Starting phenix.real_space_refine on Fri Apr 12 02:48:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq5_42461/04_2024/8uq5_42461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq5_42461/04_2024/8uq5_42461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq5_42461/04_2024/8uq5_42461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq5_42461/04_2024/8uq5_42461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq5_42461/04_2024/8uq5_42461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq5_42461/04_2024/8uq5_42461_updated.pdb" } resolution = 3.96 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= 0.008 sd= 0.022 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 920 5.16 5 C 86144 2.51 5 N 23020 2.21 5 O 25224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ASP 446": "OD1" <-> "OD2" Residue "A ARG 504": "NH1" <-> "NH2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 849": "OD1" <-> "OD2" Residue "A TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1298": "OD1" <-> "OD2" Residue "A ASP 1623": "OD1" <-> "OD2" Residue "A ASP 1681": "OD1" <-> "OD2" Residue "A TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1785": "OD1" <-> "OD2" Residue "A GLU 2294": "OE1" <-> "OE2" Residue "A GLU 2338": "OE1" <-> "OE2" Residue "A GLU 2489": "OE1" <-> "OE2" Residue "A PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3025": "OD1" <-> "OD2" Residue "A ASP 3120": "OD1" <-> "OD2" Residue "A ASP 3203": "OD1" <-> "OD2" Residue "A TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 3848": "OE1" <-> "OE2" Residue "A ASP 4030": "OD1" <-> "OD2" Residue "A GLU 4107": "OE1" <-> "OE2" Residue "A ASP 4278": "OD1" <-> "OD2" Residue "A PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4896": "OD1" <-> "OD2" Residue "A PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ASP 446": "OD1" <-> "OD2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 849": "OD1" <-> "OD2" Residue "B TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1298": "OD1" <-> "OD2" Residue "B ASP 1623": "OD1" <-> "OD2" Residue "B ASP 1681": "OD1" <-> "OD2" Residue "B TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1785": "OD1" <-> "OD2" Residue "B GLU 2294": "OE1" <-> "OE2" Residue "B GLU 2338": "OE1" <-> "OE2" Residue "B GLU 2489": "OE1" <-> "OE2" Residue "B PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3025": "OD1" <-> "OD2" Residue "B ASP 3120": "OD1" <-> "OD2" Residue "B ASP 3203": "OD1" <-> "OD2" Residue "B TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 3848": "OE1" <-> "OE2" Residue "B ASP 4030": "OD1" <-> "OD2" Residue "B GLU 4107": "OE1" <-> "OE2" Residue "B ASP 4278": "OD1" <-> "OD2" Residue "B PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4896": "OD1" <-> "OD2" Residue "B PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ASP 446": "OD1" <-> "OD2" Residue "C ARG 504": "NH1" <-> "NH2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 849": "OD1" <-> "OD2" Residue "C TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1298": "OD1" <-> "OD2" Residue "C ASP 1623": "OD1" <-> "OD2" Residue "C ASP 1681": "OD1" <-> "OD2" Residue "C TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1785": "OD1" <-> "OD2" Residue "C GLU 2294": "OE1" <-> "OE2" Residue "C GLU 2338": "OE1" <-> "OE2" Residue "C GLU 2489": "OE1" <-> "OE2" Residue "C PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3025": "OD1" <-> "OD2" Residue "C ASP 3120": "OD1" <-> "OD2" Residue "C ASP 3203": "OD1" <-> "OD2" Residue "C TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 3848": "OE1" <-> "OE2" Residue "C ASP 4030": "OD1" <-> "OD2" Residue "C GLU 4107": "OE1" <-> "OE2" Residue "C ASP 4278": "OD1" <-> "OD2" Residue "C PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4896": "OD1" <-> "OD2" Residue "C PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ASP 446": "OD1" <-> "OD2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 849": "OD1" <-> "OD2" Residue "D TYR 1094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1298": "OD1" <-> "OD2" Residue "D ASP 1623": "OD1" <-> "OD2" Residue "D ASP 1681": "OD1" <-> "OD2" Residue "D TYR 1725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1785": "OD1" <-> "OD2" Residue "D GLU 2294": "OE1" <-> "OE2" Residue "D GLU 2338": "OE1" <-> "OE2" Residue "D GLU 2489": "OE1" <-> "OE2" Residue "D PHE 2662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3025": "OD1" <-> "OD2" Residue "D ASP 3120": "OD1" <-> "OD2" Residue "D ASP 3203": "OD1" <-> "OD2" Residue "D TYR 3228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 3848": "OE1" <-> "OE2" Residue "D ASP 4030": "OD1" <-> "OD2" Residue "D GLU 4107": "OE1" <-> "OE2" Residue "D ASP 4278": "OD1" <-> "OD2" Residue "D PHE 4283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4896": "OD1" <-> "OD2" Residue "D PHE 4951": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 135336 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "B" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "C" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "D" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "A" Number of atoms: 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 33092 SG CYS A4888 178.238 177.713 87.809 1.00124.81 S ATOM 33117 SG CYS A4891 177.001 178.824 91.289 1.00121.93 S ATOM 66863 SG CYS B4888 204.191 178.235 87.823 1.00124.81 S ATOM 66888 SG CYS B4891 203.080 176.998 91.303 1.00121.93 S ATOM A00HM SG CYS C4888 203.552 204.185 87.816 1.00124.81 S ATOM A00IB SG CYS C4891 204.789 203.074 91.296 1.00121.93 S ATOM A0QJP SG CYS D4888 177.604 203.542 87.822 1.00124.81 S ATOM A0QKE SG CYS D4891 178.716 204.779 91.302 1.00121.93 S Time building chain proxies: 94.04, per 1000 atoms: 0.69 Number of scatterers: 135336 At special positions: 0 Unit cell: (382.63, 382.63, 212.48, 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 920 16.00 P 24 15.00 O 25224 8.00 N 23020 7.00 C 86144 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: 40.61 Conformation dependent library (CDL) restraints added in 33.6 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 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31712 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: 700 helices and 80 sheets defined 60.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 39.94 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.777A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.876A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TRP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.958A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 224' Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.533A pdb=" N ARG A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 259' Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.791A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 271' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 Processing helix chain 'A' and resid 441 through 446 removed outlier: 5.063A 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 509 removed outlier: 4.787A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 523 through 542 removed outlier: 4.630A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 556 removed outlier: 4.748A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.949A pdb=" N ASN A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.587A pdb=" N ILE A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.601A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.256A 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: 4.668A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.590A 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: 4.281A pdb=" N ALA A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.151A 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 876 through 900 Processing helix chain 'A' and resid 920 through 925 removed outlier: 3.576A pdb=" N LEU A 924 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Proline residue: A 925 - end of helix No H-bonds generated for 'chain 'A' and resid 920 through 925' Processing helix chain 'A' and resid 926 through 947 removed outlier: 3.534A pdb=" N GLY A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 960 removed outlier: 3.588A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 4.318A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 987' Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.148A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.791A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 6.797A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 4.119A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 5.139A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.981A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.036A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.600A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.994A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 3.987A 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 1722 removed outlier: 4.773A pdb=" N ALA A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 5.357A pdb=" N TYR A1778 " --> pdb=" O GLU A1774 " (cutoff:3.500A) 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: 4.159A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 5.508A 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: 4.149A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A1934 " --> pdb=" O ASP A1930 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1955 removed outlier: 3.748A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA A1955 " --> pdb=" O LEU A1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1950 through 1955' Processing helix chain 'A' and resid 1956 through 1966 removed outlier: 4.156A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 3.830A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.547A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.806A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 removed outlier: 3.583A 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: 3.871A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.604A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 removed outlier: 3.696A pdb=" N GLY A2166 " --> pdb=" O MET A2162 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.878A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.527A pdb=" N VAL A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.371A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.110A 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: 3.602A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A2265 " --> pdb=" O ASP A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.762A 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 2377 through 2382 removed outlier: 4.498A pdb=" N THR A2381 " --> pdb=" O GLU A2377 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2377 through 2382' 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 2439 removed outlier: 5.623A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2475 removed outlier: 4.390A pdb=" N GLY A2459 " --> pdb=" O ASP A2455 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A2460 " --> pdb=" O MET A2456 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS A2461 " --> pdb=" O SER A2457 " (cutoff:3.500A) Proline residue: A2462 - end of helix removed outlier: 3.838A 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 2504 removed outlier: 5.183A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 3.809A pdb=" N ALA A2509 " --> pdb=" O ALA A2505 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR A2510 " --> pdb=" O ALA A2506 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2505 through 2511' Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.401A 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: 4.125A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.625A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2581 through 2596 removed outlier: 4.060A pdb=" N MET A2585 " --> pdb=" O ARG A2581 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN A2586 " --> pdb=" O PRO A2582 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE A2594 " --> pdb=" O ARG A2590 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A2595 " --> pdb=" O ARG A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2603 through 2618 Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.288A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2697 removed outlier: 3.731A pdb=" N MET A2695 " --> pdb=" O LYS A2691 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER A2697 " --> pdb=" O SER A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2714 through 2740 removed outlier: 4.785A pdb=" N LYS A2723 " --> pdb=" O TYR A2719 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR A2724 " --> pdb=" O PHE A2720 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU A2726 " --> pdb=" O ASN A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.154A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2766 through 2784 removed outlier: 4.734A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TRP A2773 " --> pdb=" O GLU A2769 " (cutoff:3.500A) Proline residue: A2774 - end of helix Processing helix chain 'A' and resid 2792 through 2802 Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 4.921A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2879 through 2900 removed outlier: 4.844A pdb=" N LYS A2884 " --> pdb=" O LYS A2880 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2948 Processing helix chain 'A' and resid 2956 through 2979 removed outlier: 4.220A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix removed outlier: 3.619A pdb=" N ASP A2972 " --> pdb=" O LEU A2968 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.898A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 Processing helix chain 'A' and resid 3041 through 3049 removed outlier: 4.599A pdb=" N VAL A3045 " --> pdb=" O ASP A3041 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3078 removed outlier: 3.905A pdb=" N LEU A3061 " --> pdb=" O LEU A3057 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A3064 " --> pdb=" O PHE A3060 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 4.792A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3118 through 3123 removed outlier: 5.949A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3144 removed outlier: 6.316A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A3141 " --> pdb=" O LEU A3137 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS A3144 " --> pdb=" O LEU A3140 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 removed outlier: 4.337A pdb=" N ARG A3150 " --> pdb=" O ILE A3146 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN A3151 " --> pdb=" O TYR A3147 " (cutoff:3.500A) Processing helix chain 'A' and resid 3153 through 3167 Proline residue: A3167 - end of helix Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 4.465A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3175 through 3180' Processing helix chain 'A' and resid 3182 through 3188 removed outlier: 5.201A pdb=" N SER A3188 " --> pdb=" O TYR A3184 " (cutoff:3.500A) Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.997A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 3.628A 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: 5.181A 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 3288 Processing helix chain 'A' and resid 3294 through 3311 removed outlier: 3.555A pdb=" N VAL A3301 " --> pdb=" O LYS A3297 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.568A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3316 through 3330 removed outlier: 7.053A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 4.554A pdb=" N LYS A3325 " --> pdb=" O PRO A3321 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU A3326 " --> pdb=" O LEU A3322 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS A3328 " --> pdb=" O GLU A3324 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS A3329 " --> pdb=" O LYS A3325 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA A3330 " --> pdb=" O LEU A3326 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3606 removed outlier: 4.529A pdb=" N PHE A3603 " --> pdb=" O VAL A3599 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A3606 " --> pdb=" O CYS A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3607 through 3612 removed outlier: 3.682A pdb=" N LEU A3611 " --> pdb=" O PRO A3607 " (cutoff:3.500A) Proline residue: A3612 - end of helix No H-bonds generated for 'chain 'A' and resid 3607 through 3612' Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.665A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3647 Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.866A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3677 Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.918A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 3.545A pdb=" N LEU A3741 " --> pdb=" O ALA A3737 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A3744 " --> pdb=" O VAL A3740 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 removed outlier: 3.666A pdb=" N LYS A3760 " --> pdb=" O ALA A3756 " (cutoff:3.500A) Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.666A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 removed outlier: 3.734A pdb=" N GLY A3818 " --> pdb=" O ALA A3814 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3848 removed outlier: 3.670A pdb=" N THR A3836 " --> pdb=" O ASP A3832 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.545A pdb=" N ARG A3859 " --> pdb=" O GLN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.703A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 5.067A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3962 removed outlier: 3.793A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A3959 " --> pdb=" O GLN A3955 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.674A 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 4027 removed outlier: 3.563A pdb=" N PHE A4020 " --> pdb=" O PHE A4016 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A4022 " --> pdb=" O ASP A4018 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4029 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 removed outlier: 3.673A pdb=" N GLU A4053 " --> pdb=" O HIS A4049 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS A4056 " --> pdb=" O MET A4052 " (cutoff:3.500A) Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 5.418A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.527A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.857A 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: 5.175A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4262 removed outlier: 3.987A pdb=" N ILE A4252 " --> pdb=" O LEU A4248 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4272 removed outlier: 4.740A pdb=" N GLN A4267 " --> pdb=" O SER A4263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS A4269 " --> pdb=" O LYS A4265 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 3.639A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4521 removed outlier: 3.533A pdb=" N LEU A4507 " --> pdb=" O ARG A4503 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS A4521 " --> pdb=" O LEU A4517 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 4.369A 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: 4.581A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4662 removed outlier: 3.524A pdb=" N MET A4654 " --> pdb=" O LYS A4650 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU A4659 " --> pdb=" O ASP A4655 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A4660 " --> pdb=" O LYS A4656 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A4661 " --> pdb=" O TYR A4657 " (cutoff:3.500A) Processing helix chain 'A' and resid 4663 through 4671 Processing helix chain 'A' and resid 4673 through 4683 removed outlier: 3.507A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A4679 " --> pdb=" O ALA A4675 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.006A 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 4736 removed outlier: 3.609A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4737 through 4750 removed outlier: 4.955A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) Processing helix chain 'A' and resid 4751 through 4762 removed outlier: 3.583A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.730A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 4.251A 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: 4.357A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 3.906A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.116A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (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 2533 through 2538 removed outlier: 4.130A pdb=" N GLY A2537 " --> pdb=" O LEU A2534 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR A2538 " --> pdb=" O PHE A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.777A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.875A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TRP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.958A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.533A pdb=" N ARG B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 259' Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.791A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 271' Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 Processing helix chain 'B' and resid 441 through 446 removed outlier: 5.063A 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 509 removed outlier: 4.787A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 523 through 542 removed outlier: 4.630A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 556 removed outlier: 4.748A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ASP B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.949A pdb=" N ASN B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.587A pdb=" N ILE B 598 " --> pdb=" O ILE B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.601A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.256A 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: 4.668A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.590A 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: 4.281A pdb=" N ALA B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) removed outlier: 5.150A 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 876 through 900 Processing helix chain 'B' and resid 920 through 925 removed outlier: 3.576A pdb=" N LEU B 924 " --> pdb=" O GLU B 920 " (cutoff:3.500A) Proline residue: B 925 - end of helix No H-bonds generated for 'chain 'B' and resid 920 through 925' Processing helix chain 'B' and resid 926 through 947 removed outlier: 3.534A pdb=" N GLY B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 960 removed outlier: 3.588A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 4.318A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 987' Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 4.148A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.791A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 6.797A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 4.119A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 5.139A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.981A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.036A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.600A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.994A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 3.987A 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 1722 removed outlier: 4.773A pdb=" N ALA B1715 " --> pdb=" O LEU B1711 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 5.358A pdb=" N TYR B1778 " --> pdb=" O GLU B1774 " (cutoff:3.500A) 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: 4.159A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 5.508A 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: 4.149A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1934 " --> pdb=" O ASP B1930 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1955 removed outlier: 3.748A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B1955 " --> pdb=" O LEU B1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1950 through 1955' Processing helix chain 'B' and resid 1956 through 1966 removed outlier: 4.156A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 3.830A pdb=" N ASN B1978 " --> pdb=" O ASN B1974 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.547A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.806A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 removed outlier: 3.583A 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: 3.870A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 5.603A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 removed outlier: 3.697A pdb=" N GLY B2166 " --> pdb=" O MET B2162 " (cutoff:3.500A) Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.879A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.527A pdb=" N VAL B2193 " --> pdb=" O PHE B2189 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.371A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.111A 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: 3.602A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B2265 " --> pdb=" O ASP B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.761A 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 2377 through 2382 removed outlier: 4.498A pdb=" N THR B2381 " --> pdb=" O GLU B2377 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2377 through 2382' 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 2439 removed outlier: 5.623A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2455 through 2475 removed outlier: 4.390A pdb=" N GLY B2459 " --> pdb=" O ASP B2455 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B2460 " --> pdb=" O MET B2456 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS B2461 " --> pdb=" O SER B2457 " (cutoff:3.500A) Proline residue: B2462 - end of helix removed outlier: 3.839A 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 2504 removed outlier: 5.184A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 3.809A pdb=" N ALA B2509 " --> pdb=" O ALA B2505 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B2510 " --> pdb=" O ALA B2506 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2505 through 2511' Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.401A 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: 4.125A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.625A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2581 through 2596 removed outlier: 4.060A pdb=" N MET B2585 " --> pdb=" O ARG B2581 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN B2586 " --> pdb=" O PRO B2582 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B2594 " --> pdb=" O ARG B2590 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP B2595 " --> pdb=" O ARG B2591 " (cutoff:3.500A) Processing helix chain 'B' and resid 2603 through 2618 Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.288A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2658 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2697 removed outlier: 3.732A pdb=" N MET B2695 " --> pdb=" O LYS B2691 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER B2697 " --> pdb=" O SER B2693 " (cutoff:3.500A) Processing helix chain 'B' and resid 2714 through 2740 removed outlier: 4.785A pdb=" N LYS B2723 " --> pdb=" O TYR B2719 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B2724 " --> pdb=" O PHE B2720 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B2726 " --> pdb=" O ASN B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.154A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2766 through 2784 removed outlier: 4.734A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TRP B2773 " --> pdb=" O GLU B2769 " (cutoff:3.500A) Proline residue: B2774 - end of helix Processing helix chain 'B' and resid 2792 through 2802 Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 4.920A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2879 through 2900 removed outlier: 4.843A pdb=" N LYS B2884 " --> pdb=" O LYS B2880 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2948 Processing helix chain 'B' and resid 2956 through 2979 removed outlier: 4.220A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix removed outlier: 3.618A pdb=" N ASP B2972 " --> pdb=" O LEU B2968 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.898A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 Processing helix chain 'B' and resid 3041 through 3049 removed outlier: 4.599A pdb=" N VAL B3045 " --> pdb=" O ASP B3041 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3078 removed outlier: 3.906A pdb=" N LEU B3061 " --> pdb=" O LEU B3057 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B3064 " --> pdb=" O PHE B3060 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 4.792A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3118 through 3123 removed outlier: 5.949A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3144 removed outlier: 6.316A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B3141 " --> pdb=" O LEU B3137 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS B3144 " --> pdb=" O LEU B3140 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 removed outlier: 4.336A pdb=" N ARG B3150 " --> pdb=" O ILE B3146 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B3151 " --> pdb=" O TYR B3147 " (cutoff:3.500A) Processing helix chain 'B' and resid 3153 through 3167 Proline residue: B3167 - end of helix Processing helix chain 'B' and resid 3175 through 3180 removed outlier: 4.465A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3175 through 3180' Processing helix chain 'B' and resid 3182 through 3188 removed outlier: 5.201A pdb=" N SER B3188 " --> pdb=" O TYR B3184 " (cutoff:3.500A) Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.997A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 3.628A 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: 5.182A 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 3288 Processing helix chain 'B' and resid 3294 through 3311 removed outlier: 3.555A pdb=" N VAL B3301 " --> pdb=" O LYS B3297 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.568A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3316 through 3330 removed outlier: 7.053A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 4.554A pdb=" N LYS B3325 " --> pdb=" O PRO B3321 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU B3326 " --> pdb=" O LEU B3322 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B3328 " --> pdb=" O GLU B3324 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS B3329 " --> pdb=" O LYS B3325 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA B3330 " --> pdb=" O LEU B3326 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3606 removed outlier: 4.529A pdb=" N PHE B3603 " --> pdb=" O VAL B3599 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B3606 " --> pdb=" O CYS B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3607 through 3612 removed outlier: 3.682A pdb=" N LEU B3611 " --> pdb=" O PRO B3607 " (cutoff:3.500A) Proline residue: B3612 - end of helix No H-bonds generated for 'chain 'B' and resid 3607 through 3612' Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.665A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3647 Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.866A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3677 Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.918A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 3.545A pdb=" N LEU B3741 " --> pdb=" O ALA B3737 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B3744 " --> pdb=" O VAL B3740 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 removed outlier: 3.665A pdb=" N LYS B3760 " --> pdb=" O ALA B3756 " (cutoff:3.500A) Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.666A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 removed outlier: 3.734A pdb=" N GLY B3818 " --> pdb=" O ALA B3814 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3848 removed outlier: 3.671A pdb=" N THR B3836 " --> pdb=" O ASP B3832 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.545A pdb=" N ARG B3859 " --> pdb=" O GLN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.702A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 5.067A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3962 removed outlier: 3.794A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B3959 " --> pdb=" O GLN B3955 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.675A 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 4027 removed outlier: 3.563A pdb=" N PHE B4020 " --> pdb=" O PHE B4016 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B4022 " --> pdb=" O ASP B4018 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4029 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 removed outlier: 3.673A pdb=" N GLU B4053 " --> pdb=" O HIS B4049 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS B4056 " --> pdb=" O MET B4052 " (cutoff:3.500A) Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 5.418A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.528A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.857A 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: 5.175A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4262 removed outlier: 3.987A pdb=" N ILE B4252 " --> pdb=" O LEU B4248 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4272 removed outlier: 4.739A pdb=" N GLN B4267 " --> pdb=" O SER B4263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B4269 " --> pdb=" O LYS B4265 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 3.640A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4521 removed outlier: 3.533A pdb=" N LEU B4507 " --> pdb=" O ARG B4503 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS B4521 " --> pdb=" O LEU B4517 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 4.369A 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: 4.581A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4662 removed outlier: 3.523A pdb=" N MET B4654 " --> pdb=" O LYS B4650 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU B4659 " --> pdb=" O ASP B4655 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE B4660 " --> pdb=" O LYS B4656 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B4661 " --> pdb=" O TYR B4657 " (cutoff:3.500A) Processing helix chain 'B' and resid 4663 through 4671 Processing helix chain 'B' and resid 4673 through 4683 removed outlier: 3.507A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B4679 " --> pdb=" O ALA B4675 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.006A 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 4736 removed outlier: 3.609A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4737 through 4750 removed outlier: 4.955A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) Processing helix chain 'B' and resid 4751 through 4762 removed outlier: 3.583A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.730A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 4.252A 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: 4.356A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 3.906A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.116A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (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 2533 through 2538 removed outlier: 4.130A pdb=" N GLY B2537 " --> pdb=" O LEU B2534 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B2538 " --> pdb=" O PHE B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.777A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.876A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.958A pdb=" N ALA C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 224' Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.532A pdb=" N ARG C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 259' Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.791A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 271' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 Processing helix chain 'C' and resid 441 through 446 removed outlier: 5.063A 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 509 removed outlier: 4.787A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 523 through 542 removed outlier: 4.631A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 556 removed outlier: 4.748A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP C 556 " --> pdb=" O SER C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 3.949A pdb=" N ASN C 587 " --> pdb=" O PRO C 583 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.587A pdb=" N ILE C 598 " --> pdb=" O ILE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.602A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.257A 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: 4.667A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.590A 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: 4.281A pdb=" N ALA C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 5.151A 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 876 through 900 Processing helix chain 'C' and resid 920 through 925 removed outlier: 3.576A pdb=" N LEU C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Proline residue: C 925 - end of helix No H-bonds generated for 'chain 'C' and resid 920 through 925' Processing helix chain 'C' and resid 926 through 947 removed outlier: 3.534A pdb=" N GLY C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 960 removed outlier: 3.588A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 4.318A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 987' Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 4.148A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.791A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 6.798A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 4.119A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 5.138A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.981A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.036A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.600A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.994A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 3.987A 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 1722 removed outlier: 4.773A pdb=" N ALA C1715 " --> pdb=" O LEU C1711 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 5.358A pdb=" N TYR C1778 " --> pdb=" O GLU C1774 " (cutoff:3.500A) 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: 4.159A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.149A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C1934 " --> pdb=" O ASP C1930 " (cutoff:3.500A) Processing helix chain 'C' and resid 1950 through 1955 removed outlier: 3.748A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C1955 " --> pdb=" O LEU C1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1950 through 1955' Processing helix chain 'C' and resid 1956 through 1966 removed outlier: 4.156A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 3.830A pdb=" N ASN C1978 " --> pdb=" O ASN C1974 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.547A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.806A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 removed outlier: 3.583A 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: 3.870A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.604A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 removed outlier: 3.697A pdb=" N GLY C2166 " --> pdb=" O MET C2162 " (cutoff:3.500A) Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.877A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.527A pdb=" N VAL C2193 " --> pdb=" O PHE C2189 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.371A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.110A 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: 3.602A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C2265 " --> pdb=" O ASP C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.762A 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 2377 through 2382 removed outlier: 4.498A pdb=" N THR C2381 " --> pdb=" O GLU C2377 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C2382 " --> pdb=" O GLU C2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2377 through 2382' 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 2439 removed outlier: 5.623A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2455 through 2475 removed outlier: 4.390A pdb=" N GLY C2459 " --> pdb=" O ASP C2455 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE C2460 " --> pdb=" O MET C2456 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS C2461 " --> pdb=" O SER C2457 " (cutoff:3.500A) Proline residue: C2462 - end of helix removed outlier: 3.838A 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 2504 removed outlier: 5.183A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 3.809A pdb=" N ALA C2509 " --> pdb=" O ALA C2505 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C2510 " --> pdb=" O ALA C2506 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2505 through 2511' Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.401A 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: 4.125A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.625A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2581 through 2596 removed outlier: 4.060A pdb=" N MET C2585 " --> pdb=" O ARG C2581 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN C2586 " --> pdb=" O PRO C2582 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE C2594 " --> pdb=" O ARG C2590 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP C2595 " --> pdb=" O ARG C2591 " (cutoff:3.500A) Processing helix chain 'C' and resid 2603 through 2618 Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.289A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2658 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2697 removed outlier: 3.731A pdb=" N MET C2695 " --> pdb=" O LYS C2691 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER C2697 " --> pdb=" O SER C2693 " (cutoff:3.500A) Processing helix chain 'C' and resid 2714 through 2740 removed outlier: 4.785A pdb=" N LYS C2723 " --> pdb=" O TYR C2719 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C2724 " --> pdb=" O PHE C2720 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU C2726 " --> pdb=" O ASN C2722 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.155A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2766 through 2784 removed outlier: 4.734A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP C2773 " --> pdb=" O GLU C2769 " (cutoff:3.500A) Proline residue: C2774 - end of helix Processing helix chain 'C' and resid 2792 through 2802 Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 4.921A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2879 through 2900 removed outlier: 4.845A pdb=" N LYS C2884 " --> pdb=" O LYS C2880 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2948 Processing helix chain 'C' and resid 2956 through 2979 removed outlier: 4.219A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix removed outlier: 3.619A pdb=" N ASP C2972 " --> pdb=" O LEU C2968 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.898A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 Processing helix chain 'C' and resid 3041 through 3049 removed outlier: 4.599A pdb=" N VAL C3045 " --> pdb=" O ASP C3041 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3078 removed outlier: 3.905A pdb=" N LEU C3061 " --> pdb=" O LEU C3057 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C3064 " --> pdb=" O PHE C3060 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 4.792A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3118 through 3123 removed outlier: 5.949A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3124 through 3144 removed outlier: 6.316A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C3141 " --> pdb=" O LEU C3137 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS C3144 " --> pdb=" O LEU C3140 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 removed outlier: 4.336A pdb=" N ARG C3150 " --> pdb=" O ILE C3146 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN C3151 " --> pdb=" O TYR C3147 " (cutoff:3.500A) Processing helix chain 'C' and resid 3153 through 3167 Proline residue: C3167 - end of helix Processing helix chain 'C' and resid 3175 through 3180 removed outlier: 4.465A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3175 through 3180' Processing helix chain 'C' and resid 3182 through 3188 removed outlier: 5.201A pdb=" N SER C3188 " --> pdb=" O TYR C3184 " (cutoff:3.500A) Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.996A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 3.628A 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: 5.181A 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 3288 Processing helix chain 'C' and resid 3294 through 3311 removed outlier: 3.555A pdb=" N VAL C3301 " --> pdb=" O LYS C3297 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.568A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3316 through 3330 removed outlier: 7.052A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 4.554A pdb=" N LYS C3325 " --> pdb=" O PRO C3321 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU C3326 " --> pdb=" O LEU C3322 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS C3328 " --> pdb=" O GLU C3324 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS C3329 " --> pdb=" O LYS C3325 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA C3330 " --> pdb=" O LEU C3326 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3606 removed outlier: 4.529A pdb=" N PHE C3603 " --> pdb=" O VAL C3599 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C3606 " --> pdb=" O CYS C3602 " (cutoff:3.500A) Processing helix chain 'C' and resid 3607 through 3612 removed outlier: 3.683A pdb=" N LEU C3611 " --> pdb=" O PRO C3607 " (cutoff:3.500A) Proline residue: C3612 - end of helix No H-bonds generated for 'chain 'C' and resid 3607 through 3612' Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.665A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3647 Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.866A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3677 Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.918A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 3.544A pdb=" N LEU C3741 " --> pdb=" O ALA C3737 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C3744 " --> pdb=" O VAL C3740 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 removed outlier: 3.666A pdb=" N LYS C3760 " --> pdb=" O ALA C3756 " (cutoff:3.500A) Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.667A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 removed outlier: 3.734A pdb=" N GLY C3818 " --> pdb=" O ALA C3814 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3848 removed outlier: 3.670A pdb=" N THR C3836 " --> pdb=" O ASP C3832 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.545A pdb=" N ARG C3859 " --> pdb=" O GLN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.703A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 5.066A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3962 removed outlier: 3.793A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER C3959 " --> pdb=" O GLN C3955 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.674A 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 4027 removed outlier: 3.562A pdb=" N PHE C4020 " --> pdb=" O PHE C4016 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C4022 " --> pdb=" O ASP C4018 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4029 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 removed outlier: 3.673A pdb=" N GLU C4053 " --> pdb=" O HIS C4049 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS C4056 " --> pdb=" O MET C4052 " (cutoff:3.500A) Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 5.419A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.527A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.856A 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: 5.175A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4262 removed outlier: 3.987A pdb=" N ILE C4252 " --> pdb=" O LEU C4248 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4272 removed outlier: 4.740A pdb=" N GLN C4267 " --> pdb=" O SER C4263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS C4269 " --> pdb=" O LYS C4265 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 3.640A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4521 removed outlier: 3.533A pdb=" N LEU C4507 " --> pdb=" O ARG C4503 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS C4521 " --> pdb=" O LEU C4517 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 4.369A 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: 4.581A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4662 removed outlier: 3.523A pdb=" N MET C4654 " --> pdb=" O LYS C4650 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU C4659 " --> pdb=" O ASP C4655 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE C4660 " --> pdb=" O LYS C4656 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR C4661 " --> pdb=" O TYR C4657 " (cutoff:3.500A) Processing helix chain 'C' and resid 4663 through 4671 Processing helix chain 'C' and resid 4673 through 4683 removed outlier: 3.507A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C4679 " --> pdb=" O ALA C4675 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.006A 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 4736 removed outlier: 3.608A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4737 through 4750 removed outlier: 4.955A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) Processing helix chain 'C' and resid 4751 through 4762 removed outlier: 3.582A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.730A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 4.252A 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: 4.356A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 3.906A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.116A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (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 2533 through 2538 removed outlier: 4.129A pdb=" N GLY C2537 " --> pdb=" O LEU C2534 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR C2538 " --> pdb=" O PHE C2535 " (cutoff:3.500A) Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.777A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.876A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TRP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.958A pdb=" N ALA D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ALA D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 224' Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.532A pdb=" N ARG D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG D 258 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 259' Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.791A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 271' Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 Processing helix chain 'D' and resid 441 through 446 removed outlier: 5.064A 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 509 removed outlier: 4.788A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 523 through 542 removed outlier: 4.630A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 556 removed outlier: 4.748A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP D 556 " --> pdb=" O SER D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 3.949A pdb=" N ASN D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.587A pdb=" N ILE D 598 " --> pdb=" O ILE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.602A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.256A 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: 4.668A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.589A 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: 4.281A pdb=" N ALA D 861 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 5.150A 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 876 through 900 Processing helix chain 'D' and resid 920 through 925 removed outlier: 3.576A pdb=" N LEU D 924 " --> pdb=" O GLU D 920 " (cutoff:3.500A) Proline residue: D 925 - end of helix No H-bonds generated for 'chain 'D' and resid 920 through 925' Processing helix chain 'D' and resid 926 through 947 removed outlier: 3.534A pdb=" N GLY D 947 " --> pdb=" O LEU D 943 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 960 removed outlier: 3.588A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 4.318A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 987' Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 4.148A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.791A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 6.798A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 4.119A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 5.139A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.981A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.036A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.600A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.994A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 3.987A 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 1722 removed outlier: 4.773A pdb=" N ALA D1715 " --> pdb=" O LEU D1711 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 5.357A pdb=" N TYR D1778 " --> pdb=" O GLU D1774 " (cutoff:3.500A) 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: 4.159A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 5.507A 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: 4.149A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D1934 " --> pdb=" O ASP D1930 " (cutoff:3.500A) Processing helix chain 'D' and resid 1950 through 1955 removed outlier: 3.749A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA D1955 " --> pdb=" O LEU D1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1950 through 1955' Processing helix chain 'D' and resid 1956 through 1966 removed outlier: 4.156A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 3.829A pdb=" N ASN D1978 " --> pdb=" O ASN D1974 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.547A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.806A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 removed outlier: 3.583A 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: 3.871A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.604A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 removed outlier: 3.697A pdb=" N GLY D2166 " --> pdb=" O MET D2162 " (cutoff:3.500A) Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.877A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.528A pdb=" N VAL D2193 " --> pdb=" O PHE D2189 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.371A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.110A 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: 3.602A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D2265 " --> pdb=" O ASP D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.761A 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 2377 through 2382 removed outlier: 4.498A pdb=" N THR D2381 " --> pdb=" O GLU D2377 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2377 through 2382' 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 2439 removed outlier: 5.622A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2455 through 2475 removed outlier: 4.390A pdb=" N GLY D2459 " --> pdb=" O ASP D2455 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE D2460 " --> pdb=" O MET D2456 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS D2461 " --> pdb=" O SER D2457 " (cutoff:3.500A) Proline residue: D2462 - end of helix removed outlier: 3.839A 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 2504 removed outlier: 5.183A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 3.808A pdb=" N ALA D2509 " --> pdb=" O ALA D2505 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR D2510 " --> pdb=" O ALA D2506 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2505 through 2511' Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.401A 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: 4.125A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.625A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2581 through 2596 removed outlier: 4.059A pdb=" N MET D2585 " --> pdb=" O ARG D2581 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN D2586 " --> pdb=" O PRO D2582 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE D2594 " --> pdb=" O ARG D2590 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP D2595 " --> pdb=" O ARG D2591 " (cutoff:3.500A) Processing helix chain 'D' and resid 2603 through 2618 Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.288A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2658 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2697 removed outlier: 3.732A pdb=" N MET D2695 " --> pdb=" O LYS D2691 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N SER D2697 " --> pdb=" O SER D2693 " (cutoff:3.500A) Processing helix chain 'D' and resid 2714 through 2740 removed outlier: 4.786A pdb=" N LYS D2723 " --> pdb=" O TYR D2719 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D2724 " --> pdb=" O PHE D2720 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU D2726 " --> pdb=" O ASN D2722 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.154A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2766 through 2784 removed outlier: 4.734A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TRP D2773 " --> pdb=" O GLU D2769 " (cutoff:3.500A) Proline residue: D2774 - end of helix Processing helix chain 'D' and resid 2792 through 2802 Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 4.920A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2879 through 2900 removed outlier: 4.844A pdb=" N LYS D2884 " --> pdb=" O LYS D2880 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2948 Processing helix chain 'D' and resid 2956 through 2979 removed outlier: 4.219A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix removed outlier: 3.619A pdb=" N ASP D2972 " --> pdb=" O LEU D2968 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.898A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 Processing helix chain 'D' and resid 3041 through 3049 removed outlier: 4.599A pdb=" N VAL D3045 " --> pdb=" O ASP D3041 " (cutoff:3.500A) Processing helix chain 'D' and resid 3050 through 3078 removed outlier: 3.906A pdb=" N LEU D3061 " --> pdb=" O LEU D3057 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D3064 " --> pdb=" O PHE D3060 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 4.792A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3118 through 3123 removed outlier: 5.949A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) Processing helix chain 'D' and resid 3124 through 3144 removed outlier: 6.316A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D3141 " --> pdb=" O LEU D3137 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYS D3144 " --> pdb=" O LEU D3140 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 removed outlier: 4.337A pdb=" N ARG D3150 " --> pdb=" O ILE D3146 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLN D3151 " --> pdb=" O TYR D3147 " (cutoff:3.500A) Processing helix chain 'D' and resid 3153 through 3167 Proline residue: D3167 - end of helix Processing helix chain 'D' and resid 3175 through 3180 removed outlier: 4.465A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3175 through 3180' Processing helix chain 'D' and resid 3182 through 3188 removed outlier: 5.201A pdb=" N SER D3188 " --> pdb=" O TYR D3184 " (cutoff:3.500A) Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.997A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 3.627A 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: 5.181A 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 3288 Processing helix chain 'D' and resid 3294 through 3311 removed outlier: 3.555A pdb=" N VAL D3301 " --> pdb=" O LYS D3297 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.568A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3316 through 3330 removed outlier: 7.053A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 4.554A pdb=" N LYS D3325 " --> pdb=" O PRO D3321 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU D3326 " --> pdb=" O LEU D3322 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS D3328 " --> pdb=" O GLU D3324 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS D3329 " --> pdb=" O LYS D3325 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA D3330 " --> pdb=" O LEU D3326 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3606 removed outlier: 4.530A pdb=" N PHE D3603 " --> pdb=" O VAL D3599 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA D3606 " --> pdb=" O CYS D3602 " (cutoff:3.500A) Processing helix chain 'D' and resid 3607 through 3612 removed outlier: 3.682A pdb=" N LEU D3611 " --> pdb=" O PRO D3607 " (cutoff:3.500A) Proline residue: D3612 - end of helix No H-bonds generated for 'chain 'D' and resid 3607 through 3612' Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.666A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3647 Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.865A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3677 Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.917A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.759A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 3.544A pdb=" N LEU D3741 " --> pdb=" O ALA D3737 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D3744 " --> pdb=" O VAL D3740 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 removed outlier: 3.665A pdb=" N LYS D3760 " --> pdb=" O ALA D3756 " (cutoff:3.500A) Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.666A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 removed outlier: 3.733A pdb=" N GLY D3818 " --> pdb=" O ALA D3814 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3848 removed outlier: 3.671A pdb=" N THR D3836 " --> pdb=" O ASP D3832 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.545A pdb=" N ARG D3859 " --> pdb=" O GLN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.702A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 5.067A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3962 removed outlier: 3.793A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER D3959 " --> pdb=" O GLN D3955 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.674A 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 4027 removed outlier: 3.563A pdb=" N PHE D4020 " --> pdb=" O PHE D4016 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS D4022 " --> pdb=" O ASP D4018 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4029 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 removed outlier: 3.673A pdb=" N GLU D4053 " --> pdb=" O HIS D4049 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS D4056 " --> pdb=" O MET D4052 " (cutoff:3.500A) Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 5.419A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.527A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.857A 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: 5.175A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4262 removed outlier: 3.987A pdb=" N ILE D4252 " --> pdb=" O LEU D4248 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4272 removed outlier: 4.740A pdb=" N GLN D4267 " --> pdb=" O SER D4263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS D4269 " --> pdb=" O LYS D4265 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 3.639A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4521 removed outlier: 3.533A pdb=" N LEU D4507 " --> pdb=" O ARG D4503 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS D4521 " --> pdb=" O LEU D4517 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 4.369A 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: 4.581A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4662 removed outlier: 3.523A pdb=" N MET D4654 " --> pdb=" O LYS D4650 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLU D4659 " --> pdb=" O ASP D4655 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE D4660 " --> pdb=" O LYS D4656 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR D4661 " --> pdb=" O TYR D4657 " (cutoff:3.500A) Processing helix chain 'D' and resid 4663 through 4671 Processing helix chain 'D' and resid 4673 through 4683 removed outlier: 3.507A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D4679 " --> pdb=" O ALA D4675 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.006A 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 4736 removed outlier: 3.609A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4737 through 4750 removed outlier: 4.955A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) Processing helix chain 'D' and resid 4751 through 4762 removed outlier: 3.583A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.731A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 4.252A 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: 4.357A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 3.906A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.116A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (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 2533 through 2538 removed outlier: 4.130A pdb=" N GLY D2537 " --> pdb=" O LEU D2534 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D2538 " --> pdb=" O PHE D2535 " (cutoff:3.500A) Processing helix chain 'D' and resid 4614 through 4619 Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 52 removed outlier: 5.921A pdb=" N LYS A 34 " --> pdb=" O THR A 52 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.381A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A 25 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 211 " --> pdb=" O THR A 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 214 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP A 179 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.748A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 192 through 195 removed outlier: 4.081A pdb=" N HIS A 202 " --> pdb=" O SER A 195 " (cutoff:3.500A) 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 295 through 299 removed outlier: 4.211A pdb=" N ASP A 232 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 304 through 308 Processing sheet with id= 7, first strand: chain 'A' and resid 329 through 333 Processing sheet with id= 8, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 9, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.927A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.856A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 777 through 780 removed outlier: 3.976A pdb=" N MET A 778 " --> pdb=" O THR A1468 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.470A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 948 through 952 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'A' and resid 1016 through 1019 Processing sheet with id= 15, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 3.939A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A1248 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET A1249 " --> pdb=" O MET A1599 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.750A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A1552 " --> pdb=" O PHE A1433 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER A1424 " --> pdb=" O ALA A1513 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1513 " --> pdb=" O SER A1424 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A1505 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1307 through 1311 removed outlier: 4.949A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2741 through 2744 Processing sheet with id= 19, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.745A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.756A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'B' and resid 47 through 52 removed outlier: 5.920A pdb=" N LYS B 34 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.381A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 25 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 211 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 214 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP B 179 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.749A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 192 through 195 removed outlier: 4.081A pdb=" N HIS B 202 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 25, first strand: chain 'B' and resid 295 through 299 removed outlier: 4.211A pdb=" N ASP B 232 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 304 through 308 Processing sheet with id= 27, first strand: chain 'B' and resid 329 through 333 Processing sheet with id= 28, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 29, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.927A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.856A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 777 through 780 removed outlier: 3.976A pdb=" N MET B 778 " --> pdb=" O THR B1468 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.470A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 948 through 952 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'B' and resid 1016 through 1019 Processing sheet with id= 35, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 3.939A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR B1248 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET B1249 " --> pdb=" O MET B1599 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.750A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B1552 " --> pdb=" O PHE B1433 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER B1424 " --> pdb=" O ALA B1513 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA B1513 " --> pdb=" O SER B1424 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B1505 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1307 through 1311 removed outlier: 4.948A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 2741 through 2744 Processing sheet with id= 39, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.745A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.756A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 47 through 52 removed outlier: 5.921A pdb=" N LYS C 34 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.381A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N THR C 25 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU C 211 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 214 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP C 179 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.749A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 192 through 195 removed outlier: 4.081A pdb=" N HIS C 202 " --> pdb=" O SER C 195 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 45, first strand: chain 'C' and resid 295 through 299 removed outlier: 4.211A pdb=" N ASP C 232 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'C' and resid 304 through 308 Processing sheet with id= 47, first strand: chain 'C' and resid 329 through 333 Processing sheet with id= 48, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 49, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.927A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.856A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 777 through 780 removed outlier: 3.977A pdb=" N MET C 778 " --> pdb=" O THR C1468 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.471A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 948 through 952 No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'C' and resid 1016 through 1019 Processing sheet with id= 55, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 3.939A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR C1248 " --> pdb=" O GLU C1091 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N MET C1249 " --> pdb=" O MET C1599 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.750A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C1552 " --> pdb=" O PHE C1433 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER C1424 " --> pdb=" O ALA C1513 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C1513 " --> pdb=" O SER C1424 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C1505 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 1307 through 1311 removed outlier: 4.949A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 2741 through 2744 Processing sheet with id= 59, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.745A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.757A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.920A pdb=" N LYS D 34 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.382A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR D 25 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU D 211 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 214 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASP D 179 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.749A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'D' and resid 192 through 195 removed outlier: 4.081A pdb=" N HIS D 202 " --> pdb=" O SER D 195 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 65, first strand: chain 'D' and resid 295 through 299 removed outlier: 4.210A pdb=" N ASP D 232 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 304 through 308 Processing sheet with id= 67, first strand: chain 'D' and resid 329 through 333 Processing sheet with id= 68, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 69, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.926A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.857A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 777 through 780 removed outlier: 3.977A pdb=" N MET D 778 " --> pdb=" O THR D1468 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.469A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'D' and resid 948 through 952 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'D' and resid 1016 through 1019 Processing sheet with id= 75, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 3.939A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR D1248 " --> pdb=" O GLU D1091 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N MET D1249 " --> pdb=" O MET D1599 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.750A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL D1552 " --> pdb=" O PHE D1433 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N SER D1424 " --> pdb=" O ALA D1513 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D1513 " --> pdb=" O SER D1424 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D1505 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 1307 through 1311 removed outlier: 4.949A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 2741 through 2744 Processing sheet with id= 79, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.746A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.757A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) 7196 hydrogen bonds defined for protein. 21496 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: 100.49 Time building geometry restraints manager: 45.19 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: 44153 1.34 - 1.46: 28934 1.46 - 1.58: 63685 1.58 - 1.70: 32 1.70 - 1.82: 1488 Bond restraints: 138292 Sorted by residual: bond pdb=" C VAL D2596 " pdb=" N PRO D2597 " ideal model delta sigma weight residual 1.335 1.374 -0.040 1.19e-02 7.06e+03 1.12e+01 bond pdb=" C VAL B2596 " pdb=" N PRO B2597 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" C VAL A2596 " pdb=" N PRO A2597 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" C VAL C2596 " pdb=" N PRO C2597 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.19e-02 7.06e+03 1.09e+01 bond pdb=" C GLU C 879 " pdb=" N ARG C 880 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.25e-02 6.40e+03 4.51e+00 ... (remaining 138287 not shown) Histogram of bond angle deviations from ideal: 92.38 - 101.89: 565 101.89 - 111.41: 59739 111.41 - 120.92: 87148 120.92 - 130.44: 38648 130.44 - 139.96: 764 Bond angle restraints: 186864 Sorted by residual: angle pdb=" CB MET D1948 " pdb=" CG MET D1948 " pdb=" SD MET D1948 " ideal model delta sigma weight residual 112.70 134.09 -21.39 3.00e+00 1.11e-01 5.08e+01 angle pdb=" CB MET B1948 " pdb=" CG MET B1948 " pdb=" SD MET B1948 " ideal model delta sigma weight residual 112.70 134.07 -21.37 3.00e+00 1.11e-01 5.07e+01 angle pdb=" CB MET C1948 " pdb=" CG MET C1948 " pdb=" SD MET C1948 " ideal model delta sigma weight residual 112.70 134.07 -21.37 3.00e+00 1.11e-01 5.07e+01 angle pdb=" CB MET A1948 " pdb=" CG MET A1948 " pdb=" SD MET A1948 " ideal model delta sigma weight residual 112.70 134.06 -21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" N ARG D 880 " pdb=" CA ARG D 880 " pdb=" CB ARG D 880 " ideal model delta sigma weight residual 109.94 120.51 -10.57 1.49e+00 4.50e-01 5.03e+01 ... (remaining 186859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 75281 17.77 - 35.53: 6545 35.53 - 53.30: 1130 53.30 - 71.06: 328 71.06 - 88.83: 108 Dihedral angle restraints: 83392 sinusoidal: 34216 harmonic: 49176 Sorted by residual: dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual -180.00 -138.13 -41.87 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA PHE A4640 " pdb=" C PHE A4640 " pdb=" N PRO A4641 " pdb=" CA PRO A4641 " ideal model delta harmonic sigma weight residual -180.00 -138.13 -41.87 0 5.00e+00 4.00e-02 7.01e+01 dihedral pdb=" CA PHE C4640 " pdb=" C PHE C4640 " pdb=" N PRO C4641 " pdb=" CA PRO C4641 " ideal model delta harmonic sigma weight residual -180.00 -138.13 -41.87 0 5.00e+00 4.00e-02 7.01e+01 ... (remaining 83389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 17919 0.062 - 0.123: 2440 0.123 - 0.185: 129 0.185 - 0.247: 8 0.247 - 0.308: 4 Chirality restraints: 20500 Sorted by residual: chirality pdb=" CB ILE C2478 " pdb=" CA ILE C2478 " pdb=" CG1 ILE C2478 " pdb=" CG2 ILE C2478 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE D2478 " pdb=" CA ILE D2478 " pdb=" CG1 ILE D2478 " pdb=" CG2 ILE D2478 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE A2478 " pdb=" CA ILE A2478 " pdb=" CG1 ILE A2478 " pdb=" CG2 ILE A2478 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 20497 not shown) Planarity restraints: 23992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C3192 " 0.605 9.50e-02 1.11e+02 2.72e-01 4.80e+01 pdb=" NE ARG C3192 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG C3192 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C3192 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C3192 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B3192 " 0.605 9.50e-02 1.11e+02 2.71e-01 4.80e+01 pdb=" NE ARG B3192 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG B3192 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B3192 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B3192 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A3192 " -0.605 9.50e-02 1.11e+02 2.71e-01 4.80e+01 pdb=" NE ARG A3192 " 0.047 2.00e-02 2.50e+03 pdb=" CZ ARG A3192 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A3192 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A3192 " -0.009 2.00e-02 2.50e+03 ... (remaining 23989 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 2353 2.68 - 3.24: 139155 3.24 - 3.79: 225497 3.79 - 4.35: 297331 4.35 - 4.90: 476065 Nonbonded interactions: 1140401 Sorted by model distance: nonbonded pdb=" OE1 GLN A2659 " pdb=" NZ LYS A2663 " model vdw 2.128 2.520 nonbonded pdb=" OE1 GLN B2659 " pdb=" NZ LYS B2663 " model vdw 2.128 2.520 nonbonded pdb=" OE1 GLN D2659 " pdb=" NZ LYS D2663 " model vdw 2.128 2.520 nonbonded pdb=" OE1 GLN C2659 " pdb=" NZ LYS C2663 " model vdw 2.129 2.520 nonbonded pdb=" OD2 ASP C 982 " pdb=" OG SER C 984 " model vdw 2.138 2.440 ... (remaining 1140396 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)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 30.850 Check model and map are aligned: 1.440 Set scattering table: 0.920 Process input model: 439.940 Find NCS groups from input model: 6.970 Set up NCS constraints: 0.910 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 491.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 0.047 138292 Z= 0.182 Angle : 0.720 21.391 186864 Z= 0.408 Chirality : 0.041 0.308 20500 Planarity : 0.006 0.272 23992 Dihedral : 14.110 88.830 51668 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.30 % Rotamer: Outliers : 0.30 % Allowed : 0.27 % Favored : 99.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.06), residues: 16792 helix: 1.17 (0.06), residues: 8868 sheet: -0.13 (0.13), residues: 1596 loop : -0.61 (0.08), residues: 6328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 893 HIS 0.009 0.001 HIS A3700 PHE 0.029 0.001 PHE B4640 TYR 0.021 0.001 TYR A1703 ARG 0.031 0.001 ARG C 880 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 870 time to evaluate : 11.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.6799 (tmm) cc_final: 0.6566 (tmm) REVERT: A 678 MET cc_start: 0.8387 (tpt) cc_final: 0.8086 (tpt) REVERT: A 778 MET cc_start: 0.8370 (tpt) cc_final: 0.8146 (mmm) REVERT: A 1906 MET cc_start: 0.8553 (mmm) cc_final: 0.8345 (mmm) REVERT: A 2685 TYR cc_start: 0.7754 (t80) cc_final: 0.6655 (t80) REVERT: A 2756 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8655 (mt) REVERT: A 2757 MET cc_start: 0.7450 (mpp) cc_final: 0.6584 (mpp) REVERT: A 2840 MET cc_start: 0.8418 (mmt) cc_final: 0.7470 (mtt) REVERT: A 2844 MET cc_start: 0.9232 (ppp) cc_final: 0.8956 (ppp) REVERT: A 2932 TYR cc_start: 0.8481 (m-80) cc_final: 0.8037 (m-80) REVERT: A 2979 ARG cc_start: 0.9031 (tmm160) cc_final: 0.8766 (ttp80) REVERT: A 2982 PHE cc_start: 0.8732 (m-10) cc_final: 0.8320 (m-80) REVERT: A 3060 PHE cc_start: 0.7832 (t80) cc_final: 0.7461 (t80) REVERT: A 3121 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9087 (mt) REVERT: A 3162 PHE cc_start: 0.9130 (t80) cc_final: 0.8652 (t80) REVERT: A 3170 PHE cc_start: 0.8132 (p90) cc_final: 0.7296 (p90) REVERT: A 3245 TYR cc_start: 0.8926 (t80) cc_final: 0.8710 (t80) REVERT: A 3246 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8219 (mpp) REVERT: A 3304 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8696 (tp-100) REVERT: A 4057 HIS cc_start: 0.8438 (m90) cc_final: 0.8187 (m170) REVERT: A 4080 TYR cc_start: 0.8410 (p90) cc_final: 0.7574 (p90) REVERT: A 4504 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7519 (ppp) REVERT: A 4804 MET cc_start: 0.7867 (mmm) cc_final: 0.7630 (mmm) REVERT: A 4879 GLN cc_start: 0.8259 (tp40) cc_final: 0.7454 (tp-100) REVERT: B 317 MET cc_start: 0.6923 (tmm) cc_final: 0.6697 (tmm) REVERT: B 1906 MET cc_start: 0.8417 (mmm) cc_final: 0.8153 (mmt) REVERT: B 2685 TYR cc_start: 0.7566 (t80) cc_final: 0.6495 (t80) REVERT: B 2689 MET cc_start: 0.3641 (ptt) cc_final: 0.2851 (tmm) REVERT: B 2757 MET cc_start: 0.7441 (mpp) cc_final: 0.6631 (mpp) REVERT: B 2840 MET cc_start: 0.8323 (mmt) cc_final: 0.7363 (mtt) REVERT: B 2844 MET cc_start: 0.9162 (ppp) cc_final: 0.8904 (ppp) REVERT: B 2932 TYR cc_start: 0.8444 (m-80) cc_final: 0.8068 (m-80) REVERT: B 2979 ARG cc_start: 0.9043 (tmm160) cc_final: 0.8786 (ttp80) REVERT: B 2982 PHE cc_start: 0.8706 (m-10) cc_final: 0.8333 (m-80) REVERT: B 3060 PHE cc_start: 0.7838 (t80) cc_final: 0.7455 (t80) REVERT: B 3072 MET cc_start: 0.8812 (mpp) cc_final: 0.8603 (ptp) REVERT: B 3121 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9070 (mt) REVERT: B 3147 TYR cc_start: 0.8205 (m-80) cc_final: 0.7971 (m-80) REVERT: B 3162 PHE cc_start: 0.9145 (t80) cc_final: 0.8622 (t80) REVERT: B 3170 PHE cc_start: 0.8199 (p90) cc_final: 0.7415 (p90) REVERT: B 3246 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8234 (mpp) REVERT: B 3304 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8754 (tp-100) REVERT: B 3689 MET cc_start: 0.8274 (mtm) cc_final: 0.8045 (mtm) REVERT: B 4052 MET cc_start: 0.8334 (mtp) cc_final: 0.8094 (mtp) REVERT: B 4057 HIS cc_start: 0.8497 (m90) cc_final: 0.8226 (m170) REVERT: B 4080 TYR cc_start: 0.8402 (p90) cc_final: 0.7639 (p90) REVERT: B 4502 MET cc_start: 0.7891 (mtm) cc_final: 0.7648 (ptp) REVERT: B 4504 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7420 (ppp) REVERT: B 4654 MET cc_start: 0.9031 (tpp) cc_final: 0.8785 (tpp) REVERT: B 4748 MET cc_start: 0.8180 (mpp) cc_final: 0.7738 (mpp) REVERT: B 4879 GLN cc_start: 0.8307 (tp40) cc_final: 0.7515 (tp40) REVERT: C 317 MET cc_start: 0.6921 (tmm) cc_final: 0.6676 (tmm) REVERT: C 999 LEU cc_start: 0.9090 (mt) cc_final: 0.8851 (mt) REVERT: C 1906 MET cc_start: 0.8414 (mmm) cc_final: 0.8144 (mmt) REVERT: C 2685 TYR cc_start: 0.7566 (t80) cc_final: 0.6480 (t80) REVERT: C 2689 MET cc_start: 0.3717 (ptt) cc_final: 0.2943 (tmm) REVERT: C 2757 MET cc_start: 0.7444 (mpp) cc_final: 0.6639 (mpp) REVERT: C 2840 MET cc_start: 0.8359 (mmt) cc_final: 0.7396 (mtt) REVERT: C 2844 MET cc_start: 0.9162 (ppp) cc_final: 0.8903 (ppp) REVERT: C 2932 TYR cc_start: 0.8433 (m-80) cc_final: 0.8063 (m-80) REVERT: C 2979 ARG cc_start: 0.9031 (tmm160) cc_final: 0.8774 (ttp80) REVERT: C 2982 PHE cc_start: 0.8732 (m-10) cc_final: 0.8339 (m-80) REVERT: C 3060 PHE cc_start: 0.7846 (t80) cc_final: 0.7458 (t80) REVERT: C 3121 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9054 (mt) REVERT: C 3162 PHE cc_start: 0.9145 (t80) cc_final: 0.8628 (t80) REVERT: C 3170 PHE cc_start: 0.8207 (p90) cc_final: 0.7414 (p90) REVERT: C 3246 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8224 (mpp) REVERT: C 3304 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8757 (tp-100) REVERT: C 3689 MET cc_start: 0.8285 (mtm) cc_final: 0.8028 (mtm) REVERT: C 4057 HIS cc_start: 0.8470 (m90) cc_final: 0.8192 (m170) REVERT: C 4080 TYR cc_start: 0.8380 (p90) cc_final: 0.7625 (p90) REVERT: C 4502 MET cc_start: 0.7877 (mtm) cc_final: 0.7634 (ptp) REVERT: C 4504 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7429 (ppp) REVERT: C 4654 MET cc_start: 0.9037 (tpp) cc_final: 0.8774 (tpp) REVERT: C 4748 MET cc_start: 0.8173 (mpp) cc_final: 0.7783 (mpp) REVERT: C 4879 GLN cc_start: 0.8279 (tp40) cc_final: 0.7438 (tp-100) REVERT: D 317 MET cc_start: 0.6926 (tmm) cc_final: 0.6701 (tmm) REVERT: D 678 MET cc_start: 0.8360 (tpt) cc_final: 0.8031 (tpt) REVERT: D 999 LEU cc_start: 0.9088 (mt) cc_final: 0.8852 (mt) REVERT: D 1906 MET cc_start: 0.8408 (mmm) cc_final: 0.8145 (mmt) REVERT: D 2685 TYR cc_start: 0.7569 (t80) cc_final: 0.6514 (t80) REVERT: D 2756 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8658 (mt) REVERT: D 2757 MET cc_start: 0.7438 (mpp) cc_final: 0.6624 (mpp) REVERT: D 2840 MET cc_start: 0.8318 (mmt) cc_final: 0.7327 (mtt) REVERT: D 2844 MET cc_start: 0.9179 (ppp) cc_final: 0.8893 (ppp) REVERT: D 2932 TYR cc_start: 0.8425 (m-80) cc_final: 0.8070 (m-80) REVERT: D 2979 ARG cc_start: 0.9075 (tmm160) cc_final: 0.8814 (ttp80) REVERT: D 2982 PHE cc_start: 0.8716 (m-10) cc_final: 0.8343 (m-80) REVERT: D 3060 PHE cc_start: 0.7833 (t80) cc_final: 0.7455 (t80) REVERT: D 3072 MET cc_start: 0.8805 (mpp) cc_final: 0.8583 (ptp) REVERT: D 3121 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9042 (mt) REVERT: D 3147 TYR cc_start: 0.8194 (m-80) cc_final: 0.7960 (m-80) REVERT: D 3162 PHE cc_start: 0.9147 (t80) cc_final: 0.8607 (t80) REVERT: D 3170 PHE cc_start: 0.8204 (p90) cc_final: 0.7429 (p90) REVERT: D 3246 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8253 (mpp) REVERT: D 3304 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8727 (tp-100) REVERT: D 3689 MET cc_start: 0.8289 (mtm) cc_final: 0.8059 (mtm) REVERT: D 4052 MET cc_start: 0.8312 (mtp) cc_final: 0.8055 (mtp) REVERT: D 4080 TYR cc_start: 0.8367 (p90) cc_final: 0.7631 (p90) REVERT: D 4502 MET cc_start: 0.7882 (mtm) cc_final: 0.7646 (ptp) REVERT: D 4504 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7372 (ppp) REVERT: D 4654 MET cc_start: 0.9044 (tpp) cc_final: 0.8645 (tpp) REVERT: D 4748 MET cc_start: 0.8192 (mpp) cc_final: 0.7748 (mpp) REVERT: D 4879 GLN cc_start: 0.8297 (tp40) cc_final: 0.7442 (tp-100) outliers start: 44 outliers final: 0 residues processed: 878 average time/residue: 1.1238 time to fit residues: 1753.6337 Evaluate side-chains 777 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 763 time to evaluate : 10.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2756 LEU Chi-restraints excluded: chain A residue 3121 LEU Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 4504 MET Chi-restraints excluded: chain B residue 3121 LEU Chi-restraints excluded: chain B residue 3246 MET Chi-restraints excluded: chain B residue 4504 MET Chi-restraints excluded: chain C residue 3121 LEU Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4504 MET Chi-restraints excluded: chain D residue 2756 LEU Chi-restraints excluded: chain D residue 3121 LEU Chi-restraints excluded: chain D residue 3246 MET Chi-restraints excluded: chain D residue 4504 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1425 optimal weight: 8.9990 chunk 1279 optimal weight: 20.0000 chunk 709 optimal weight: 7.9990 chunk 437 optimal weight: 9.9990 chunk 863 optimal weight: 6.9990 chunk 683 optimal weight: 5.9990 chunk 1323 optimal weight: 7.9990 chunk 511 optimal weight: 20.0000 chunk 804 optimal weight: 5.9990 chunk 984 optimal weight: 10.0000 chunk 1532 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS A 914 GLN A 927 GLN A 932 ASN A1498 GLN ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3079 GLN ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4296 HIS ** A4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS B 927 GLN B 932 ASN B1498 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3079 GLN ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS C 927 GLN C 932 ASN C1498 GLN ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3079 GLN ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS D 927 GLN D 932 ASN D1498 GLN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3079 GLN ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 138292 Z= 0.438 Angle : 0.692 10.885 186864 Z= 0.357 Chirality : 0.043 0.222 20500 Planarity : 0.005 0.143 23992 Dihedral : 6.559 87.080 18612 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 0.41 % Allowed : 4.07 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.06), residues: 16792 helix: 1.39 (0.06), residues: 8972 sheet: -0.19 (0.13), residues: 1676 loop : -0.58 (0.08), residues: 6144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B2732 HIS 0.008 0.002 HIS D3665 PHE 0.040 0.002 PHE C3117 TYR 0.041 0.002 TYR C1703 ARG 0.014 0.001 ARG A3260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 820 time to evaluate : 11.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.7897 (ppp) cc_final: 0.7649 (ppp) REVERT: A 655 MET cc_start: 0.9253 (mmp) cc_final: 0.8947 (mmp) REVERT: A 678 MET cc_start: 0.8338 (tpt) cc_final: 0.7894 (tpt) REVERT: A 778 MET cc_start: 0.8319 (tpt) cc_final: 0.8021 (mmm) REVERT: A 895 MET cc_start: 0.8963 (mtt) cc_final: 0.8724 (mmm) REVERT: A 902 TRP cc_start: 0.5438 (t-100) cc_final: 0.4712 (t-100) REVERT: A 1498 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8080 (pm20) REVERT: A 1948 MET cc_start: 0.8265 (mmm) cc_final: 0.7841 (mmm) REVERT: A 2605 MET cc_start: 0.9152 (ppp) cc_final: 0.8865 (ppp) REVERT: A 2681 MET cc_start: 0.8193 (tpp) cc_final: 0.7418 (tmm) REVERT: A 2685 TYR cc_start: 0.7805 (t80) cc_final: 0.7170 (t80) REVERT: A 2689 MET cc_start: 0.3795 (ptt) cc_final: 0.2856 (tmm) REVERT: A 2757 MET cc_start: 0.7426 (mpp) cc_final: 0.6782 (mpp) REVERT: A 2840 MET cc_start: 0.8336 (mmt) cc_final: 0.7819 (mmm) REVERT: A 2844 MET cc_start: 0.9201 (ppp) cc_final: 0.8952 (ppp) REVERT: A 2874 TYR cc_start: 0.8510 (t80) cc_final: 0.8164 (t80) REVERT: A 2932 TYR cc_start: 0.8613 (m-80) cc_final: 0.8375 (m-80) REVERT: A 2979 ARG cc_start: 0.9079 (tmm160) cc_final: 0.8828 (ttp80) REVERT: A 2982 PHE cc_start: 0.8912 (m-10) cc_final: 0.8566 (m-80) REVERT: A 3060 PHE cc_start: 0.8079 (t80) cc_final: 0.7684 (t80) REVERT: A 3131 TYR cc_start: 0.9156 (m-80) cc_final: 0.8550 (m-80) REVERT: A 3138 TYR cc_start: 0.9269 (t80) cc_final: 0.8805 (t80) REVERT: A 3162 PHE cc_start: 0.9165 (t80) cc_final: 0.8782 (t80) REVERT: A 3170 PHE cc_start: 0.8146 (p90) cc_final: 0.7383 (p90) REVERT: A 3245 TYR cc_start: 0.9050 (t80) cc_final: 0.8815 (t80) REVERT: A 3246 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8251 (mpp) REVERT: A 3304 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8788 (tp-100) REVERT: A 3954 MET cc_start: 0.8666 (mmp) cc_final: 0.8372 (mmm) REVERT: A 4057 HIS cc_start: 0.8442 (m90) cc_final: 0.8241 (m170) REVERT: A 4080 TYR cc_start: 0.8477 (p90) cc_final: 0.7656 (p90) REVERT: A 4258 MET cc_start: 0.3665 (ppp) cc_final: 0.3294 (ppp) REVERT: A 4748 MET cc_start: 0.8064 (mpp) cc_final: 0.7657 (mpp) REVERT: A 4879 GLN cc_start: 0.8170 (tp40) cc_final: 0.7315 (tp-100) REVERT: A 4943 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: B 655 MET cc_start: 0.9292 (mmp) cc_final: 0.8622 (mmp) REVERT: B 778 MET cc_start: 0.8240 (tpt) cc_final: 0.7829 (mmm) REVERT: B 895 MET cc_start: 0.8999 (mtt) cc_final: 0.8771 (mmm) REVERT: B 1498 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: B 1948 MET cc_start: 0.8232 (mmm) cc_final: 0.8000 (mmm) REVERT: B 2681 MET cc_start: 0.8075 (tpp) cc_final: 0.7322 (tmm) REVERT: B 2685 TYR cc_start: 0.7793 (t80) cc_final: 0.7116 (t80) REVERT: B 2757 MET cc_start: 0.7182 (mpp) cc_final: 0.6645 (mpp) REVERT: B 2840 MET cc_start: 0.8226 (mmt) cc_final: 0.7709 (mmm) REVERT: B 2844 MET cc_start: 0.9192 (ppp) cc_final: 0.8940 (ppp) REVERT: B 2874 TYR cc_start: 0.8654 (t80) cc_final: 0.8336 (t80) REVERT: B 2884 LYS cc_start: 0.9345 (pptt) cc_final: 0.8887 (pptt) REVERT: B 2932 TYR cc_start: 0.8595 (m-80) cc_final: 0.8188 (m-80) REVERT: B 2979 ARG cc_start: 0.9085 (tmm160) cc_final: 0.8816 (ttp80) REVERT: B 2982 PHE cc_start: 0.8923 (m-10) cc_final: 0.8581 (m-80) REVERT: B 3060 PHE cc_start: 0.8110 (t80) cc_final: 0.7701 (t80) REVERT: B 3114 GLN cc_start: 0.8789 (pp30) cc_final: 0.8574 (pp30) REVERT: B 3131 TYR cc_start: 0.9177 (m-80) cc_final: 0.8573 (m-80) REVERT: B 3138 TYR cc_start: 0.9327 (t80) cc_final: 0.8864 (t80) REVERT: B 3147 TYR cc_start: 0.8420 (m-80) cc_final: 0.8135 (m-80) REVERT: B 3162 PHE cc_start: 0.9170 (t80) cc_final: 0.8825 (t80) REVERT: B 3246 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8219 (mpp) REVERT: B 3954 MET cc_start: 0.8668 (mmp) cc_final: 0.8400 (mmm) REVERT: B 4057 HIS cc_start: 0.8444 (m90) cc_final: 0.8222 (m170) REVERT: B 4080 TYR cc_start: 0.8464 (p90) cc_final: 0.7709 (p90) REVERT: B 4748 MET cc_start: 0.8254 (mpp) cc_final: 0.7796 (mpp) REVERT: B 4879 GLN cc_start: 0.8113 (tp40) cc_final: 0.7199 (tp-100) REVERT: C 81 MET cc_start: 0.7856 (ppp) cc_final: 0.7617 (ppp) REVERT: C 655 MET cc_start: 0.9280 (mmp) cc_final: 0.8634 (mmp) REVERT: C 778 MET cc_start: 0.8248 (tpt) cc_final: 0.7910 (mmm) REVERT: C 895 MET cc_start: 0.8947 (mtt) cc_final: 0.8727 (mmm) REVERT: C 1498 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8106 (pm20) REVERT: C 1948 MET cc_start: 0.8279 (mmm) cc_final: 0.7963 (tpp) REVERT: C 2681 MET cc_start: 0.8117 (tpp) cc_final: 0.7319 (tmm) REVERT: C 2685 TYR cc_start: 0.7768 (t80) cc_final: 0.7096 (t80) REVERT: C 2757 MET cc_start: 0.7200 (mpp) cc_final: 0.6668 (mpp) REVERT: C 2840 MET cc_start: 0.8217 (mmt) cc_final: 0.7670 (mmm) REVERT: C 2844 MET cc_start: 0.9188 (ppp) cc_final: 0.8948 (ppp) REVERT: C 2874 TYR cc_start: 0.8635 (t80) cc_final: 0.8313 (t80) REVERT: C 2932 TYR cc_start: 0.8587 (m-80) cc_final: 0.8191 (m-80) REVERT: C 2979 ARG cc_start: 0.9093 (tmm160) cc_final: 0.8817 (ttp80) REVERT: C 2982 PHE cc_start: 0.8912 (m-10) cc_final: 0.8562 (m-80) REVERT: C 3060 PHE cc_start: 0.8129 (t80) cc_final: 0.7730 (t80) REVERT: C 3114 GLN cc_start: 0.8781 (pp30) cc_final: 0.8573 (pp30) REVERT: C 3131 TYR cc_start: 0.9183 (m-80) cc_final: 0.8570 (m-80) REVERT: C 3138 TYR cc_start: 0.9299 (t80) cc_final: 0.8879 (t80) REVERT: C 3162 PHE cc_start: 0.9143 (t80) cc_final: 0.8716 (t80) REVERT: C 3170 PHE cc_start: 0.8470 (p90) cc_final: 0.7938 (p90) REVERT: C 3954 MET cc_start: 0.8659 (mmp) cc_final: 0.8389 (mmm) REVERT: C 4080 TYR cc_start: 0.8453 (p90) cc_final: 0.7699 (p90) REVERT: C 4748 MET cc_start: 0.8252 (mpp) cc_final: 0.7762 (mpp) REVERT: C 4879 GLN cc_start: 0.8130 (tp40) cc_final: 0.7235 (tp-100) REVERT: D 81 MET cc_start: 0.7857 (ppp) cc_final: 0.7619 (ppp) REVERT: D 393 MET cc_start: 0.8357 (tpt) cc_final: 0.7386 (mmm) REVERT: D 655 MET cc_start: 0.9276 (mmp) cc_final: 0.8608 (mmp) REVERT: D 778 MET cc_start: 0.8246 (tpt) cc_final: 0.7840 (mmm) REVERT: D 895 MET cc_start: 0.8952 (mtt) cc_final: 0.8743 (mmm) REVERT: D 1498 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: D 1948 MET cc_start: 0.8274 (mmm) cc_final: 0.7954 (tpp) REVERT: D 1953 MET cc_start: 0.7396 (mmt) cc_final: 0.7166 (mpp) REVERT: D 2681 MET cc_start: 0.8099 (tpp) cc_final: 0.7253 (tmm) REVERT: D 2685 TYR cc_start: 0.7804 (t80) cc_final: 0.7136 (t80) REVERT: D 2689 MET cc_start: 0.3557 (ptt) cc_final: 0.2652 (tmm) REVERT: D 2757 MET cc_start: 0.7347 (mpp) cc_final: 0.6761 (mpp) REVERT: D 2840 MET cc_start: 0.8204 (mmt) cc_final: 0.7668 (mmm) REVERT: D 2844 MET cc_start: 0.9181 (ppp) cc_final: 0.8918 (ppp) REVERT: D 2932 TYR cc_start: 0.8578 (m-80) cc_final: 0.8340 (m-80) REVERT: D 2979 ARG cc_start: 0.9095 (tmm160) cc_final: 0.8833 (ttp80) REVERT: D 2982 PHE cc_start: 0.8919 (m-10) cc_final: 0.8565 (m-80) REVERT: D 3060 PHE cc_start: 0.8062 (t80) cc_final: 0.7657 (t80) REVERT: D 3131 TYR cc_start: 0.9173 (m-80) cc_final: 0.8583 (m-80) REVERT: D 3147 TYR cc_start: 0.8395 (m-80) cc_final: 0.8108 (m-80) REVERT: D 3162 PHE cc_start: 0.9181 (t80) cc_final: 0.8721 (t80) REVERT: D 3170 PHE cc_start: 0.8468 (p90) cc_final: 0.7933 (p90) REVERT: D 3246 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8237 (mpp) REVERT: D 3304 GLN cc_start: 0.9172 (tp-100) cc_final: 0.8791 (tp-100) REVERT: D 3954 MET cc_start: 0.8665 (mmp) cc_final: 0.8395 (mmm) REVERT: D 4080 TYR cc_start: 0.8456 (p90) cc_final: 0.7705 (p90) REVERT: D 4748 MET cc_start: 0.8201 (mpp) cc_final: 0.7705 (mpp) REVERT: D 4879 GLN cc_start: 0.8143 (tp40) cc_final: 0.7254 (tp-100) outliers start: 61 outliers final: 27 residues processed: 836 average time/residue: 1.1063 time to fit residues: 1657.9829 Evaluate side-chains 812 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 777 time to evaluate : 11.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 927 GLN Chi-restraints excluded: chain A residue 1498 GLN Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3246 MET Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 927 GLN Chi-restraints excluded: chain B residue 1498 GLN Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 3246 MET Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 927 GLN Chi-restraints excluded: chain C residue 1498 GLN Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 3246 MET Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain D residue 469 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 927 GLN Chi-restraints excluded: chain D residue 1498 GLN Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 3246 MET Chi-restraints excluded: chain D residue 4274 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 851 optimal weight: 20.0000 chunk 475 optimal weight: 0.9990 chunk 1275 optimal weight: 3.9990 chunk 1043 optimal weight: 9.9990 chunk 422 optimal weight: 10.0000 chunk 1535 optimal weight: 5.9990 chunk 1658 optimal weight: 6.9990 chunk 1367 optimal weight: 20.0000 chunk 1522 optimal weight: 8.9990 chunk 523 optimal weight: 40.0000 chunk 1231 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS A 927 GLN ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2729 HIS ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4879 GLN ** A4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS B 927 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2464 HIS ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4879 GLN ** B4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS C 927 GLN ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4879 GLN ** C4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS D 927 GLN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2464 HIS ** D2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4879 GLN ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 138292 Z= 0.261 Angle : 0.607 13.342 186864 Z= 0.310 Chirality : 0.040 0.214 20500 Planarity : 0.005 0.132 23992 Dihedral : 6.293 89.765 18588 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 0.36 % Allowed : 5.77 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.07), residues: 16792 helix: 1.58 (0.06), residues: 8972 sheet: -0.22 (0.13), residues: 1680 loop : -0.56 (0.08), residues: 6140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C2732 HIS 0.007 0.001 HIS D3700 PHE 0.047 0.001 PHE C2943 TYR 0.035 0.001 TYR C1703 ARG 0.006 0.000 ARG D3192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 795 time to evaluate : 11.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8474 (tpt) cc_final: 0.7876 (mmm) REVERT: A 655 MET cc_start: 0.9273 (mmp) cc_final: 0.8844 (mmp) REVERT: A 678 MET cc_start: 0.8322 (tpt) cc_final: 0.7843 (tpt) REVERT: A 778 MET cc_start: 0.8281 (tpt) cc_final: 0.7988 (mmm) REVERT: A 895 MET cc_start: 0.9048 (mtt) cc_final: 0.8797 (mmt) REVERT: A 902 TRP cc_start: 0.5712 (t-100) cc_final: 0.5123 (t-100) REVERT: A 1948 MET cc_start: 0.8146 (mmm) cc_final: 0.7729 (ppp) REVERT: A 2605 MET cc_start: 0.9131 (ppp) cc_final: 0.8792 (ppp) REVERT: A 2685 TYR cc_start: 0.7791 (t80) cc_final: 0.7105 (t80) REVERT: A 2757 MET cc_start: 0.7322 (mpp) cc_final: 0.6649 (mpp) REVERT: A 2840 MET cc_start: 0.8300 (mmt) cc_final: 0.7879 (mmm) REVERT: A 2844 MET cc_start: 0.9096 (ppp) cc_final: 0.8868 (ppp) REVERT: A 2874 TYR cc_start: 0.8610 (t80) cc_final: 0.8384 (t80) REVERT: A 2932 TYR cc_start: 0.8627 (m-80) cc_final: 0.8325 (m-80) REVERT: A 2979 ARG cc_start: 0.9070 (tmm160) cc_final: 0.8809 (ttp80) REVERT: A 2982 PHE cc_start: 0.8872 (m-10) cc_final: 0.8536 (m-80) REVERT: A 3060 PHE cc_start: 0.8086 (t80) cc_final: 0.7317 (t80) REVERT: A 3131 TYR cc_start: 0.9166 (m-80) cc_final: 0.8679 (m-80) REVERT: A 3138 TYR cc_start: 0.9266 (t80) cc_final: 0.8796 (t80) REVERT: A 3162 PHE cc_start: 0.9104 (t80) cc_final: 0.8714 (t80) REVERT: A 3170 PHE cc_start: 0.8163 (p90) cc_final: 0.7143 (p90) REVERT: A 3245 TYR cc_start: 0.9010 (t80) cc_final: 0.8793 (t80) REVERT: A 3304 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8735 (tp-100) REVERT: A 4057 HIS cc_start: 0.8389 (m90) cc_final: 0.8177 (m170) REVERT: A 4080 TYR cc_start: 0.8485 (p90) cc_final: 0.7709 (p90) REVERT: A 4258 MET cc_start: 0.3736 (ppp) cc_final: 0.3421 (ppp) REVERT: A 4748 MET cc_start: 0.8094 (mpp) cc_final: 0.7683 (mpp) REVERT: A 4879 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7385 (tp40) REVERT: A 4943 MET cc_start: 0.8075 (mtp) cc_final: 0.7613 (mtp) REVERT: B 393 MET cc_start: 0.8447 (tpt) cc_final: 0.7825 (mmm) REVERT: B 655 MET cc_start: 0.9301 (mmp) cc_final: 0.8699 (mmp) REVERT: B 678 MET cc_start: 0.8286 (tpt) cc_final: 0.7860 (tpt) REVERT: B 778 MET cc_start: 0.8197 (tpt) cc_final: 0.7907 (mmm) REVERT: B 999 LEU cc_start: 0.9144 (mt) cc_final: 0.8803 (mt) REVERT: B 1948 MET cc_start: 0.8156 (mmm) cc_final: 0.7820 (mmm) REVERT: B 2142 MET cc_start: 0.8587 (tpp) cc_final: 0.8352 (tpp) REVERT: B 2681 MET cc_start: 0.8006 (tpp) cc_final: 0.7187 (tmm) REVERT: B 2685 TYR cc_start: 0.7792 (t80) cc_final: 0.7097 (t80) REVERT: B 2689 MET cc_start: 0.3718 (ptt) cc_final: 0.3070 (tmm) REVERT: B 2727 HIS cc_start: 0.9164 (t-90) cc_final: 0.8743 (t-90) REVERT: B 2731 LYS cc_start: 0.9447 (pttm) cc_final: 0.9096 (pttm) REVERT: B 2757 MET cc_start: 0.7327 (mpp) cc_final: 0.6567 (mpp) REVERT: B 2798 MET cc_start: 0.7803 (mmp) cc_final: 0.7575 (mmm) REVERT: B 2840 MET cc_start: 0.8137 (mmt) cc_final: 0.7744 (mmm) REVERT: B 2932 TYR cc_start: 0.8621 (m-80) cc_final: 0.8220 (m-80) REVERT: B 2979 ARG cc_start: 0.9082 (tmm160) cc_final: 0.8801 (ttp80) REVERT: B 2982 PHE cc_start: 0.8866 (m-10) cc_final: 0.8516 (m-80) REVERT: B 3060 PHE cc_start: 0.8072 (t80) cc_final: 0.7669 (t80) REVERT: B 3114 GLN cc_start: 0.8776 (pp30) cc_final: 0.8464 (pp30) REVERT: B 3131 TYR cc_start: 0.9167 (m-80) cc_final: 0.8629 (m-80) REVERT: B 3138 TYR cc_start: 0.9308 (t80) cc_final: 0.8869 (t80) REVERT: B 3147 TYR cc_start: 0.8384 (m-80) cc_final: 0.8136 (m-80) REVERT: B 3162 PHE cc_start: 0.9126 (t80) cc_final: 0.8851 (t80) REVERT: B 3170 PHE cc_start: 0.8698 (p90) cc_final: 0.8060 (p90) REVERT: B 3304 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8758 (tp-100) REVERT: B 3819 MET cc_start: 0.6958 (ptt) cc_final: 0.6706 (ptt) REVERT: B 4057 HIS cc_start: 0.8406 (m90) cc_final: 0.8200 (m170) REVERT: B 4080 TYR cc_start: 0.8469 (p90) cc_final: 0.7687 (p90) REVERT: B 4258 MET cc_start: 0.3442 (ppp) cc_final: 0.3049 (ppp) REVERT: B 4654 MET cc_start: 0.9112 (tpp) cc_final: 0.8748 (tpp) REVERT: B 4748 MET cc_start: 0.8261 (mpp) cc_final: 0.7781 (mpp) REVERT: B 4879 GLN cc_start: 0.7976 (tp-100) cc_final: 0.7274 (tp40) REVERT: C 393 MET cc_start: 0.8454 (tpt) cc_final: 0.7830 (mmm) REVERT: C 655 MET cc_start: 0.9306 (mmp) cc_final: 0.8729 (mmp) REVERT: C 778 MET cc_start: 0.8206 (tpt) cc_final: 0.7905 (mmm) REVERT: C 999 LEU cc_start: 0.9159 (mt) cc_final: 0.8832 (mt) REVERT: C 1948 MET cc_start: 0.8275 (mmm) cc_final: 0.7963 (tpp) REVERT: C 1953 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7298 (mpp) REVERT: C 2666 LEU cc_start: 0.9454 (tt) cc_final: 0.9252 (pp) REVERT: C 2681 MET cc_start: 0.7991 (tpp) cc_final: 0.7140 (tmm) REVERT: C 2685 TYR cc_start: 0.7789 (t80) cc_final: 0.7084 (t80) REVERT: C 2689 MET cc_start: 0.3735 (ptt) cc_final: 0.3072 (tmm) REVERT: C 2727 HIS cc_start: 0.9173 (t-90) cc_final: 0.8734 (t-90) REVERT: C 2731 LYS cc_start: 0.9453 (pttm) cc_final: 0.9107 (pttm) REVERT: C 2757 MET cc_start: 0.7303 (mpp) cc_final: 0.6550 (mpp) REVERT: C 2840 MET cc_start: 0.8193 (mmt) cc_final: 0.7765 (mmm) REVERT: C 2844 MET cc_start: 0.9060 (ppp) cc_final: 0.8803 (ppp) REVERT: C 2932 TYR cc_start: 0.8612 (m-80) cc_final: 0.8186 (m-80) REVERT: C 2979 ARG cc_start: 0.9083 (tmm160) cc_final: 0.8800 (ttp80) REVERT: C 2982 PHE cc_start: 0.8878 (m-10) cc_final: 0.8511 (m-80) REVERT: C 3060 PHE cc_start: 0.8078 (t80) cc_final: 0.7679 (t80) REVERT: C 3114 GLN cc_start: 0.8783 (pp30) cc_final: 0.8467 (pp30) REVERT: C 3131 TYR cc_start: 0.9157 (m-80) cc_final: 0.8608 (m-80) REVERT: C 3162 PHE cc_start: 0.9159 (t80) cc_final: 0.8721 (t80) REVERT: C 3170 PHE cc_start: 0.8583 (p90) cc_final: 0.8080 (p90) REVERT: C 3304 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8759 (tp-100) REVERT: C 3819 MET cc_start: 0.6958 (ptt) cc_final: 0.6705 (ptt) REVERT: C 4080 TYR cc_start: 0.8470 (p90) cc_final: 0.7703 (p90) REVERT: C 4258 MET cc_start: 0.3439 (ppp) cc_final: 0.3035 (ppp) REVERT: C 4654 MET cc_start: 0.9109 (tpp) cc_final: 0.8732 (tpp) REVERT: C 4748 MET cc_start: 0.8255 (mpp) cc_final: 0.7760 (mpp) REVERT: C 4879 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7282 (tp40) REVERT: D 393 MET cc_start: 0.8438 (tpt) cc_final: 0.7745 (mmm) REVERT: D 655 MET cc_start: 0.9281 (mmp) cc_final: 0.8695 (mmp) REVERT: D 778 MET cc_start: 0.8200 (tpt) cc_final: 0.7905 (mmm) REVERT: D 999 LEU cc_start: 0.9154 (mt) cc_final: 0.8829 (mt) REVERT: D 1948 MET cc_start: 0.8238 (mmm) cc_final: 0.7936 (tpp) REVERT: D 1953 MET cc_start: 0.7437 (mmt) cc_final: 0.7209 (mpp) REVERT: D 2681 MET cc_start: 0.7970 (tpp) cc_final: 0.7118 (tmm) REVERT: D 2685 TYR cc_start: 0.7772 (t80) cc_final: 0.7074 (t80) REVERT: D 2689 MET cc_start: 0.3956 (ptt) cc_final: 0.3009 (tmm) REVERT: D 2727 HIS cc_start: 0.9158 (t-90) cc_final: 0.8709 (t-90) REVERT: D 2731 LYS cc_start: 0.9448 (pttm) cc_final: 0.9089 (pttm) REVERT: D 2757 MET cc_start: 0.7401 (mpp) cc_final: 0.6635 (mpp) REVERT: D 2798 MET cc_start: 0.7787 (mmp) cc_final: 0.7537 (mmm) REVERT: D 2840 MET cc_start: 0.8171 (mmt) cc_final: 0.7753 (mmm) REVERT: D 2844 MET cc_start: 0.9043 (ppp) cc_final: 0.8722 (ppp) REVERT: D 2874 TYR cc_start: 0.8634 (t80) cc_final: 0.8346 (t80) REVERT: D 2932 TYR cc_start: 0.8618 (m-80) cc_final: 0.8340 (m-80) REVERT: D 2979 ARG cc_start: 0.9093 (tmm160) cc_final: 0.8821 (ttp80) REVERT: D 2982 PHE cc_start: 0.8882 (m-10) cc_final: 0.8519 (m-80) REVERT: D 3060 PHE cc_start: 0.8050 (t80) cc_final: 0.7648 (t80) REVERT: D 3131 TYR cc_start: 0.9157 (m-80) cc_final: 0.8668 (m-80) REVERT: D 3138 TYR cc_start: 0.9292 (t80) cc_final: 0.8873 (t80) REVERT: D 3147 TYR cc_start: 0.8348 (m-80) cc_final: 0.8108 (m-80) REVERT: D 3162 PHE cc_start: 0.9098 (t80) cc_final: 0.8670 (t80) REVERT: D 3170 PHE cc_start: 0.8578 (p90) cc_final: 0.8072 (p90) REVERT: D 3304 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8754 (tp-100) REVERT: D 3819 MET cc_start: 0.6977 (ptt) cc_final: 0.6724 (ptt) REVERT: D 4080 TYR cc_start: 0.8469 (p90) cc_final: 0.7693 (p90) REVERT: D 4258 MET cc_start: 0.3445 (ppp) cc_final: 0.3044 (ppp) REVERT: D 4654 MET cc_start: 0.9138 (tpp) cc_final: 0.8727 (tpp) REVERT: D 4748 MET cc_start: 0.8190 (mpp) cc_final: 0.7706 (mpp) REVERT: D 4879 GLN cc_start: 0.7992 (tp-100) cc_final: 0.7298 (tp40) outliers start: 54 outliers final: 32 residues processed: 810 average time/residue: 1.1523 time to fit residues: 1673.9494 Evaluate side-chains 804 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 771 time to evaluate : 11.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 HIS Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2859 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain C residue 469 HIS Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain D residue 469 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4572 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1517 optimal weight: 5.9990 chunk 1154 optimal weight: 9.9990 chunk 796 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 732 optimal weight: 9.9990 chunk 1031 optimal weight: 4.9990 chunk 1541 optimal weight: 20.0000 chunk 1631 optimal weight: 8.9990 chunk 805 optimal weight: 9.9990 chunk 1460 optimal weight: 3.9990 chunk 439 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2550 HIS ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3806 ASN ** A3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4296 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 GLN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2464 HIS ** B2550 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2729 HIS ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3806 ASN ** B3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 240 HIS ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2464 HIS ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2729 HIS ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3806 ASN ** C3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS D 914 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2464 HIS D2550 HIS ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2729 HIS ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3806 ASN ** D3925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 138292 Z= 0.412 Angle : 0.656 16.417 186864 Z= 0.336 Chirality : 0.041 0.199 20500 Planarity : 0.005 0.129 23992 Dihedral : 6.176 86.587 18576 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.59 % Rotamer: Outliers : 0.57 % Allowed : 6.96 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.07), residues: 16792 helix: 1.54 (0.06), residues: 9024 sheet: -0.33 (0.13), residues: 1596 loop : -0.54 (0.08), residues: 6172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B3250 HIS 0.008 0.001 HIS D3665 PHE 0.027 0.002 PHE A3117 TYR 0.035 0.002 TYR C1703 ARG 0.008 0.001 ARG A1960 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 800 time to evaluate : 11.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8463 (tpt) cc_final: 0.7871 (mmm) REVERT: A 655 MET cc_start: 0.9274 (mmp) cc_final: 0.8623 (mmp) REVERT: A 678 MET cc_start: 0.8354 (tpt) cc_final: 0.7836 (tpt) REVERT: A 895 MET cc_start: 0.9088 (mtt) cc_final: 0.8839 (mmt) REVERT: A 902 TRP cc_start: 0.5949 (t-100) cc_final: 0.5188 (t-100) REVERT: A 1948 MET cc_start: 0.8094 (mmm) cc_final: 0.7676 (ppp) REVERT: A 2605 MET cc_start: 0.9171 (ppp) cc_final: 0.8823 (ppp) REVERT: A 2685 TYR cc_start: 0.7932 (t80) cc_final: 0.7357 (t80) REVERT: A 2688 MET cc_start: 0.7821 (mpp) cc_final: 0.7500 (mmp) REVERT: A 2689 MET cc_start: 0.4589 (ptt) cc_final: 0.3843 (tmm) REVERT: A 2727 HIS cc_start: 0.9114 (t-90) cc_final: 0.8779 (t-90) REVERT: A 2731 LYS cc_start: 0.9473 (ptpp) cc_final: 0.8943 (ptpp) REVERT: A 2757 MET cc_start: 0.7119 (mpp) cc_final: 0.6399 (mpp) REVERT: A 2840 MET cc_start: 0.8310 (mmt) cc_final: 0.7798 (mmm) REVERT: A 2932 TYR cc_start: 0.8700 (m-80) cc_final: 0.8354 (m-80) REVERT: A 2979 ARG cc_start: 0.9092 (tmm160) cc_final: 0.8867 (ttp80) REVERT: A 2982 PHE cc_start: 0.8974 (m-10) cc_final: 0.8649 (m-80) REVERT: A 3060 PHE cc_start: 0.8161 (t80) cc_final: 0.7807 (t80) REVERT: A 3131 TYR cc_start: 0.9161 (m-80) cc_final: 0.8690 (m-80) REVERT: A 3138 TYR cc_start: 0.9322 (t80) cc_final: 0.8832 (t80) REVERT: A 3162 PHE cc_start: 0.9100 (t80) cc_final: 0.8722 (t80) REVERT: A 3170 PHE cc_start: 0.8230 (p90) cc_final: 0.7479 (p90) REVERT: A 3245 TYR cc_start: 0.9088 (t80) cc_final: 0.8861 (t80) REVERT: A 3246 MET cc_start: 0.9036 (mtm) cc_final: 0.8497 (mpp) REVERT: A 3304 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8731 (tp-100) REVERT: A 4057 HIS cc_start: 0.8393 (m90) cc_final: 0.8134 (m170) REVERT: A 4080 TYR cc_start: 0.8526 (p90) cc_final: 0.7813 (p90) REVERT: A 4258 MET cc_start: 0.3723 (ppp) cc_final: 0.3440 (ppp) REVERT: A 4654 MET cc_start: 0.8855 (tpp) cc_final: 0.8455 (tpp) REVERT: A 4748 MET cc_start: 0.8055 (mpp) cc_final: 0.7713 (mpp) REVERT: A 4879 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7342 (tp-100) REVERT: A 4943 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7684 (mtp) REVERT: B 393 MET cc_start: 0.8420 (tpt) cc_final: 0.7811 (mmm) REVERT: B 655 MET cc_start: 0.9251 (mmp) cc_final: 0.8743 (mmp) REVERT: B 778 MET cc_start: 0.8231 (tpt) cc_final: 0.7838 (mmm) REVERT: B 935 MET cc_start: 0.9334 (ppp) cc_final: 0.9111 (ppp) REVERT: B 1948 MET cc_start: 0.8042 (mmm) cc_final: 0.7593 (ppp) REVERT: B 2681 MET cc_start: 0.8078 (tpp) cc_final: 0.7411 (tmm) REVERT: B 2685 TYR cc_start: 0.7830 (t80) cc_final: 0.7520 (t80) REVERT: B 2689 MET cc_start: 0.4070 (ptt) cc_final: 0.2961 (tmm) REVERT: B 2719 TYR cc_start: 0.9114 (t80) cc_final: 0.8779 (t80) REVERT: B 2727 HIS cc_start: 0.9216 (t-90) cc_final: 0.8685 (t-90) REVERT: B 2731 LYS cc_start: 0.9435 (pttm) cc_final: 0.8901 (pttm) REVERT: B 2757 MET cc_start: 0.7330 (mpp) cc_final: 0.6867 (mpp) REVERT: B 2844 MET cc_start: 0.9135 (ppp) cc_final: 0.8878 (ppp) REVERT: B 2848 TYR cc_start: 0.8367 (m-10) cc_final: 0.7912 (m-10) REVERT: B 2932 TYR cc_start: 0.8658 (m-80) cc_final: 0.8330 (m-80) REVERT: B 2979 ARG cc_start: 0.9104 (tmm160) cc_final: 0.8867 (ttp80) REVERT: B 2982 PHE cc_start: 0.8978 (m-10) cc_final: 0.8638 (m-80) REVERT: B 3060 PHE cc_start: 0.8163 (t80) cc_final: 0.7791 (t80) REVERT: B 3114 GLN cc_start: 0.8773 (pp30) cc_final: 0.8421 (pp30) REVERT: B 3131 TYR cc_start: 0.9161 (m-80) cc_final: 0.8686 (m-80) REVERT: B 3138 TYR cc_start: 0.9306 (t80) cc_final: 0.8886 (t80) REVERT: B 3147 TYR cc_start: 0.8415 (m-80) cc_final: 0.8157 (m-80) REVERT: B 3162 PHE cc_start: 0.9140 (t80) cc_final: 0.8897 (t80) REVERT: B 3304 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8764 (tp-100) REVERT: B 3819 MET cc_start: 0.7079 (ptt) cc_final: 0.6865 (ptt) REVERT: B 4057 HIS cc_start: 0.8453 (m90) cc_final: 0.8237 (m170) REVERT: B 4080 TYR cc_start: 0.8501 (p90) cc_final: 0.7767 (p90) REVERT: B 4258 MET cc_start: 0.3701 (ppp) cc_final: 0.3364 (ppp) REVERT: B 4654 MET cc_start: 0.9150 (tpp) cc_final: 0.8658 (tpp) REVERT: B 4748 MET cc_start: 0.8175 (mpp) cc_final: 0.7701 (mpp) REVERT: B 4879 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7433 (tp40) REVERT: C 393 MET cc_start: 0.8415 (tpt) cc_final: 0.7807 (mmm) REVERT: C 655 MET cc_start: 0.9246 (mmp) cc_final: 0.8766 (mmp) REVERT: C 778 MET cc_start: 0.8226 (tpt) cc_final: 0.7830 (mmm) REVERT: C 935 MET cc_start: 0.9341 (ppp) cc_final: 0.9137 (ppp) REVERT: C 1948 MET cc_start: 0.8218 (mmm) cc_final: 0.7907 (tpp) REVERT: C 2681 MET cc_start: 0.8101 (tpp) cc_final: 0.7378 (tmm) REVERT: C 2685 TYR cc_start: 0.7824 (t80) cc_final: 0.7513 (t80) REVERT: C 2689 MET cc_start: 0.4084 (ptt) cc_final: 0.2964 (tmm) REVERT: C 2727 HIS cc_start: 0.9221 (t-90) cc_final: 0.8683 (t-90) REVERT: C 2731 LYS cc_start: 0.9441 (pttm) cc_final: 0.8897 (pttm) REVERT: C 2757 MET cc_start: 0.7280 (mpp) cc_final: 0.6838 (mpp) REVERT: C 2840 MET cc_start: 0.8228 (mmt) cc_final: 0.7754 (mmm) REVERT: C 2932 TYR cc_start: 0.8667 (m-80) cc_final: 0.8338 (m-80) REVERT: C 2979 ARG cc_start: 0.9099 (tmm160) cc_final: 0.8870 (ttp80) REVERT: C 2982 PHE cc_start: 0.8977 (m-10) cc_final: 0.8637 (m-80) REVERT: C 3060 PHE cc_start: 0.8142 (t80) cc_final: 0.7772 (t80) REVERT: C 3114 GLN cc_start: 0.8764 (pp30) cc_final: 0.8506 (pp30) REVERT: C 3131 TYR cc_start: 0.9158 (m-80) cc_final: 0.8705 (m-80) REVERT: C 3162 PHE cc_start: 0.9129 (t80) cc_final: 0.8763 (t80) REVERT: C 3170 PHE cc_start: 0.8558 (p90) cc_final: 0.8072 (p90) REVERT: C 3304 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8765 (tp-100) REVERT: C 3819 MET cc_start: 0.7110 (ptt) cc_final: 0.6908 (ptt) REVERT: C 4080 TYR cc_start: 0.8503 (p90) cc_final: 0.7740 (p90) REVERT: C 4258 MET cc_start: 0.3672 (ppp) cc_final: 0.3340 (ppp) REVERT: C 4654 MET cc_start: 0.9144 (tpp) cc_final: 0.8646 (tpp) REVERT: C 4748 MET cc_start: 0.8171 (mpp) cc_final: 0.7692 (mpp) REVERT: C 4879 GLN cc_start: 0.8172 (tp-100) cc_final: 0.7447 (tp40) REVERT: D 393 MET cc_start: 0.8386 (tpt) cc_final: 0.7692 (mmm) REVERT: D 655 MET cc_start: 0.9256 (mmp) cc_final: 0.8743 (mmp) REVERT: D 678 MET cc_start: 0.8307 (tpt) cc_final: 0.7869 (tpt) REVERT: D 778 MET cc_start: 0.8230 (tpt) cc_final: 0.7840 (mmm) REVERT: D 1948 MET cc_start: 0.8142 (mmm) cc_final: 0.7842 (tpp) REVERT: D 1953 MET cc_start: 0.7450 (mmt) cc_final: 0.7199 (mpp) REVERT: D 2134 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8739 (tpt) REVERT: D 2681 MET cc_start: 0.8094 (tpp) cc_final: 0.7362 (tmm) REVERT: D 2685 TYR cc_start: 0.7903 (t80) cc_final: 0.7300 (t80) REVERT: D 2688 MET cc_start: 0.7703 (mpp) cc_final: 0.7495 (mmp) REVERT: D 2727 HIS cc_start: 0.9213 (t-90) cc_final: 0.8680 (t-90) REVERT: D 2731 LYS cc_start: 0.9447 (pttm) cc_final: 0.8898 (pttm) REVERT: D 2757 MET cc_start: 0.7211 (mpp) cc_final: 0.6478 (mpp) REVERT: D 2840 MET cc_start: 0.8198 (mmt) cc_final: 0.7697 (mmm) REVERT: D 2874 TYR cc_start: 0.8733 (t80) cc_final: 0.8493 (t80) REVERT: D 2932 TYR cc_start: 0.8658 (m-80) cc_final: 0.8328 (m-80) REVERT: D 2979 ARG cc_start: 0.9110 (tmm160) cc_final: 0.8883 (ttp80) REVERT: D 2982 PHE cc_start: 0.9001 (m-10) cc_final: 0.8661 (m-80) REVERT: D 3060 PHE cc_start: 0.8126 (t80) cc_final: 0.7767 (t80) REVERT: D 3131 TYR cc_start: 0.9168 (m-80) cc_final: 0.8686 (m-80) REVERT: D 3138 TYR cc_start: 0.9304 (t80) cc_final: 0.8913 (t80) REVERT: D 3147 TYR cc_start: 0.8395 (m-80) cc_final: 0.8140 (m-80) REVERT: D 3162 PHE cc_start: 0.9116 (t80) cc_final: 0.8690 (t80) REVERT: D 3304 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8777 (tp-100) REVERT: D 3819 MET cc_start: 0.7096 (ptt) cc_final: 0.6884 (ptt) REVERT: D 4080 TYR cc_start: 0.8496 (p90) cc_final: 0.7749 (p90) REVERT: D 4258 MET cc_start: 0.3599 (ppp) cc_final: 0.3258 (ppp) REVERT: D 4748 MET cc_start: 0.8173 (mpp) cc_final: 0.7690 (mpp) REVERT: D 4879 GLN cc_start: 0.8178 (tp-100) cc_final: 0.7460 (tp40) outliers start: 84 outliers final: 41 residues processed: 848 average time/residue: 1.1359 time to fit residues: 1724.5764 Evaluate side-chains 819 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 776 time to evaluate : 11.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2745 GLU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2893 LEU Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 3073 GLU Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 883 GLU Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 3073 GLU Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 3073 GLU Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4572 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1358 optimal weight: 30.0000 chunk 926 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 1214 optimal weight: 50.0000 chunk 673 optimal weight: 20.0000 chunk 1392 optimal weight: 6.9990 chunk 1127 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 833 optimal weight: 10.0000 chunk 1464 optimal weight: 7.9990 chunk 411 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 HIS A 409 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2464 HIS ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3287 ASN ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3774 GLN A3851 ASN A3865 ASN A3955 GLN A3975 GLN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4296 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS B 409 GLN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1620 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2464 HIS ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3774 GLN B3851 ASN B3865 ASN B3955 GLN B3975 GLN B4296 HIS ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2464 HIS ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3774 GLN C3851 ASN C3865 ASN C3955 GLN C3975 GLN C4296 HIS D 409 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1620 GLN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2464 HIS ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3774 GLN D3851 ASN D3865 ASN D3955 GLN D3975 GLN D4296 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 138292 Z= 0.502 Angle : 0.694 12.334 186864 Z= 0.357 Chirality : 0.043 0.212 20500 Planarity : 0.005 0.128 23992 Dihedral : 6.144 85.189 18576 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 0.53 % Allowed : 8.10 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.07), residues: 16792 helix: 1.48 (0.06), residues: 9016 sheet: -0.42 (0.13), residues: 1572 loop : -0.55 (0.08), residues: 6204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A2732 HIS 0.010 0.001 HIS C3665 PHE 0.049 0.002 PHE A2943 TYR 0.038 0.002 TYR A2760 ARG 0.012 0.001 ARG D3192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 789 time to evaluate : 11.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8446 (tpt) cc_final: 0.7833 (mmm) REVERT: A 655 MET cc_start: 0.9234 (mmp) cc_final: 0.8778 (mmp) REVERT: A 678 MET cc_start: 0.8380 (tpt) cc_final: 0.7814 (tpt) REVERT: A 778 MET cc_start: 0.8547 (tpt) cc_final: 0.8123 (mmm) REVERT: A 895 MET cc_start: 0.9169 (mtt) cc_final: 0.8875 (mmt) REVERT: A 902 TRP cc_start: 0.6318 (t-100) cc_final: 0.5643 (t-100) REVERT: A 981 MET cc_start: 0.8664 (tmm) cc_final: 0.8367 (tmm) REVERT: A 1948 MET cc_start: 0.8044 (mmm) cc_final: 0.7536 (ppp) REVERT: A 1953 MET cc_start: 0.7397 (mmt) cc_final: 0.7163 (mpp) REVERT: A 2605 MET cc_start: 0.9200 (ppp) cc_final: 0.8842 (ppp) REVERT: A 2685 TYR cc_start: 0.7848 (t80) cc_final: 0.7220 (t80) REVERT: A 2689 MET cc_start: 0.5250 (ptt) cc_final: 0.4788 (tmm) REVERT: A 2727 HIS cc_start: 0.9123 (t-90) cc_final: 0.8592 (t-90) REVERT: A 2731 LYS cc_start: 0.9459 (ptpp) cc_final: 0.8692 (ptpp) REVERT: A 2757 MET cc_start: 0.7153 (mpp) cc_final: 0.6303 (mpp) REVERT: A 2844 MET cc_start: 0.9191 (ppp) cc_final: 0.8745 (ppp) REVERT: A 2848 TYR cc_start: 0.8539 (m-10) cc_final: 0.7899 (m-10) REVERT: A 2874 TYR cc_start: 0.8715 (t80) cc_final: 0.8452 (t80) REVERT: A 2921 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7571 (p90) REVERT: A 2932 TYR cc_start: 0.8794 (m-80) cc_final: 0.8408 (m-80) REVERT: A 2979 ARG cc_start: 0.9122 (tmm160) cc_final: 0.8881 (ttp80) REVERT: A 2982 PHE cc_start: 0.9031 (m-10) cc_final: 0.8732 (m-80) REVERT: A 3060 PHE cc_start: 0.8208 (t80) cc_final: 0.7536 (t80) REVERT: A 3131 TYR cc_start: 0.9124 (m-80) cc_final: 0.8688 (m-80) REVERT: A 3138 TYR cc_start: 0.9327 (t80) cc_final: 0.8874 (t80) REVERT: A 3162 PHE cc_start: 0.9094 (t80) cc_final: 0.8745 (t80) REVERT: A 3170 PHE cc_start: 0.8263 (p90) cc_final: 0.7449 (p90) REVERT: A 3245 TYR cc_start: 0.9084 (t80) cc_final: 0.8790 (t80) REVERT: A 3304 GLN cc_start: 0.9080 (tp-100) cc_final: 0.8756 (tp-100) REVERT: A 3819 MET cc_start: 0.7268 (ptt) cc_final: 0.7048 (ptt) REVERT: A 4080 TYR cc_start: 0.8549 (p90) cc_final: 0.7841 (p90) REVERT: A 4258 MET cc_start: 0.3858 (ppp) cc_final: 0.3250 (ptt) REVERT: A 4654 MET cc_start: 0.8903 (tpp) cc_final: 0.8499 (tpp) REVERT: A 4748 MET cc_start: 0.8078 (mpp) cc_final: 0.7801 (mpp) REVERT: A 4879 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7436 (tp40) REVERT: A 4943 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: B 393 MET cc_start: 0.8456 (tpt) cc_final: 0.7834 (mmm) REVERT: B 655 MET cc_start: 0.9219 (mmp) cc_final: 0.8874 (mmp) REVERT: B 778 MET cc_start: 0.8263 (tpt) cc_final: 0.7791 (mmm) REVERT: B 981 MET cc_start: 0.8782 (tmm) cc_final: 0.8489 (tmm) REVERT: B 1953 MET cc_start: 0.7394 (mmt) cc_final: 0.7188 (mpp) REVERT: B 2681 MET cc_start: 0.8152 (tpp) cc_final: 0.7618 (tmm) REVERT: B 2685 TYR cc_start: 0.7864 (t80) cc_final: 0.7542 (t80) REVERT: B 2689 MET cc_start: 0.4474 (ptt) cc_final: 0.3484 (tmm) REVERT: B 2719 TYR cc_start: 0.9143 (t80) cc_final: 0.8847 (t80) REVERT: B 2727 HIS cc_start: 0.9260 (t-90) cc_final: 0.8688 (t-90) REVERT: B 2731 LYS cc_start: 0.9451 (pttm) cc_final: 0.8877 (pttm) REVERT: B 2757 MET cc_start: 0.7110 (mpp) cc_final: 0.6682 (mpp) REVERT: B 2844 MET cc_start: 0.9197 (ppp) cc_final: 0.8988 (ppp) REVERT: B 2848 TYR cc_start: 0.8438 (m-10) cc_final: 0.8178 (m-10) REVERT: B 2921 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7691 (p90) REVERT: B 2932 TYR cc_start: 0.8739 (m-80) cc_final: 0.8359 (m-80) REVERT: B 2979 ARG cc_start: 0.9129 (tmm160) cc_final: 0.8895 (ttp80) REVERT: B 2982 PHE cc_start: 0.9061 (m-10) cc_final: 0.8744 (m-80) REVERT: B 3060 PHE cc_start: 0.8246 (t80) cc_final: 0.7580 (t80) REVERT: B 3114 GLN cc_start: 0.8794 (pp30) cc_final: 0.8487 (pp30) REVERT: B 3131 TYR cc_start: 0.9167 (m-80) cc_final: 0.8728 (m-80) REVERT: B 3147 TYR cc_start: 0.8453 (m-80) cc_final: 0.8175 (m-80) REVERT: B 3162 PHE cc_start: 0.9133 (t80) cc_final: 0.8717 (t80) REVERT: B 3170 PHE cc_start: 0.8711 (p90) cc_final: 0.8153 (p90) REVERT: B 3263 MET cc_start: 0.9221 (ppp) cc_final: 0.8288 (pmm) REVERT: B 3304 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8787 (tp-100) REVERT: B 4080 TYR cc_start: 0.8548 (p90) cc_final: 0.7848 (p90) REVERT: B 4258 MET cc_start: 0.3574 (ppp) cc_final: 0.3261 (ppp) REVERT: B 4654 MET cc_start: 0.9160 (tpp) cc_final: 0.8624 (tpp) REVERT: B 4748 MET cc_start: 0.8148 (mpp) cc_final: 0.7763 (mpp) REVERT: B 4879 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7597 (tp40) REVERT: B 4943 MET cc_start: 0.8345 (mtm) cc_final: 0.8135 (mtp) REVERT: C 393 MET cc_start: 0.8450 (tpt) cc_final: 0.7821 (mmm) REVERT: C 655 MET cc_start: 0.9224 (mmp) cc_final: 0.8885 (mmp) REVERT: C 778 MET cc_start: 0.8254 (tpt) cc_final: 0.7781 (mmm) REVERT: C 981 MET cc_start: 0.8767 (tmm) cc_final: 0.8471 (tmm) REVERT: C 1948 MET cc_start: 0.8122 (mmm) cc_final: 0.7821 (tpp) REVERT: C 1953 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7319 (mpp) REVERT: C 2681 MET cc_start: 0.8172 (tpp) cc_final: 0.7527 (tmm) REVERT: C 2685 TYR cc_start: 0.7853 (t80) cc_final: 0.7534 (t80) REVERT: C 2689 MET cc_start: 0.4487 (ptt) cc_final: 0.3480 (tmm) REVERT: C 2727 HIS cc_start: 0.9258 (t-90) cc_final: 0.8661 (t-90) REVERT: C 2731 LYS cc_start: 0.9436 (pttm) cc_final: 0.8848 (pttm) REVERT: C 2757 MET cc_start: 0.7110 (mpp) cc_final: 0.6398 (mpp) REVERT: C 2844 MET cc_start: 0.9133 (ppp) cc_final: 0.8704 (ppp) REVERT: C 2848 TYR cc_start: 0.8412 (m-10) cc_final: 0.7760 (m-10) REVERT: C 2921 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7691 (p90) REVERT: C 2932 TYR cc_start: 0.8731 (m-80) cc_final: 0.8347 (m-80) REVERT: C 2979 ARG cc_start: 0.9133 (tmm160) cc_final: 0.8900 (ttp80) REVERT: C 2982 PHE cc_start: 0.9046 (m-10) cc_final: 0.8730 (m-80) REVERT: C 3060 PHE cc_start: 0.8240 (t80) cc_final: 0.7556 (t80) REVERT: C 3114 GLN cc_start: 0.8786 (pp30) cc_final: 0.8412 (pp30) REVERT: C 3131 TYR cc_start: 0.9168 (m-80) cc_final: 0.8726 (m-80) REVERT: C 3162 PHE cc_start: 0.9120 (t80) cc_final: 0.8724 (t80) REVERT: C 3263 MET cc_start: 0.9213 (ppp) cc_final: 0.8335 (pmm) REVERT: C 3304 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8782 (tp-100) REVERT: C 4080 TYR cc_start: 0.8539 (p90) cc_final: 0.7826 (p90) REVERT: C 4258 MET cc_start: 0.3507 (ppp) cc_final: 0.3196 (ppp) REVERT: C 4654 MET cc_start: 0.9160 (tpp) cc_final: 0.8607 (tpp) REVERT: C 4748 MET cc_start: 0.8147 (mpp) cc_final: 0.7784 (mpp) REVERT: C 4879 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7610 (tp40) REVERT: D 393 MET cc_start: 0.8424 (tpt) cc_final: 0.7718 (mmm) REVERT: D 655 MET cc_start: 0.9226 (mmp) cc_final: 0.8874 (mmp) REVERT: D 678 MET cc_start: 0.8328 (tpt) cc_final: 0.7846 (tpt) REVERT: D 778 MET cc_start: 0.8262 (tpt) cc_final: 0.7797 (mmm) REVERT: D 981 MET cc_start: 0.8795 (tmm) cc_final: 0.8509 (tmm) REVERT: D 1948 MET cc_start: 0.8113 (mmm) cc_final: 0.7780 (tpp) REVERT: D 2681 MET cc_start: 0.8157 (tpp) cc_final: 0.7500 (tmm) REVERT: D 2685 TYR cc_start: 0.7889 (t80) cc_final: 0.7222 (t80) REVERT: D 2689 MET cc_start: 0.4758 (ptt) cc_final: 0.4305 (tmm) REVERT: D 2727 HIS cc_start: 0.9256 (t-90) cc_final: 0.8652 (t-90) REVERT: D 2731 LYS cc_start: 0.9442 (pttm) cc_final: 0.8846 (pttm) REVERT: D 2757 MET cc_start: 0.7216 (mpp) cc_final: 0.6500 (mpp) REVERT: D 2844 MET cc_start: 0.9136 (ppp) cc_final: 0.8683 (ppp) REVERT: D 2848 TYR cc_start: 0.8475 (m-10) cc_final: 0.7820 (m-10) REVERT: D 2884 LYS cc_start: 0.9375 (pptt) cc_final: 0.8988 (pptt) REVERT: D 2921 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7685 (p90) REVERT: D 2932 TYR cc_start: 0.8731 (m-80) cc_final: 0.8345 (m-80) REVERT: D 2982 PHE cc_start: 0.9054 (m-10) cc_final: 0.8723 (m-80) REVERT: D 3060 PHE cc_start: 0.8210 (t80) cc_final: 0.7892 (t80) REVERT: D 3131 TYR cc_start: 0.9152 (m-80) cc_final: 0.8731 (m-80) REVERT: D 3147 TYR cc_start: 0.8435 (m-80) cc_final: 0.8159 (m-80) REVERT: D 3162 PHE cc_start: 0.9090 (t80) cc_final: 0.8730 (t80) REVERT: D 3170 PHE cc_start: 0.8656 (p90) cc_final: 0.8367 (p90) REVERT: D 3263 MET cc_start: 0.9221 (ppp) cc_final: 0.8286 (pmm) REVERT: D 3304 GLN cc_start: 0.9100 (tp-100) cc_final: 0.8785 (tp-100) REVERT: D 4080 TYR cc_start: 0.8536 (p90) cc_final: 0.7822 (p90) REVERT: D 4258 MET cc_start: 0.3651 (ppp) cc_final: 0.3338 (ppp) REVERT: D 4654 MET cc_start: 0.9121 (tpp) cc_final: 0.8642 (tpp) REVERT: D 4748 MET cc_start: 0.8150 (mpp) cc_final: 0.7759 (mpp) REVERT: D 4879 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7574 (tp40) REVERT: D 4943 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8145 (mtp) outliers start: 79 outliers final: 55 residues processed: 824 average time/residue: 1.1225 time to fit residues: 1655.6542 Evaluate side-chains 835 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 773 time to evaluate : 11.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2745 GLU Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2921 PHE Chi-restraints excluded: chain A residue 2972 ASP Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2921 PHE Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2972 ASP Chi-restraints excluded: chain B residue 3073 GLU Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 883 GLU Chi-restraints excluded: chain C residue 985 PHE Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2921 PHE Chi-restraints excluded: chain C residue 2972 ASP Chi-restraints excluded: chain C residue 3073 GLU Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2921 PHE Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2972 ASP Chi-restraints excluded: chain D residue 3073 GLU Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4572 LEU Chi-restraints excluded: chain D residue 4943 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 548 optimal weight: 3.9990 chunk 1469 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 957 optimal weight: 8.9990 chunk 402 optimal weight: 9.9990 chunk 1633 optimal weight: 0.9990 chunk 1355 optimal weight: 0.0370 chunk 756 optimal weight: 0.9980 chunk 135 optimal weight: 6.9990 chunk 540 optimal weight: 9.9990 chunk 857 optimal weight: 7.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 HIS ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3774 GLN A3851 ASN A3955 GLN A3975 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 HIS B1620 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3287 ASN ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3774 GLN B3851 ASN B3955 GLN B3975 GLN C 914 GLN ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2464 HIS ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3287 ASN ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3774 GLN C3851 ASN C3955 GLN C3975 GLN ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3287 ASN D3774 GLN D3851 ASN D3955 GLN D3975 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 138292 Z= 0.193 Angle : 0.605 19.261 186864 Z= 0.304 Chirality : 0.039 0.216 20500 Planarity : 0.004 0.125 23992 Dihedral : 5.955 81.432 18576 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.76 % Rotamer: Outliers : 0.70 % Allowed : 8.42 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.07), residues: 16792 helix: 1.67 (0.06), residues: 9004 sheet: -0.37 (0.13), residues: 1572 loop : -0.46 (0.08), residues: 6216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C3250 HIS 0.008 0.001 HIS A4057 PHE 0.022 0.001 PHE C3117 TYR 0.036 0.001 TYR B2760 ARG 0.009 0.000 ARG C1960 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 768 time to evaluate : 13.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8488 (tpt) cc_final: 0.7912 (mmm) REVERT: A 655 MET cc_start: 0.9273 (mmp) cc_final: 0.8693 (mmp) REVERT: A 678 MET cc_start: 0.8348 (tpt) cc_final: 0.7792 (tpt) REVERT: A 778 MET cc_start: 0.8482 (tpt) cc_final: 0.8019 (mmm) REVERT: A 895 MET cc_start: 0.9153 (mtt) cc_final: 0.8865 (mmt) REVERT: A 902 TRP cc_start: 0.6108 (t-100) cc_final: 0.5522 (t-100) REVERT: A 981 MET cc_start: 0.8697 (tmm) cc_final: 0.8495 (tmm) REVERT: A 1842 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8816 (pt) REVERT: A 1948 MET cc_start: 0.8036 (mmm) cc_final: 0.7503 (ppp) REVERT: A 2384 MET cc_start: 0.9000 (mmm) cc_final: 0.8764 (mmm) REVERT: A 2605 MET cc_start: 0.9186 (ppp) cc_final: 0.8843 (ppp) REVERT: A 2685 TYR cc_start: 0.7822 (t80) cc_final: 0.7188 (t80) REVERT: A 2689 MET cc_start: 0.5211 (ptt) cc_final: 0.4761 (ttm) REVERT: A 2727 HIS cc_start: 0.9112 (t-90) cc_final: 0.8508 (t-90) REVERT: A 2731 LYS cc_start: 0.9436 (ptpp) cc_final: 0.8671 (ptpp) REVERT: A 2757 MET cc_start: 0.7011 (mpp) cc_final: 0.6309 (mpp) REVERT: A 2844 MET cc_start: 0.9225 (ppp) cc_final: 0.8756 (ppp) REVERT: A 2848 TYR cc_start: 0.8461 (m-10) cc_final: 0.7987 (m-10) REVERT: A 2874 TYR cc_start: 0.8709 (t80) cc_final: 0.8482 (t80) REVERT: A 2921 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7404 (p90) REVERT: A 2932 TYR cc_start: 0.8747 (m-80) cc_final: 0.8343 (m-80) REVERT: A 2979 ARG cc_start: 0.9087 (tmm160) cc_final: 0.8824 (ttp80) REVERT: A 2982 PHE cc_start: 0.8919 (m-10) cc_final: 0.8594 (m-80) REVERT: A 3060 PHE cc_start: 0.8135 (t80) cc_final: 0.7473 (t80) REVERT: A 3131 TYR cc_start: 0.9083 (m-80) cc_final: 0.8637 (m-80) REVERT: A 3138 TYR cc_start: 0.9289 (t80) cc_final: 0.8877 (t80) REVERT: A 3162 PHE cc_start: 0.9037 (t80) cc_final: 0.8699 (t80) REVERT: A 3170 PHE cc_start: 0.8271 (p90) cc_final: 0.7416 (p90) REVERT: A 3245 TYR cc_start: 0.9032 (t80) cc_final: 0.8793 (t80) REVERT: A 3246 MET cc_start: 0.8978 (mtm) cc_final: 0.8400 (mpp) REVERT: A 3296 MET cc_start: 0.9323 (pmm) cc_final: 0.9006 (pmm) REVERT: A 3304 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8704 (tp-100) REVERT: A 3819 MET cc_start: 0.7080 (ptt) cc_final: 0.6842 (ptt) REVERT: A 4080 TYR cc_start: 0.8510 (p90) cc_final: 0.7811 (p90) REVERT: A 4258 MET cc_start: 0.3881 (ppp) cc_final: 0.3272 (ptt) REVERT: A 4654 MET cc_start: 0.8897 (tpp) cc_final: 0.8480 (tpp) REVERT: A 4748 MET cc_start: 0.8107 (mpp) cc_final: 0.7758 (mpp) REVERT: A 4879 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7447 (tp40) REVERT: A 4943 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7648 (mtp) REVERT: B 393 MET cc_start: 0.8462 (tpt) cc_final: 0.7876 (mmm) REVERT: B 655 MET cc_start: 0.9306 (mmp) cc_final: 0.8926 (mmp) REVERT: B 778 MET cc_start: 0.8232 (tpt) cc_final: 0.7724 (mmm) REVERT: B 981 MET cc_start: 0.8788 (tmm) cc_final: 0.8586 (tmm) REVERT: B 1842 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8816 (pt) REVERT: B 1948 MET cc_start: 0.7841 (mmm) cc_final: 0.7484 (ppp) REVERT: B 2681 MET cc_start: 0.8034 (tpp) cc_final: 0.7427 (tmm) REVERT: B 2685 TYR cc_start: 0.7796 (t80) cc_final: 0.7468 (t80) REVERT: B 2689 MET cc_start: 0.4538 (ptt) cc_final: 0.3654 (tmm) REVERT: B 2727 HIS cc_start: 0.9225 (t-90) cc_final: 0.8694 (t-90) REVERT: B 2731 LYS cc_start: 0.9413 (pttm) cc_final: 0.8790 (pttm) REVERT: B 2757 MET cc_start: 0.7306 (mpp) cc_final: 0.6699 (mpp) REVERT: B 2844 MET cc_start: 0.9185 (ppp) cc_final: 0.8760 (ppp) REVERT: B 2848 TYR cc_start: 0.8360 (m-10) cc_final: 0.8045 (m-10) REVERT: B 2890 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8844 (pm20) REVERT: B 2921 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7472 (p90) REVERT: B 2932 TYR cc_start: 0.8699 (m-80) cc_final: 0.8314 (m-80) REVERT: B 2979 ARG cc_start: 0.9108 (tmm160) cc_final: 0.8847 (ttp80) REVERT: B 2982 PHE cc_start: 0.8937 (m-10) cc_final: 0.8587 (m-80) REVERT: B 3060 PHE cc_start: 0.8138 (t80) cc_final: 0.7446 (t80) REVERT: B 3131 TYR cc_start: 0.9126 (m-80) cc_final: 0.8666 (m-80) REVERT: B 3147 TYR cc_start: 0.8370 (m-80) cc_final: 0.8107 (m-80) REVERT: B 3162 PHE cc_start: 0.9062 (t80) cc_final: 0.8689 (t80) REVERT: B 3170 PHE cc_start: 0.8654 (p90) cc_final: 0.8137 (p90) REVERT: B 3263 MET cc_start: 0.9144 (ppp) cc_final: 0.8222 (pmm) REVERT: B 3296 MET cc_start: 0.9301 (pmm) cc_final: 0.8939 (pmm) REVERT: B 3304 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8716 (tp-100) REVERT: B 3819 MET cc_start: 0.6989 (ptt) cc_final: 0.6715 (ptt) REVERT: B 4080 TYR cc_start: 0.8507 (p90) cc_final: 0.7847 (p90) REVERT: B 4258 MET cc_start: 0.3632 (ppp) cc_final: 0.3353 (ppp) REVERT: B 4654 MET cc_start: 0.9168 (tpp) cc_final: 0.8607 (tpp) REVERT: B 4748 MET cc_start: 0.8157 (mpp) cc_final: 0.7776 (mpp) REVERT: B 4879 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7415 (tp40) REVERT: B 4943 MET cc_start: 0.8328 (ttm) cc_final: 0.8120 (mtp) REVERT: C 393 MET cc_start: 0.8461 (tpt) cc_final: 0.7901 (mmm) REVERT: C 655 MET cc_start: 0.9298 (mmp) cc_final: 0.8925 (mmp) REVERT: C 778 MET cc_start: 0.8227 (tpt) cc_final: 0.7722 (mmm) REVERT: C 981 MET cc_start: 0.8768 (tmm) cc_final: 0.8542 (tmm) REVERT: C 1842 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8817 (pt) REVERT: C 1948 MET cc_start: 0.8124 (mmm) cc_final: 0.7805 (tpp) REVERT: C 1953 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7333 (mpp) REVERT: C 2384 MET cc_start: 0.9040 (mmm) cc_final: 0.8809 (mmm) REVERT: C 2681 MET cc_start: 0.8014 (tpp) cc_final: 0.7331 (tmm) REVERT: C 2685 TYR cc_start: 0.7799 (t80) cc_final: 0.7474 (t80) REVERT: C 2689 MET cc_start: 0.4608 (ptt) cc_final: 0.3716 (tmm) REVERT: C 2727 HIS cc_start: 0.9230 (t-90) cc_final: 0.8683 (t-90) REVERT: C 2731 LYS cc_start: 0.9417 (pttm) cc_final: 0.8785 (pttm) REVERT: C 2757 MET cc_start: 0.7269 (mpp) cc_final: 0.6676 (mpp) REVERT: C 2844 MET cc_start: 0.9167 (ppp) cc_final: 0.8479 (ppp) REVERT: C 2848 TYR cc_start: 0.8341 (m-10) cc_final: 0.7624 (m-10) REVERT: C 2921 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7482 (p90) REVERT: C 2932 TYR cc_start: 0.8697 (m-80) cc_final: 0.8211 (m-80) REVERT: C 2935 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: C 2979 ARG cc_start: 0.9100 (tmm160) cc_final: 0.8843 (ttp80) REVERT: C 2982 PHE cc_start: 0.8922 (m-10) cc_final: 0.8578 (m-80) REVERT: C 3060 PHE cc_start: 0.8147 (t80) cc_final: 0.7463 (t80) REVERT: C 3131 TYR cc_start: 0.9113 (m-80) cc_final: 0.8659 (m-80) REVERT: C 3162 PHE cc_start: 0.9043 (t80) cc_final: 0.8688 (t80) REVERT: C 3170 PHE cc_start: 0.8592 (p90) cc_final: 0.8080 (p90) REVERT: C 3246 MET cc_start: 0.8670 (mtp) cc_final: 0.8417 (ptp) REVERT: C 3263 MET cc_start: 0.9144 (ppp) cc_final: 0.8314 (pmm) REVERT: C 3296 MET cc_start: 0.9301 (pmm) cc_final: 0.8948 (pmm) REVERT: C 3304 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8730 (tp-100) REVERT: C 4080 TYR cc_start: 0.8493 (p90) cc_final: 0.7825 (p90) REVERT: C 4258 MET cc_start: 0.3650 (ppp) cc_final: 0.3372 (ppp) REVERT: C 4654 MET cc_start: 0.9142 (tpp) cc_final: 0.8578 (tpp) REVERT: C 4748 MET cc_start: 0.8153 (mpp) cc_final: 0.7761 (mpp) REVERT: C 4879 GLN cc_start: 0.8165 (tp-100) cc_final: 0.7410 (tp40) REVERT: D 393 MET cc_start: 0.8438 (tpt) cc_final: 0.7778 (mmm) REVERT: D 655 MET cc_start: 0.9307 (mmp) cc_final: 0.8923 (mmp) REVERT: D 678 MET cc_start: 0.8304 (tpt) cc_final: 0.7798 (tpt) REVERT: D 778 MET cc_start: 0.8231 (tpt) cc_final: 0.7732 (mmm) REVERT: D 981 MET cc_start: 0.8802 (tmm) cc_final: 0.8578 (tmm) REVERT: D 1842 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8814 (pt) REVERT: D 1948 MET cc_start: 0.8109 (mmm) cc_final: 0.7792 (tpp) REVERT: D 2681 MET cc_start: 0.7997 (tpp) cc_final: 0.7295 (tmm) REVERT: D 2685 TYR cc_start: 0.7880 (t80) cc_final: 0.7196 (t80) REVERT: D 2689 MET cc_start: 0.5027 (ptt) cc_final: 0.4562 (ttm) REVERT: D 2727 HIS cc_start: 0.9219 (t-90) cc_final: 0.8679 (t-90) REVERT: D 2731 LYS cc_start: 0.9413 (pttm) cc_final: 0.8775 (pttm) REVERT: D 2757 MET cc_start: 0.7264 (mpp) cc_final: 0.6348 (mpp) REVERT: D 2844 MET cc_start: 0.9176 (ppp) cc_final: 0.8571 (ppp) REVERT: D 2848 TYR cc_start: 0.8432 (m-10) cc_final: 0.7825 (m-10) REVERT: D 2921 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7502 (p90) REVERT: D 2932 TYR cc_start: 0.8692 (m-80) cc_final: 0.8308 (m-80) REVERT: D 2982 PHE cc_start: 0.8940 (m-10) cc_final: 0.8613 (m-80) REVERT: D 3060 PHE cc_start: 0.8123 (t80) cc_final: 0.7431 (t80) REVERT: D 3131 TYR cc_start: 0.9120 (m-80) cc_final: 0.8671 (m-80) REVERT: D 3147 TYR cc_start: 0.8353 (m-80) cc_final: 0.8086 (m-80) REVERT: D 3246 MET cc_start: 0.8654 (mtp) cc_final: 0.8377 (ptp) REVERT: D 3296 MET cc_start: 0.9304 (pmm) cc_final: 0.8941 (pmm) REVERT: D 3304 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8732 (tp-100) REVERT: D 4080 TYR cc_start: 0.8488 (p90) cc_final: 0.7819 (p90) REVERT: D 4258 MET cc_start: 0.3624 (ppp) cc_final: 0.3338 (ppp) REVERT: D 4283 PHE cc_start: 0.3525 (OUTLIER) cc_final: 0.3154 (m-80) REVERT: D 4654 MET cc_start: 0.9120 (tpp) cc_final: 0.8575 (tpp) REVERT: D 4748 MET cc_start: 0.8156 (mpp) cc_final: 0.7767 (mpp) REVERT: D 4879 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7433 (tp40) REVERT: D 4943 MET cc_start: 0.8356 (mtm) cc_final: 0.8103 (mtp) outliers start: 104 outliers final: 54 residues processed: 840 average time/residue: 1.1505 time to fit residues: 1736.3483 Evaluate side-chains 827 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 760 time to evaluate : 11.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2921 PHE Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2972 ASP Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4283 PHE Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 883 GLU Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2893 LEU Chi-restraints excluded: chain B residue 2921 PHE Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2972 ASP Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4283 PHE Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 883 GLU Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2893 LEU Chi-restraints excluded: chain C residue 2921 PHE Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4283 PHE Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 985 PHE Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2921 PHE Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2972 ASP Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4283 PHE Chi-restraints excluded: chain D residue 4572 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1574 optimal weight: 0.4980 chunk 184 optimal weight: 10.0000 chunk 930 optimal weight: 40.0000 chunk 1192 optimal weight: 10.0000 chunk 924 optimal weight: 4.9990 chunk 1374 optimal weight: 5.9990 chunk 911 optimal weight: 9.9990 chunk 1626 optimal weight: 10.0000 chunk 1018 optimal weight: 0.8980 chunk 991 optimal weight: 6.9990 chunk 751 optimal weight: 10.0000 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 927 GLN ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 138292 Z= 0.270 Angle : 0.621 15.947 186864 Z= 0.311 Chirality : 0.040 0.231 20500 Planarity : 0.004 0.163 23992 Dihedral : 5.853 80.689 18576 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 0.71 % Allowed : 8.93 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 1.04 (0.07), residues: 16792 helix: 1.70 (0.06), residues: 8996 sheet: -0.32 (0.13), residues: 1536 loop : -0.48 (0.08), residues: 6260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B3250 HIS 0.006 0.001 HIS C 692 PHE 0.025 0.001 PHE D3162 TYR 0.029 0.001 TYR B2760 ARG 0.010 0.000 ARG B1960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 773 time to evaluate : 11.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8473 (tpt) cc_final: 0.7908 (mmm) REVERT: A 655 MET cc_start: 0.9263 (mmp) cc_final: 0.8707 (mmp) REVERT: A 678 MET cc_start: 0.8353 (tpt) cc_final: 0.7817 (tpt) REVERT: A 778 MET cc_start: 0.8478 (tpt) cc_final: 0.7755 (mmm) REVERT: A 895 MET cc_start: 0.9143 (mtt) cc_final: 0.8879 (mmt) REVERT: A 902 TRP cc_start: 0.6213 (t-100) cc_final: 0.5615 (t-100) REVERT: A 1842 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8833 (pt) REVERT: A 1948 MET cc_start: 0.7999 (mmm) cc_final: 0.7461 (ppp) REVERT: A 1953 MET cc_start: 0.7335 (mmt) cc_final: 0.7121 (mpp) REVERT: A 2442 MET cc_start: 0.8726 (mmp) cc_final: 0.8443 (mmm) REVERT: A 2685 TYR cc_start: 0.7738 (t80) cc_final: 0.7099 (t80) REVERT: A 2689 MET cc_start: 0.5463 (ptt) cc_final: 0.5060 (ttm) REVERT: A 2727 HIS cc_start: 0.9127 (t-90) cc_final: 0.8481 (t-90) REVERT: A 2731 LYS cc_start: 0.9470 (ptpp) cc_final: 0.8626 (ptpp) REVERT: A 2757 MET cc_start: 0.7032 (mpp) cc_final: 0.6307 (mpp) REVERT: A 2844 MET cc_start: 0.9250 (ppp) cc_final: 0.8752 (ppp) REVERT: A 2848 TYR cc_start: 0.8539 (m-10) cc_final: 0.8156 (m-10) REVERT: A 2874 TYR cc_start: 0.8714 (t80) cc_final: 0.8481 (t80) REVERT: A 2921 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7418 (p90) REVERT: A 2932 TYR cc_start: 0.8778 (m-80) cc_final: 0.8345 (m-80) REVERT: A 2979 ARG cc_start: 0.9091 (tmm160) cc_final: 0.8827 (ttp80) REVERT: A 2982 PHE cc_start: 0.8959 (m-10) cc_final: 0.8644 (m-80) REVERT: A 3060 PHE cc_start: 0.8158 (t80) cc_final: 0.7495 (t80) REVERT: A 3131 TYR cc_start: 0.9090 (m-80) cc_final: 0.8662 (m-80) REVERT: A 3138 TYR cc_start: 0.9306 (t80) cc_final: 0.8897 (t80) REVERT: A 3162 PHE cc_start: 0.9045 (t80) cc_final: 0.8720 (t80) REVERT: A 3170 PHE cc_start: 0.8281 (p90) cc_final: 0.7435 (p90) REVERT: A 3245 TYR cc_start: 0.9036 (t80) cc_final: 0.8818 (t80) REVERT: A 3246 MET cc_start: 0.8977 (mtm) cc_final: 0.8417 (mpp) REVERT: A 3304 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8716 (tp-100) REVERT: A 3819 MET cc_start: 0.7128 (ptt) cc_final: 0.6879 (ptt) REVERT: A 4080 TYR cc_start: 0.8541 (p90) cc_final: 0.7846 (p90) REVERT: A 4258 MET cc_start: 0.3953 (ppp) cc_final: 0.3350 (ptt) REVERT: A 4505 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 4654 MET cc_start: 0.8916 (tpp) cc_final: 0.8488 (tpp) REVERT: A 4748 MET cc_start: 0.8124 (mpp) cc_final: 0.7778 (mpp) REVERT: A 4879 GLN cc_start: 0.8177 (tp-100) cc_final: 0.7453 (tp40) REVERT: A 4943 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7694 (mtp) REVERT: B 393 MET cc_start: 0.8473 (tpt) cc_final: 0.7904 (mmm) REVERT: B 655 MET cc_start: 0.9290 (mmp) cc_final: 0.8914 (mmp) REVERT: B 778 MET cc_start: 0.8221 (tpt) cc_final: 0.7709 (mmm) REVERT: B 1842 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8828 (pt) REVERT: B 1948 MET cc_start: 0.7813 (mmm) cc_final: 0.7391 (mmm) REVERT: B 2172 MET cc_start: 0.8983 (tpp) cc_final: 0.8681 (tpp) REVERT: B 2681 MET cc_start: 0.8059 (tpp) cc_final: 0.7513 (tmm) REVERT: B 2685 TYR cc_start: 0.7696 (t80) cc_final: 0.7379 (t80) REVERT: B 2689 MET cc_start: 0.4705 (ptt) cc_final: 0.3801 (tmm) REVERT: B 2719 TYR cc_start: 0.9079 (t80) cc_final: 0.8803 (t80) REVERT: B 2727 HIS cc_start: 0.9245 (t-90) cc_final: 0.8625 (t-90) REVERT: B 2731 LYS cc_start: 0.9434 (pttm) cc_final: 0.8862 (pttm) REVERT: B 2757 MET cc_start: 0.6999 (mpp) cc_final: 0.6705 (mpp) REVERT: B 2848 TYR cc_start: 0.8362 (m-10) cc_final: 0.8150 (m-10) REVERT: B 2890 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8852 (pm20) REVERT: B 2921 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7496 (p90) REVERT: B 2932 TYR cc_start: 0.8728 (m-80) cc_final: 0.8318 (m-80) REVERT: B 2979 ARG cc_start: 0.9111 (tmm160) cc_final: 0.8855 (ttp80) REVERT: B 2982 PHE cc_start: 0.8966 (m-10) cc_final: 0.8630 (m-80) REVERT: B 3060 PHE cc_start: 0.8173 (t80) cc_final: 0.7492 (t80) REVERT: B 3131 TYR cc_start: 0.9123 (m-80) cc_final: 0.8680 (m-80) REVERT: B 3147 TYR cc_start: 0.8406 (m-80) cc_final: 0.8132 (m-80) REVERT: B 3246 MET cc_start: 0.8655 (mtp) cc_final: 0.8390 (ptp) REVERT: B 3263 MET cc_start: 0.9114 (ppp) cc_final: 0.8258 (pmm) REVERT: B 3304 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8733 (tp-100) REVERT: B 3819 MET cc_start: 0.7028 (ptt) cc_final: 0.6809 (ptt) REVERT: B 4080 TYR cc_start: 0.8546 (p90) cc_final: 0.7889 (p90) REVERT: B 4258 MET cc_start: 0.3596 (ppp) cc_final: 0.2894 (ptt) REVERT: B 4505 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8029 (tp) REVERT: B 4654 MET cc_start: 0.9162 (tpp) cc_final: 0.8608 (tpp) REVERT: B 4748 MET cc_start: 0.8164 (mpp) cc_final: 0.7779 (mpp) REVERT: B 4879 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7433 (tp40) REVERT: B 4943 MET cc_start: 0.8329 (ttm) cc_final: 0.8112 (mtp) REVERT: C 393 MET cc_start: 0.8469 (tpt) cc_final: 0.7894 (mmm) REVERT: C 655 MET cc_start: 0.9290 (mmp) cc_final: 0.8926 (mmp) REVERT: C 778 MET cc_start: 0.8219 (tpt) cc_final: 0.7702 (mmm) REVERT: C 1842 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8831 (pt) REVERT: C 1948 MET cc_start: 0.8128 (mmm) cc_final: 0.7862 (tpp) REVERT: C 1953 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: C 2442 MET cc_start: 0.8727 (mmp) cc_final: 0.8426 (mmm) REVERT: C 2681 MET cc_start: 0.8022 (tpp) cc_final: 0.7422 (tmm) REVERT: C 2685 TYR cc_start: 0.7683 (t80) cc_final: 0.7377 (t80) REVERT: C 2689 MET cc_start: 0.4739 (ptt) cc_final: 0.3855 (tmm) REVERT: C 2719 TYR cc_start: 0.9106 (t80) cc_final: 0.8822 (t80) REVERT: C 2727 HIS cc_start: 0.9250 (t-90) cc_final: 0.8624 (t-90) REVERT: C 2731 LYS cc_start: 0.9424 (pttm) cc_final: 0.8851 (pttm) REVERT: C 2757 MET cc_start: 0.7015 (mpp) cc_final: 0.6398 (mpp) REVERT: C 2844 MET cc_start: 0.9192 (ppp) cc_final: 0.8526 (ppp) REVERT: C 2848 TYR cc_start: 0.8389 (m-10) cc_final: 0.7826 (m-10) REVERT: C 2921 PHE cc_start: 0.7824 (OUTLIER) cc_final: 0.7511 (p90) REVERT: C 2932 TYR cc_start: 0.8718 (m-80) cc_final: 0.8309 (m-80) REVERT: C 2979 ARG cc_start: 0.9106 (tmm160) cc_final: 0.8850 (ttp80) REVERT: C 2982 PHE cc_start: 0.8973 (m-10) cc_final: 0.8635 (m-80) REVERT: C 3060 PHE cc_start: 0.8181 (t80) cc_final: 0.7509 (t80) REVERT: C 3131 TYR cc_start: 0.9118 (m-80) cc_final: 0.8678 (m-80) REVERT: C 3162 PHE cc_start: 0.9055 (t80) cc_final: 0.8708 (t80) REVERT: C 3170 PHE cc_start: 0.8613 (p90) cc_final: 0.8031 (p90) REVERT: C 3246 MET cc_start: 0.8668 (mtp) cc_final: 0.8408 (ptp) REVERT: C 3304 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8745 (tp-100) REVERT: C 4080 TYR cc_start: 0.8500 (p90) cc_final: 0.7823 (p90) REVERT: C 4258 MET cc_start: 0.3642 (ppp) cc_final: 0.2943 (ptt) REVERT: C 4505 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8033 (tp) REVERT: C 4654 MET cc_start: 0.9163 (tpp) cc_final: 0.8601 (tpp) REVERT: C 4748 MET cc_start: 0.8170 (mpp) cc_final: 0.7781 (mpp) REVERT: C 4879 GLN cc_start: 0.8171 (tp-100) cc_final: 0.7427 (tp40) REVERT: D 393 MET cc_start: 0.8446 (tpt) cc_final: 0.7783 (mmm) REVERT: D 655 MET cc_start: 0.9288 (mmp) cc_final: 0.8916 (mmp) REVERT: D 678 MET cc_start: 0.8298 (tpt) cc_final: 0.7791 (tpt) REVERT: D 778 MET cc_start: 0.8219 (tpt) cc_final: 0.7711 (mmm) REVERT: D 1842 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8827 (pt) REVERT: D 1948 MET cc_start: 0.8198 (mmm) cc_final: 0.7915 (tpp) REVERT: D 2442 MET cc_start: 0.8728 (mmp) cc_final: 0.8410 (mmm) REVERT: D 2681 MET cc_start: 0.8008 (tpp) cc_final: 0.7384 (tmm) REVERT: D 2685 TYR cc_start: 0.7862 (t80) cc_final: 0.7189 (t80) REVERT: D 2689 MET cc_start: 0.5006 (ptt) cc_final: 0.4588 (ttm) REVERT: D 2727 HIS cc_start: 0.9243 (t-90) cc_final: 0.8626 (t-90) REVERT: D 2731 LYS cc_start: 0.9430 (pttm) cc_final: 0.8850 (pttm) REVERT: D 2757 MET cc_start: 0.7049 (mpp) cc_final: 0.6449 (mpp) REVERT: D 2844 MET cc_start: 0.9200 (ppp) cc_final: 0.8584 (ppp) REVERT: D 2848 TYR cc_start: 0.8448 (m-10) cc_final: 0.7909 (m-10) REVERT: D 2921 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7515 (p90) REVERT: D 2932 TYR cc_start: 0.8717 (m-80) cc_final: 0.8311 (m-80) REVERT: D 2982 PHE cc_start: 0.8985 (m-10) cc_final: 0.8652 (m-80) REVERT: D 3060 PHE cc_start: 0.8164 (t80) cc_final: 0.7476 (t80) REVERT: D 3114 GLN cc_start: 0.8540 (pp30) cc_final: 0.8286 (pp30) REVERT: D 3131 TYR cc_start: 0.9132 (m-80) cc_final: 0.8692 (m-80) REVERT: D 3147 TYR cc_start: 0.8374 (m-80) cc_final: 0.8112 (m-80) REVERT: D 3162 PHE cc_start: 0.9111 (t80) cc_final: 0.8815 (t80) REVERT: D 3170 PHE cc_start: 0.8644 (p90) cc_final: 0.8111 (p90) REVERT: D 3246 MET cc_start: 0.8636 (mtp) cc_final: 0.8345 (ptp) REVERT: D 3304 GLN cc_start: 0.9083 (tp-100) cc_final: 0.8736 (tp-100) REVERT: D 4080 TYR cc_start: 0.8498 (p90) cc_final: 0.7847 (p90) REVERT: D 4258 MET cc_start: 0.3665 (ppp) cc_final: 0.3394 (ppp) REVERT: D 4505 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8023 (tp) REVERT: D 4654 MET cc_start: 0.9115 (tpp) cc_final: 0.8586 (tpp) REVERT: D 4748 MET cc_start: 0.8159 (mpp) cc_final: 0.7771 (mpp) REVERT: D 4879 GLN cc_start: 0.8175 (tp-100) cc_final: 0.7433 (tp40) REVERT: D 4943 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8134 (mtp) outliers start: 106 outliers final: 72 residues processed: 843 average time/residue: 1.1238 time to fit residues: 1704.4376 Evaluate side-chains 854 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 766 time to evaluate : 10.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2734 MET Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2921 PHE Chi-restraints excluded: chain A residue 2929 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2972 ASP Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4283 PHE Chi-restraints excluded: chain A residue 4505 LEU Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4615 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 986 ILE Chi-restraints excluded: chain B residue 1215 MET Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2893 LEU Chi-restraints excluded: chain B residue 2921 PHE Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2972 ASP Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4283 PHE Chi-restraints excluded: chain B residue 4505 LEU Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain B residue 4615 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 883 GLU Chi-restraints excluded: chain C residue 1215 MET Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2921 PHE Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2972 ASP Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4283 PHE Chi-restraints excluded: chain C residue 4505 LEU Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain C residue 4615 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 883 GLU Chi-restraints excluded: chain D residue 985 PHE Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2921 PHE Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2972 ASP Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4283 PHE Chi-restraints excluded: chain D residue 4505 LEU Chi-restraints excluded: chain D residue 4572 LEU Chi-restraints excluded: chain D residue 4615 LEU Chi-restraints excluded: chain D residue 4943 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1006 optimal weight: 8.9990 chunk 649 optimal weight: 20.0000 chunk 971 optimal weight: 10.0000 chunk 490 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 315 optimal weight: 0.9990 chunk 1034 optimal weight: 9.9990 chunk 1108 optimal weight: 2.9990 chunk 804 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 1278 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2868 HIS ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 138292 Z= 0.271 Angle : 0.624 15.354 186864 Z= 0.312 Chirality : 0.040 0.250 20500 Planarity : 0.004 0.150 23992 Dihedral : 5.748 80.485 18576 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 0.71 % Allowed : 9.05 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 1.07 (0.07), residues: 16792 helix: 1.71 (0.06), residues: 8996 sheet: -0.31 (0.13), residues: 1536 loop : -0.46 (0.08), residues: 6260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2732 HIS 0.006 0.001 HIS D 692 PHE 0.024 0.001 PHE B3162 TYR 0.028 0.001 TYR C4939 ARG 0.007 0.000 ARG B1960 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 773 time to evaluate : 11.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8442 (tpt) cc_final: 0.7881 (mmm) REVERT: A 655 MET cc_start: 0.9268 (mmp) cc_final: 0.8727 (mmp) REVERT: A 678 MET cc_start: 0.8359 (tpt) cc_final: 0.7812 (tpt) REVERT: A 778 MET cc_start: 0.8466 (tpt) cc_final: 0.7750 (mmm) REVERT: A 895 MET cc_start: 0.9162 (mtt) cc_final: 0.8886 (mmt) REVERT: A 902 TRP cc_start: 0.6228 (t-100) cc_final: 0.5679 (t-100) REVERT: A 1842 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8832 (pt) REVERT: A 1948 MET cc_start: 0.8016 (mmm) cc_final: 0.7488 (ppp) REVERT: A 1953 MET cc_start: 0.7363 (mmt) cc_final: 0.7144 (mpp) REVERT: A 2689 MET cc_start: 0.5496 (ptt) cc_final: 0.5225 (tmm) REVERT: A 2727 HIS cc_start: 0.9136 (t-90) cc_final: 0.8483 (t-90) REVERT: A 2731 LYS cc_start: 0.9471 (ptpp) cc_final: 0.8588 (ptpp) REVERT: A 2757 MET cc_start: 0.7049 (mpp) cc_final: 0.6322 (mpp) REVERT: A 2844 MET cc_start: 0.9254 (ppp) cc_final: 0.8733 (ppp) REVERT: A 2848 TYR cc_start: 0.8523 (m-10) cc_final: 0.8153 (m-10) REVERT: A 2858 MET cc_start: 0.9447 (mmt) cc_final: 0.9187 (mpp) REVERT: A 2874 TYR cc_start: 0.8700 (t80) cc_final: 0.8459 (t80) REVERT: A 2921 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7420 (p90) REVERT: A 2932 TYR cc_start: 0.8787 (m-80) cc_final: 0.8332 (m-80) REVERT: A 2979 ARG cc_start: 0.9094 (tmm160) cc_final: 0.8835 (ttp80) REVERT: A 2982 PHE cc_start: 0.8966 (m-10) cc_final: 0.8651 (m-80) REVERT: A 3060 PHE cc_start: 0.8161 (t80) cc_final: 0.7497 (t80) REVERT: A 3131 TYR cc_start: 0.9078 (m-80) cc_final: 0.8698 (m-80) REVERT: A 3138 TYR cc_start: 0.9295 (t80) cc_final: 0.8919 (t80) REVERT: A 3170 PHE cc_start: 0.8297 (p90) cc_final: 0.7448 (p90) REVERT: A 3245 TYR cc_start: 0.9019 (t80) cc_final: 0.8741 (t80) REVERT: A 3296 MET cc_start: 0.9352 (pmm) cc_final: 0.9059 (pmm) REVERT: A 3304 GLN cc_start: 0.9045 (tp-100) cc_final: 0.8706 (tp-100) REVERT: A 3819 MET cc_start: 0.7190 (ptt) cc_final: 0.6957 (ptt) REVERT: A 4080 TYR cc_start: 0.8551 (p90) cc_final: 0.7843 (p90) REVERT: A 4258 MET cc_start: 0.3939 (ppp) cc_final: 0.3357 (ptt) REVERT: A 4505 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8035 (tp) REVERT: A 4654 MET cc_start: 0.8936 (tpp) cc_final: 0.8500 (tpp) REVERT: A 4748 MET cc_start: 0.8123 (mpp) cc_final: 0.7850 (mpp) REVERT: A 4879 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7450 (tp40) REVERT: A 4943 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7693 (mtp) REVERT: B 393 MET cc_start: 0.8470 (tpt) cc_final: 0.7909 (mmm) REVERT: B 655 MET cc_start: 0.9286 (mmp) cc_final: 0.8923 (mmp) REVERT: B 778 MET cc_start: 0.8214 (tpt) cc_final: 0.7696 (mmm) REVERT: B 1842 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8829 (pt) REVERT: B 1948 MET cc_start: 0.7824 (mmm) cc_final: 0.7373 (mmm) REVERT: B 2150 MET cc_start: 0.8655 (mmm) cc_final: 0.8336 (mmm) REVERT: B 2172 MET cc_start: 0.8975 (tpp) cc_final: 0.8720 (tpp) REVERT: B 2442 MET cc_start: 0.8731 (mmp) cc_final: 0.8370 (mmm) REVERT: B 2681 MET cc_start: 0.8044 (tpp) cc_final: 0.7474 (tmm) REVERT: B 2685 TYR cc_start: 0.7976 (t80) cc_final: 0.7303 (t80) REVERT: B 2689 MET cc_start: 0.5035 (ptt) cc_final: 0.4313 (tmm) REVERT: B 2719 TYR cc_start: 0.9087 (t80) cc_final: 0.8810 (t80) REVERT: B 2727 HIS cc_start: 0.9254 (t-90) cc_final: 0.8627 (t-90) REVERT: B 2731 LYS cc_start: 0.9445 (pttm) cc_final: 0.8848 (pttm) REVERT: B 2757 MET cc_start: 0.7056 (mpp) cc_final: 0.6729 (mpp) REVERT: B 2890 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8837 (pm20) REVERT: B 2921 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7488 (p90) REVERT: B 2932 TYR cc_start: 0.8743 (m-80) cc_final: 0.8314 (m-80) REVERT: B 2979 ARG cc_start: 0.9108 (tmm160) cc_final: 0.8849 (ttp80) REVERT: B 2982 PHE cc_start: 0.8975 (m-10) cc_final: 0.8647 (m-80) REVERT: B 3060 PHE cc_start: 0.8183 (t80) cc_final: 0.7519 (t80) REVERT: B 3072 MET cc_start: 0.9399 (ptp) cc_final: 0.9185 (pmm) REVERT: B 3131 TYR cc_start: 0.9117 (m-80) cc_final: 0.8727 (m-80) REVERT: B 3147 TYR cc_start: 0.8408 (m-80) cc_final: 0.8129 (m-80) REVERT: B 3162 PHE cc_start: 0.9114 (t80) cc_final: 0.8816 (t80) REVERT: B 3246 MET cc_start: 0.8647 (mtp) cc_final: 0.8362 (ptp) REVERT: B 3263 MET cc_start: 0.9058 (ppp) cc_final: 0.8208 (pmm) REVERT: B 3304 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8723 (tp-100) REVERT: B 4080 TYR cc_start: 0.8557 (p90) cc_final: 0.7892 (p90) REVERT: B 4258 MET cc_start: 0.3652 (ppp) cc_final: 0.2957 (ptt) REVERT: B 4505 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8028 (tp) REVERT: B 4654 MET cc_start: 0.9166 (tpp) cc_final: 0.8611 (tpp) REVERT: B 4748 MET cc_start: 0.8163 (mpp) cc_final: 0.7816 (mpp) REVERT: B 4879 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7427 (tp40) REVERT: B 4943 MET cc_start: 0.8324 (ttm) cc_final: 0.8108 (mtp) REVERT: C 393 MET cc_start: 0.8469 (tpt) cc_final: 0.7913 (mmm) REVERT: C 655 MET cc_start: 0.9292 (mmp) cc_final: 0.8936 (mmp) REVERT: C 778 MET cc_start: 0.8216 (tpt) cc_final: 0.7702 (mmm) REVERT: C 1842 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8832 (pt) REVERT: C 1948 MET cc_start: 0.8188 (mmm) cc_final: 0.7916 (tpp) REVERT: C 1953 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7406 (mpp) REVERT: C 2150 MET cc_start: 0.8652 (mmm) cc_final: 0.8335 (mmm) REVERT: C 2681 MET cc_start: 0.8031 (tpp) cc_final: 0.7448 (tmm) REVERT: C 2689 MET cc_start: 0.4967 (ptt) cc_final: 0.4258 (tmm) REVERT: C 2719 TYR cc_start: 0.9097 (t80) cc_final: 0.8824 (t80) REVERT: C 2727 HIS cc_start: 0.9258 (t-90) cc_final: 0.8591 (t-90) REVERT: C 2731 LYS cc_start: 0.9443 (pttm) cc_final: 0.8838 (pttm) REVERT: C 2757 MET cc_start: 0.7061 (mpp) cc_final: 0.6736 (mpp) REVERT: C 2844 MET cc_start: 0.9213 (ppp) cc_final: 0.8465 (ppp) REVERT: C 2848 TYR cc_start: 0.8366 (m-10) cc_final: 0.7761 (m-10) REVERT: C 2921 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7484 (p90) REVERT: C 2932 TYR cc_start: 0.8745 (m-80) cc_final: 0.8318 (m-80) REVERT: C 2979 ARG cc_start: 0.9113 (tmm160) cc_final: 0.8853 (ttp80) REVERT: C 2982 PHE cc_start: 0.8963 (m-10) cc_final: 0.8642 (m-80) REVERT: C 3060 PHE cc_start: 0.8170 (t80) cc_final: 0.7498 (t80) REVERT: C 3072 MET cc_start: 0.9377 (ptp) cc_final: 0.9170 (ptp) REVERT: C 3131 TYR cc_start: 0.9111 (m-80) cc_final: 0.8713 (m-80) REVERT: C 3170 PHE cc_start: 0.8589 (p90) cc_final: 0.8014 (p90) REVERT: C 3246 MET cc_start: 0.8683 (mtp) cc_final: 0.8413 (ptp) REVERT: C 3304 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8737 (tp-100) REVERT: C 3689 MET cc_start: 0.8777 (mmm) cc_final: 0.8289 (mmp) REVERT: C 3819 MET cc_start: 0.7011 (ptt) cc_final: 0.6765 (ptt) REVERT: C 4080 TYR cc_start: 0.8541 (p90) cc_final: 0.7862 (p90) REVERT: C 4258 MET cc_start: 0.3672 (ppp) cc_final: 0.2977 (ptt) REVERT: C 4505 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8031 (tp) REVERT: C 4654 MET cc_start: 0.9167 (tpp) cc_final: 0.8606 (tpp) REVERT: C 4748 MET cc_start: 0.8170 (mpp) cc_final: 0.7819 (mpp) REVERT: C 4879 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7443 (tp40) REVERT: D 393 MET cc_start: 0.8431 (tpt) cc_final: 0.7778 (mmm) REVERT: D 655 MET cc_start: 0.9283 (mmp) cc_final: 0.8917 (mmp) REVERT: D 678 MET cc_start: 0.8308 (tpt) cc_final: 0.7823 (tpt) REVERT: D 778 MET cc_start: 0.8216 (tpt) cc_final: 0.7706 (mmm) REVERT: D 1842 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8829 (pt) REVERT: D 1948 MET cc_start: 0.8186 (mmm) cc_final: 0.7906 (tpp) REVERT: D 1953 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7380 (mpp) REVERT: D 2150 MET cc_start: 0.8646 (mmm) cc_final: 0.8329 (mmm) REVERT: D 2681 MET cc_start: 0.8007 (tpp) cc_final: 0.7407 (tmm) REVERT: D 2689 MET cc_start: 0.5134 (ptt) cc_final: 0.4734 (ttm) REVERT: D 2719 TYR cc_start: 0.9062 (t80) cc_final: 0.8771 (t80) REVERT: D 2727 HIS cc_start: 0.9254 (t-90) cc_final: 0.8594 (t-90) REVERT: D 2731 LYS cc_start: 0.9446 (pttm) cc_final: 0.8835 (pttm) REVERT: D 2757 MET cc_start: 0.7124 (mpp) cc_final: 0.6497 (mpp) REVERT: D 2844 MET cc_start: 0.9218 (ppp) cc_final: 0.8583 (ppp) REVERT: D 2848 TYR cc_start: 0.8391 (m-10) cc_final: 0.7885 (m-10) REVERT: D 2921 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7474 (p90) REVERT: D 2932 TYR cc_start: 0.8735 (m-80) cc_final: 0.8309 (m-80) REVERT: D 2982 PHE cc_start: 0.8979 (m-10) cc_final: 0.8658 (m-80) REVERT: D 3060 PHE cc_start: 0.8169 (t80) cc_final: 0.7498 (t80) REVERT: D 3114 GLN cc_start: 0.8520 (pp30) cc_final: 0.8276 (pp30) REVERT: D 3131 TYR cc_start: 0.9113 (m-80) cc_final: 0.8724 (m-80) REVERT: D 3147 TYR cc_start: 0.8382 (m-80) cc_final: 0.8114 (m-80) REVERT: D 3162 PHE cc_start: 0.9106 (t80) cc_final: 0.8826 (t80) REVERT: D 3170 PHE cc_start: 0.8632 (p90) cc_final: 0.8115 (p90) REVERT: D 3246 MET cc_start: 0.8633 (mtp) cc_final: 0.8336 (ptp) REVERT: D 3304 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8731 (tp-100) REVERT: D 3689 MET cc_start: 0.8777 (mmm) cc_final: 0.8303 (mmp) REVERT: D 3819 MET cc_start: 0.7010 (ptt) cc_final: 0.6779 (ptt) REVERT: D 4080 TYR cc_start: 0.8510 (p90) cc_final: 0.7827 (p90) REVERT: D 4258 MET cc_start: 0.3673 (ppp) cc_final: 0.3002 (ptt) REVERT: D 4505 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8026 (tp) REVERT: D 4654 MET cc_start: 0.9130 (tpp) cc_final: 0.8580 (tpp) REVERT: D 4748 MET cc_start: 0.8172 (mpp) cc_final: 0.7800 (mpp) REVERT: D 4879 GLN cc_start: 0.8182 (tp-100) cc_final: 0.7445 (tp40) REVERT: D 4943 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (mtp) outliers start: 106 outliers final: 77 residues processed: 832 average time/residue: 1.1234 time to fit residues: 1678.6545 Evaluate side-chains 864 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 770 time to evaluate : 11.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2734 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2893 LEU Chi-restraints excluded: chain A residue 2921 PHE Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2972 ASP Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4283 PHE Chi-restraints excluded: chain A residue 4505 LEU Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4615 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1720 MET Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2893 LEU Chi-restraints excluded: chain B residue 2921 PHE Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2972 ASP Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4283 PHE Chi-restraints excluded: chain B residue 4505 LEU Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain B residue 4615 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2734 MET Chi-restraints excluded: chain C residue 2921 PHE Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2972 ASP Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4283 PHE Chi-restraints excluded: chain C residue 4505 LEU Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain C residue 4615 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1215 MET Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1953 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2921 PHE Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2972 ASP Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4283 PHE Chi-restraints excluded: chain D residue 4505 LEU Chi-restraints excluded: chain D residue 4572 LEU Chi-restraints excluded: chain D residue 4615 LEU Chi-restraints excluded: chain D residue 4943 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1479 optimal weight: 9.9990 chunk 1558 optimal weight: 30.0000 chunk 1422 optimal weight: 5.9990 chunk 1516 optimal weight: 10.0000 chunk 912 optimal weight: 0.9990 chunk 660 optimal weight: 10.0000 chunk 1190 optimal weight: 3.9990 chunk 465 optimal weight: 7.9990 chunk 1370 optimal weight: 10.0000 chunk 1433 optimal weight: 6.9990 chunk 1510 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 GLN ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 138292 Z= 0.315 Angle : 0.638 14.896 186864 Z= 0.320 Chirality : 0.040 0.242 20500 Planarity : 0.004 0.143 23992 Dihedral : 5.679 79.601 18576 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 0.73 % Allowed : 9.10 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 1.04 (0.07), residues: 16792 helix: 1.70 (0.06), residues: 9020 sheet: -0.39 (0.13), residues: 1580 loop : -0.48 (0.08), residues: 6192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2732 HIS 0.009 0.001 HIS C2868 PHE 0.026 0.001 PHE C3162 TYR 0.031 0.001 TYR C2685 ARG 0.006 0.000 ARG C1960 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 770 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 393 MET cc_start: 0.8453 (tpt) cc_final: 0.7900 (mmm) REVERT: A 655 MET cc_start: 0.9261 (mmp) cc_final: 0.8717 (mmp) REVERT: A 678 MET cc_start: 0.8367 (tpt) cc_final: 0.7819 (tpt) REVERT: A 778 MET cc_start: 0.8476 (tpt) cc_final: 0.7735 (mmm) REVERT: A 895 MET cc_start: 0.9171 (mtt) cc_final: 0.8883 (mmt) REVERT: A 902 TRP cc_start: 0.6385 (t-100) cc_final: 0.5831 (t-100) REVERT: A 981 MET cc_start: 0.8582 (tmm) cc_final: 0.8257 (tmm) REVERT: A 1842 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8840 (pt) REVERT: A 2442 MET cc_start: 0.8739 (mmp) cc_final: 0.8447 (mmm) REVERT: A 2689 MET cc_start: 0.5650 (ptt) cc_final: 0.5231 (tmm) REVERT: A 2727 HIS cc_start: 0.9131 (t-90) cc_final: 0.8490 (t-90) REVERT: A 2731 LYS cc_start: 0.9473 (ptpp) cc_final: 0.8610 (ptpp) REVERT: A 2757 MET cc_start: 0.7001 (mpp) cc_final: 0.6295 (mpp) REVERT: A 2844 MET cc_start: 0.9263 (ppp) cc_final: 0.8723 (ppp) REVERT: A 2848 TYR cc_start: 0.8572 (m-10) cc_final: 0.8236 (m-10) REVERT: A 2874 TYR cc_start: 0.8708 (t80) cc_final: 0.8459 (t80) REVERT: A 2921 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7408 (p90) REVERT: A 2932 TYR cc_start: 0.8800 (m-80) cc_final: 0.8338 (m-80) REVERT: A 2979 ARG cc_start: 0.9094 (tmm160) cc_final: 0.8837 (ttp80) REVERT: A 2982 PHE cc_start: 0.8994 (m-10) cc_final: 0.8686 (m-80) REVERT: A 3060 PHE cc_start: 0.8188 (t80) cc_final: 0.7523 (t80) REVERT: A 3131 TYR cc_start: 0.9073 (m-80) cc_final: 0.8702 (m-80) REVERT: A 3138 TYR cc_start: 0.9302 (t80) cc_final: 0.8963 (t80) REVERT: A 3162 PHE cc_start: 0.9111 (t80) cc_final: 0.8828 (t80) REVERT: A 3170 PHE cc_start: 0.8312 (p90) cc_final: 0.7440 (p90) REVERT: A 3245 TYR cc_start: 0.9033 (t80) cc_final: 0.8737 (t80) REVERT: A 3296 MET cc_start: 0.9355 (pmm) cc_final: 0.9069 (pmm) REVERT: A 3304 GLN cc_start: 0.9056 (tp-100) cc_final: 0.8714 (tp-100) REVERT: A 3819 MET cc_start: 0.7255 (ptt) cc_final: 0.7048 (ptt) REVERT: A 4080 TYR cc_start: 0.8556 (p90) cc_final: 0.7854 (p90) REVERT: A 4258 MET cc_start: 0.4036 (ppp) cc_final: 0.3462 (ptt) REVERT: A 4505 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8030 (tp) REVERT: A 4654 MET cc_start: 0.8939 (tpp) cc_final: 0.8523 (tpp) REVERT: A 4748 MET cc_start: 0.8106 (mpp) cc_final: 0.7838 (mpp) REVERT: A 4879 GLN cc_start: 0.8218 (tp-100) cc_final: 0.7482 (tp40) REVERT: A 4943 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7705 (mtp) REVERT: B 393 MET cc_start: 0.8444 (tpt) cc_final: 0.7873 (mmm) REVERT: B 655 MET cc_start: 0.9269 (mmp) cc_final: 0.8921 (mmp) REVERT: B 778 MET cc_start: 0.8227 (tpt) cc_final: 0.7700 (mmm) REVERT: B 1842 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8832 (pt) REVERT: B 1948 MET cc_start: 0.7834 (mmm) cc_final: 0.7386 (mmm) REVERT: B 2172 MET cc_start: 0.8986 (tpp) cc_final: 0.8696 (tpp) REVERT: B 2214 MET cc_start: 0.9149 (mmm) cc_final: 0.8582 (mmm) REVERT: B 2681 MET cc_start: 0.8063 (tpp) cc_final: 0.7463 (tmm) REVERT: B 2685 TYR cc_start: 0.7820 (t80) cc_final: 0.7158 (t80) REVERT: B 2689 MET cc_start: 0.5191 (ptt) cc_final: 0.4543 (tmm) REVERT: B 2719 TYR cc_start: 0.9073 (t80) cc_final: 0.8823 (t80) REVERT: B 2727 HIS cc_start: 0.9265 (t-90) cc_final: 0.8634 (t-90) REVERT: B 2731 LYS cc_start: 0.9444 (pttm) cc_final: 0.8852 (pttm) REVERT: B 2757 MET cc_start: 0.7056 (mpp) cc_final: 0.6733 (mpp) REVERT: B 2840 MET cc_start: 0.8159 (mmt) cc_final: 0.7851 (mmt) REVERT: B 2890 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8836 (pm20) REVERT: B 2921 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7497 (p90) REVERT: B 2932 TYR cc_start: 0.8775 (m-80) cc_final: 0.8334 (m-80) REVERT: B 2979 ARG cc_start: 0.9111 (tmm160) cc_final: 0.8852 (ttp80) REVERT: B 2982 PHE cc_start: 0.9002 (m-10) cc_final: 0.8687 (m-80) REVERT: B 3060 PHE cc_start: 0.8203 (t80) cc_final: 0.7542 (t80) REVERT: B 3072 MET cc_start: 0.9408 (ptp) cc_final: 0.9191 (pmm) REVERT: B 3131 TYR cc_start: 0.9096 (m-80) cc_final: 0.8717 (m-80) REVERT: B 3147 TYR cc_start: 0.8427 (m-80) cc_final: 0.8147 (m-80) REVERT: B 3162 PHE cc_start: 0.9144 (t80) cc_final: 0.8823 (t80) REVERT: B 3246 MET cc_start: 0.8645 (mtp) cc_final: 0.8355 (ptp) REVERT: B 3263 MET cc_start: 0.9055 (ppp) cc_final: 0.8190 (pmm) REVERT: B 3304 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8719 (tp-100) REVERT: B 3689 MET cc_start: 0.8797 (mmp) cc_final: 0.8438 (mmm) REVERT: B 3819 MET cc_start: 0.7063 (ptt) cc_final: 0.6794 (ptt) REVERT: B 4080 TYR cc_start: 0.8562 (p90) cc_final: 0.7887 (p90) REVERT: B 4258 MET cc_start: 0.3790 (ppp) cc_final: 0.3121 (ptt) REVERT: B 4505 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8028 (tp) REVERT: B 4654 MET cc_start: 0.9169 (tpp) cc_final: 0.8584 (tpp) REVERT: B 4748 MET cc_start: 0.8168 (mpp) cc_final: 0.7830 (mpp) REVERT: B 4879 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7455 (tp40) REVERT: B 4943 MET cc_start: 0.8329 (ttm) cc_final: 0.8116 (mtp) REVERT: C 393 MET cc_start: 0.8434 (tpt) cc_final: 0.7869 (mmm) REVERT: C 655 MET cc_start: 0.9274 (mmp) cc_final: 0.8932 (mmp) REVERT: C 678 MET cc_start: 0.8299 (tpt) cc_final: 0.7831 (tpt) REVERT: C 778 MET cc_start: 0.8224 (tpt) cc_final: 0.7702 (mmm) REVERT: C 1842 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8837 (pt) REVERT: C 1948 MET cc_start: 0.8190 (mmm) cc_final: 0.7905 (tpp) REVERT: C 1953 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7416 (mpp) REVERT: C 2442 MET cc_start: 0.8742 (mmp) cc_final: 0.8404 (mmm) REVERT: C 2681 MET cc_start: 0.8057 (tpp) cc_final: 0.7522 (tmm) REVERT: C 2685 TYR cc_start: 0.8194 (t80) cc_final: 0.7332 (t80) REVERT: C 2689 MET cc_start: 0.5166 (ptt) cc_final: 0.4418 (tmm) REVERT: C 2719 TYR cc_start: 0.9076 (t80) cc_final: 0.8818 (t80) REVERT: C 2727 HIS cc_start: 0.9272 (t-90) cc_final: 0.8609 (t-90) REVERT: C 2731 LYS cc_start: 0.9443 (pttm) cc_final: 0.8843 (pttm) REVERT: C 2757 MET cc_start: 0.7042 (mpp) cc_final: 0.6723 (mpp) REVERT: C 2921 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7454 (p90) REVERT: C 2932 TYR cc_start: 0.8767 (m-80) cc_final: 0.8325 (m-80) REVERT: C 2979 ARG cc_start: 0.9118 (tmm160) cc_final: 0.8895 (ttp80) REVERT: C 2982 PHE cc_start: 0.8992 (m-10) cc_final: 0.8662 (m-80) REVERT: C 3060 PHE cc_start: 0.8208 (t80) cc_final: 0.7536 (t80) REVERT: C 3131 TYR cc_start: 0.9108 (m-80) cc_final: 0.8716 (m-80) REVERT: C 3162 PHE cc_start: 0.9082 (t80) cc_final: 0.8837 (t80) REVERT: C 3170 PHE cc_start: 0.8605 (p90) cc_final: 0.8075 (p90) REVERT: C 3246 MET cc_start: 0.8700 (mtp) cc_final: 0.8424 (ptp) REVERT: C 3304 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8733 (tp-100) REVERT: C 3689 MET cc_start: 0.8791 (mmm) cc_final: 0.8308 (mmp) REVERT: C 3819 MET cc_start: 0.7096 (ptt) cc_final: 0.6877 (ptt) REVERT: C 4080 TYR cc_start: 0.8565 (p90) cc_final: 0.7891 (p90) REVERT: C 4258 MET cc_start: 0.3745 (ppp) cc_final: 0.3060 (ptt) REVERT: C 4505 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8032 (tp) REVERT: C 4654 MET cc_start: 0.9180 (tpp) cc_final: 0.8584 (tpp) REVERT: C 4748 MET cc_start: 0.8173 (mpp) cc_final: 0.7833 (mpp) REVERT: C 4879 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7602 (tp40) REVERT: D 393 MET cc_start: 0.8418 (tpt) cc_final: 0.7776 (mmm) REVERT: D 655 MET cc_start: 0.9269 (mmp) cc_final: 0.8918 (mmp) REVERT: D 678 MET cc_start: 0.8314 (tpt) cc_final: 0.7826 (tpt) REVERT: D 778 MET cc_start: 0.8230 (tpt) cc_final: 0.7706 (mmm) REVERT: D 1842 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8836 (pt) REVERT: D 1948 MET cc_start: 0.8188 (mmm) cc_final: 0.7901 (tpp) REVERT: D 1953 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: D 2442 MET cc_start: 0.8745 (mmp) cc_final: 0.8397 (mmm) REVERT: D 2681 MET cc_start: 0.8035 (tpp) cc_final: 0.7456 (tmm) REVERT: D 2689 MET cc_start: 0.5236 (ptt) cc_final: 0.4809 (ttm) REVERT: D 2719 TYR cc_start: 0.9070 (t80) cc_final: 0.8782 (t80) REVERT: D 2727 HIS cc_start: 0.9273 (t-90) cc_final: 0.8619 (t-90) REVERT: D 2731 LYS cc_start: 0.9447 (pttm) cc_final: 0.8843 (pttm) REVERT: D 2757 MET cc_start: 0.7140 (mpp) cc_final: 0.6469 (mpp) REVERT: D 2844 MET cc_start: 0.9222 (ppp) cc_final: 0.8534 (ppp) REVERT: D 2848 TYR cc_start: 0.8419 (m-10) cc_final: 0.7949 (m-10) REVERT: D 2921 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7487 (p90) REVERT: D 2932 TYR cc_start: 0.8757 (m-80) cc_final: 0.8324 (m-80) REVERT: D 2982 PHE cc_start: 0.9007 (m-10) cc_final: 0.8703 (m-80) REVERT: D 3060 PHE cc_start: 0.8186 (t80) cc_final: 0.7511 (t80) REVERT: D 3114 GLN cc_start: 0.8519 (pp30) cc_final: 0.8283 (pp30) REVERT: D 3131 TYR cc_start: 0.9109 (m-80) cc_final: 0.8734 (m-80) REVERT: D 3147 TYR cc_start: 0.8409 (m-80) cc_final: 0.8128 (m-80) REVERT: D 3162 PHE cc_start: 0.9114 (t80) cc_final: 0.8834 (t80) REVERT: D 3170 PHE cc_start: 0.8631 (p90) cc_final: 0.8127 (p90) REVERT: D 3246 MET cc_start: 0.8658 (mtp) cc_final: 0.8356 (ptp) REVERT: D 3304 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8733 (tp-100) REVERT: D 3689 MET cc_start: 0.8791 (mmm) cc_final: 0.8337 (mmp) REVERT: D 3819 MET cc_start: 0.7101 (ptt) cc_final: 0.6880 (ptt) REVERT: D 4080 TYR cc_start: 0.8551 (p90) cc_final: 0.7869 (p90) REVERT: D 4258 MET cc_start: 0.3753 (ppp) cc_final: 0.3069 (ptt) REVERT: D 4505 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8027 (tp) REVERT: D 4654 MET cc_start: 0.9133 (tpp) cc_final: 0.8633 (tpp) REVERT: D 4748 MET cc_start: 0.8173 (mpp) cc_final: 0.7836 (mpp) REVERT: D 4879 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7598 (tp40) REVERT: D 4943 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8121 (mtp) outliers start: 109 outliers final: 79 residues processed: 831 average time/residue: 1.1373 time to fit residues: 1698.5405 Evaluate side-chains 863 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 767 time to evaluate : 11.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2734 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2921 PHE Chi-restraints excluded: chain A residue 2929 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2972 ASP Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4283 PHE Chi-restraints excluded: chain A residue 4505 LEU Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4615 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 986 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2893 LEU Chi-restraints excluded: chain B residue 2921 PHE Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2972 ASP Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4283 PHE Chi-restraints excluded: chain B residue 4505 LEU Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain B residue 4615 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2734 MET Chi-restraints excluded: chain C residue 2921 PHE Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2972 ASP Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4283 PHE Chi-restraints excluded: chain C residue 4505 LEU Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain C residue 4615 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1953 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2921 PHE Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2972 ASP Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4283 PHE Chi-restraints excluded: chain D residue 4505 LEU Chi-restraints excluded: chain D residue 4572 LEU Chi-restraints excluded: chain D residue 4615 LEU Chi-restraints excluded: chain D residue 4943 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 995 optimal weight: 7.9990 chunk 1603 optimal weight: 6.9990 chunk 978 optimal weight: 2.9990 chunk 760 optimal weight: 9.9990 chunk 1114 optimal weight: 8.9990 chunk 1681 optimal weight: 9.9990 chunk 1547 optimal weight: 5.9990 chunk 1339 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 1034 optimal weight: 5.9990 chunk 821 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3774 GLN A3851 ASN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN B1620 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3774 GLN B3851 ASN C 927 GLN ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3230 GLN ** C3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3774 GLN C3851 ASN C3955 GLN C3975 GLN C4296 HIS D 927 GLN ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3774 GLN D3851 ASN D4296 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 138292 Z= 0.369 Angle : 0.666 21.252 186864 Z= 0.334 Chirality : 0.041 0.357 20500 Planarity : 0.004 0.140 23992 Dihedral : 5.666 78.170 18576 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 0.73 % Allowed : 9.24 % Favored : 90.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.07), residues: 16792 helix: 1.66 (0.06), residues: 9048 sheet: -0.44 (0.13), residues: 1552 loop : -0.50 (0.08), residues: 6192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2732 HIS 0.007 0.001 HIS D3665 PHE 0.021 0.002 PHE D3117 TYR 0.035 0.002 TYR C2848 ARG 0.006 0.000 ARG B1960 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33584 Ramachandran restraints generated. 16792 Oldfield, 0 Emsley, 16792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 773 time to evaluate : 11.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.8434 (tpt) cc_final: 0.7849 (mmm) REVERT: A 655 MET cc_start: 0.9250 (mmp) cc_final: 0.8833 (mmp) REVERT: A 678 MET cc_start: 0.8379 (tpt) cc_final: 0.7852 (tpt) REVERT: A 778 MET cc_start: 0.8488 (tpt) cc_final: 0.7747 (mmm) REVERT: A 895 MET cc_start: 0.9177 (mtt) cc_final: 0.8870 (mmt) REVERT: A 902 TRP cc_start: 0.6512 (t-100) cc_final: 0.5941 (t-100) REVERT: A 981 MET cc_start: 0.8593 (tmm) cc_final: 0.8266 (tmm) REVERT: A 1842 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8844 (pt) REVERT: A 1948 MET cc_start: 0.7809 (mmm) cc_final: 0.7418 (ppp) REVERT: A 2689 MET cc_start: 0.5717 (ptt) cc_final: 0.5506 (tmm) REVERT: A 2727 HIS cc_start: 0.9156 (t-90) cc_final: 0.8511 (t-90) REVERT: A 2731 LYS cc_start: 0.9477 (ptpp) cc_final: 0.8572 (ptpp) REVERT: A 2757 MET cc_start: 0.7054 (mpp) cc_final: 0.6327 (mpp) REVERT: A 2844 MET cc_start: 0.9260 (ppp) cc_final: 0.8607 (ppp) REVERT: A 2848 TYR cc_start: 0.8565 (m-10) cc_final: 0.8162 (m-10) REVERT: A 2874 TYR cc_start: 0.8726 (t80) cc_final: 0.8474 (t80) REVERT: A 2921 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7435 (p90) REVERT: A 2932 TYR cc_start: 0.8824 (m-80) cc_final: 0.8354 (m-80) REVERT: A 2979 ARG cc_start: 0.9104 (tmm160) cc_final: 0.8854 (ttp80) REVERT: A 2982 PHE cc_start: 0.9038 (m-10) cc_final: 0.8740 (m-80) REVERT: A 3060 PHE cc_start: 0.8231 (t80) cc_final: 0.7571 (t80) REVERT: A 3131 TYR cc_start: 0.9065 (m-80) cc_final: 0.8692 (m-80) REVERT: A 3138 TYR cc_start: 0.9307 (t80) cc_final: 0.8971 (t80) REVERT: A 3162 PHE cc_start: 0.9126 (t80) cc_final: 0.8835 (t80) REVERT: A 3296 MET cc_start: 0.9383 (pmm) cc_final: 0.9103 (pmm) REVERT: A 3304 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8730 (tp-100) REVERT: A 3819 MET cc_start: 0.7345 (ptt) cc_final: 0.7084 (ptt) REVERT: A 4080 TYR cc_start: 0.8569 (p90) cc_final: 0.7870 (p90) REVERT: A 4186 MET cc_start: 0.8533 (mmm) cc_final: 0.7805 (mmm) REVERT: A 4258 MET cc_start: 0.4061 (ppp) cc_final: 0.3489 (ptt) REVERT: A 4505 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8046 (tp) REVERT: A 4654 MET cc_start: 0.8935 (tpp) cc_final: 0.8520 (tpp) REVERT: A 4748 MET cc_start: 0.8125 (mpp) cc_final: 0.7897 (mpp) REVERT: A 4879 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7566 (tp40) REVERT: A 4943 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7696 (mtp) REVERT: B 393 MET cc_start: 0.8420 (tpt) cc_final: 0.7840 (mmm) REVERT: B 655 MET cc_start: 0.9258 (mmp) cc_final: 0.8914 (mmp) REVERT: B 778 MET cc_start: 0.8243 (tpt) cc_final: 0.7706 (mmm) REVERT: B 1842 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8836 (pt) REVERT: B 1948 MET cc_start: 0.7822 (mmm) cc_final: 0.7356 (mmm) REVERT: B 2150 MET cc_start: 0.8652 (mmm) cc_final: 0.8349 (mmm) REVERT: B 2172 MET cc_start: 0.9006 (tpp) cc_final: 0.8734 (tpp) REVERT: B 2681 MET cc_start: 0.8085 (tpp) cc_final: 0.7485 (tmm) REVERT: B 2689 MET cc_start: 0.5404 (ptt) cc_final: 0.4764 (tmm) REVERT: B 2719 TYR cc_start: 0.9102 (t80) cc_final: 0.8856 (t80) REVERT: B 2727 HIS cc_start: 0.9290 (t-90) cc_final: 0.8644 (t-90) REVERT: B 2731 LYS cc_start: 0.9450 (pttm) cc_final: 0.8842 (pttm) REVERT: B 2757 MET cc_start: 0.7117 (mpp) cc_final: 0.6780 (mpp) REVERT: B 2782 MET cc_start: 0.8896 (ppp) cc_final: 0.8689 (pmm) REVERT: B 2840 MET cc_start: 0.8145 (mmt) cc_final: 0.7883 (mmt) REVERT: B 2890 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8845 (pm20) REVERT: B 2921 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7528 (p90) REVERT: B 2932 TYR cc_start: 0.8797 (m-80) cc_final: 0.8349 (m-80) REVERT: B 2979 ARG cc_start: 0.9125 (tmm160) cc_final: 0.8911 (ttp80) REVERT: B 2982 PHE cc_start: 0.9028 (m-10) cc_final: 0.8699 (m-80) REVERT: B 3060 PHE cc_start: 0.8230 (t80) cc_final: 0.7563 (t80) REVERT: B 3072 MET cc_start: 0.9426 (ptp) cc_final: 0.9207 (pmm) REVERT: B 3131 TYR cc_start: 0.9090 (m-80) cc_final: 0.8723 (m-80) REVERT: B 3147 TYR cc_start: 0.8458 (m-80) cc_final: 0.8172 (m-80) REVERT: B 3162 PHE cc_start: 0.9144 (t80) cc_final: 0.8842 (t80) REVERT: B 3304 GLN cc_start: 0.9065 (tp-100) cc_final: 0.8727 (tp-100) REVERT: B 4080 TYR cc_start: 0.8569 (p90) cc_final: 0.7903 (p90) REVERT: B 4258 MET cc_start: 0.3686 (ppp) cc_final: 0.3069 (ptt) REVERT: B 4505 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8044 (tp) REVERT: B 4654 MET cc_start: 0.9168 (tpp) cc_final: 0.8574 (tpp) REVERT: B 4748 MET cc_start: 0.8153 (mpp) cc_final: 0.7812 (mpp) REVERT: B 4879 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7618 (tp40) REVERT: B 4943 MET cc_start: 0.8335 (ttm) cc_final: 0.8129 (mtp) REVERT: C 393 MET cc_start: 0.8418 (tpt) cc_final: 0.7844 (mmm) REVERT: C 655 MET cc_start: 0.9252 (mmp) cc_final: 0.8925 (mmp) REVERT: C 678 MET cc_start: 0.8319 (tpt) cc_final: 0.7837 (tpt) REVERT: C 778 MET cc_start: 0.8240 (tpt) cc_final: 0.7696 (mmm) REVERT: C 1842 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8843 (pt) REVERT: C 1948 MET cc_start: 0.8179 (mmm) cc_final: 0.7891 (tpp) REVERT: C 1953 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7429 (mpp) REVERT: C 2150 MET cc_start: 0.8651 (mmm) cc_final: 0.8350 (mmm) REVERT: C 2681 MET cc_start: 0.8075 (tpp) cc_final: 0.7526 (tmm) REVERT: C 2685 TYR cc_start: 0.8210 (t80) cc_final: 0.7313 (t80) REVERT: C 2689 MET cc_start: 0.5373 (ptt) cc_final: 0.4799 (tmm) REVERT: C 2719 TYR cc_start: 0.9097 (t80) cc_final: 0.8854 (t80) REVERT: C 2727 HIS cc_start: 0.9301 (t-90) cc_final: 0.8626 (t-90) REVERT: C 2731 LYS cc_start: 0.9436 (pttm) cc_final: 0.8826 (pttm) REVERT: C 2757 MET cc_start: 0.7075 (mpp) cc_final: 0.6725 (mpp) REVERT: C 2844 MET cc_start: 0.9219 (ppp) cc_final: 0.8972 (ppp) REVERT: C 2921 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7484 (p90) REVERT: C 2932 TYR cc_start: 0.8791 (m-80) cc_final: 0.8350 (m-80) REVERT: C 2979 ARG cc_start: 0.9127 (tmm160) cc_final: 0.8906 (ttp80) REVERT: C 2982 PHE cc_start: 0.9026 (m-10) cc_final: 0.8699 (m-80) REVERT: C 3060 PHE cc_start: 0.8239 (t80) cc_final: 0.7557 (t80) REVERT: C 3072 MET cc_start: 0.9381 (ptp) cc_final: 0.9180 (ptp) REVERT: C 3131 TYR cc_start: 0.9103 (m-80) cc_final: 0.8729 (m-80) REVERT: C 3162 PHE cc_start: 0.9115 (t80) cc_final: 0.8848 (t80) REVERT: C 3170 PHE cc_start: 0.8636 (p90) cc_final: 0.8103 (p90) REVERT: C 3246 MET cc_start: 0.8685 (mtp) cc_final: 0.8396 (ptp) REVERT: C 3304 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8748 (tp-100) REVERT: C 3689 MET cc_start: 0.8768 (mmm) cc_final: 0.8292 (mmp) REVERT: C 3819 MET cc_start: 0.7212 (ptt) cc_final: 0.7001 (ptt) REVERT: C 4080 TYR cc_start: 0.8570 (p90) cc_final: 0.7888 (p90) REVERT: C 4186 MET cc_start: 0.8519 (mmm) cc_final: 0.7795 (mmm) REVERT: C 4258 MET cc_start: 0.3745 (ppp) cc_final: 0.3121 (ptt) REVERT: C 4505 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8052 (tp) REVERT: C 4654 MET cc_start: 0.9161 (tpp) cc_final: 0.8550 (tpp) REVERT: C 4748 MET cc_start: 0.8158 (mpp) cc_final: 0.7810 (mpp) REVERT: C 4879 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7619 (tp40) REVERT: D 393 MET cc_start: 0.8389 (tpt) cc_final: 0.7702 (mmm) REVERT: D 655 MET cc_start: 0.9258 (mmp) cc_final: 0.8909 (mmp) REVERT: D 678 MET cc_start: 0.8329 (tpt) cc_final: 0.7808 (tpt) REVERT: D 778 MET cc_start: 0.8244 (tpt) cc_final: 0.7711 (mmm) REVERT: D 1842 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8840 (pt) REVERT: D 1948 MET cc_start: 0.8187 (mmm) cc_final: 0.7888 (tpp) REVERT: D 1953 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7422 (mpp) REVERT: D 2150 MET cc_start: 0.8649 (mmm) cc_final: 0.8349 (mmm) REVERT: D 2681 MET cc_start: 0.8045 (tpp) cc_final: 0.7450 (tmm) REVERT: D 2689 MET cc_start: 0.5386 (ptt) cc_final: 0.4975 (ttm) REVERT: D 2719 TYR cc_start: 0.9081 (t80) cc_final: 0.8793 (t80) REVERT: D 2727 HIS cc_start: 0.9301 (t-90) cc_final: 0.8635 (t-90) REVERT: D 2731 LYS cc_start: 0.9446 (pttm) cc_final: 0.8840 (pttm) REVERT: D 2757 MET cc_start: 0.7199 (mpp) cc_final: 0.6544 (mpp) REVERT: D 2782 MET cc_start: 0.8905 (ppp) cc_final: 0.8695 (pmm) REVERT: D 2844 MET cc_start: 0.9220 (ppp) cc_final: 0.8439 (ppp) REVERT: D 2848 TYR cc_start: 0.8440 (m-10) cc_final: 0.7739 (m-10) REVERT: D 2921 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7515 (p90) REVERT: D 2932 TYR cc_start: 0.8788 (m-80) cc_final: 0.8345 (m-80) REVERT: D 2982 PHE cc_start: 0.9033 (m-10) cc_final: 0.8744 (m-80) REVERT: D 3060 PHE cc_start: 0.8231 (t80) cc_final: 0.7564 (t80) REVERT: D 3114 GLN cc_start: 0.8522 (pp30) cc_final: 0.8294 (pp30) REVERT: D 3131 TYR cc_start: 0.9102 (m-80) cc_final: 0.8737 (m-80) REVERT: D 3147 TYR cc_start: 0.8449 (m-80) cc_final: 0.8158 (m-80) REVERT: D 3162 PHE cc_start: 0.9135 (t80) cc_final: 0.8840 (t80) REVERT: D 3170 PHE cc_start: 0.8634 (p90) cc_final: 0.8149 (p90) REVERT: D 3246 MET cc_start: 0.8675 (mtp) cc_final: 0.8362 (ptp) REVERT: D 3304 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8736 (tp-100) REVERT: D 3689 MET cc_start: 0.8796 (mmm) cc_final: 0.8345 (mmp) REVERT: D 4080 TYR cc_start: 0.8555 (p90) cc_final: 0.7890 (p90) REVERT: D 4258 MET cc_start: 0.3668 (ppp) cc_final: 0.3053 (ptt) REVERT: D 4505 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8034 (tp) REVERT: D 4654 MET cc_start: 0.9148 (tpp) cc_final: 0.8632 (tpp) REVERT: D 4748 MET cc_start: 0.8139 (mpp) cc_final: 0.7765 (mpp) REVERT: D 4879 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7631 (tp40) REVERT: D 4943 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8134 (mtp) outliers start: 108 outliers final: 78 residues processed: 836 average time/residue: 1.1656 time to fit residues: 1753.4743 Evaluate side-chains 863 residues out of total 14836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 768 time to evaluate : 11.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 880 ARG Chi-restraints excluded: chain A residue 883 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1842 ILE Chi-restraints excluded: chain A residue 1975 MET Chi-restraints excluded: chain A residue 2192 MET Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2695 MET Chi-restraints excluded: chain A residue 2734 MET Chi-restraints excluded: chain A residue 2737 LEU Chi-restraints excluded: chain A residue 2921 PHE Chi-restraints excluded: chain A residue 2929 LEU Chi-restraints excluded: chain A residue 2935 GLU Chi-restraints excluded: chain A residue 2972 ASP Chi-restraints excluded: chain A residue 3073 GLU Chi-restraints excluded: chain A residue 3147 TYR Chi-restraints excluded: chain A residue 3739 MET Chi-restraints excluded: chain A residue 3956 MET Chi-restraints excluded: chain A residue 4075 ASN Chi-restraints excluded: chain A residue 4283 PHE Chi-restraints excluded: chain A residue 4505 LEU Chi-restraints excluded: chain A residue 4572 LEU Chi-restraints excluded: chain A residue 4615 LEU Chi-restraints excluded: chain A residue 4943 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 880 ARG Chi-restraints excluded: chain B residue 986 ILE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1842 ILE Chi-restraints excluded: chain B residue 1975 MET Chi-restraints excluded: chain B residue 2192 MET Chi-restraints excluded: chain B residue 2355 GLU Chi-restraints excluded: chain B residue 2695 MET Chi-restraints excluded: chain B residue 2734 MET Chi-restraints excluded: chain B residue 2890 GLN Chi-restraints excluded: chain B residue 2893 LEU Chi-restraints excluded: chain B residue 2921 PHE Chi-restraints excluded: chain B residue 2935 GLU Chi-restraints excluded: chain B residue 2972 ASP Chi-restraints excluded: chain B residue 3956 MET Chi-restraints excluded: chain B residue 4075 ASN Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4283 PHE Chi-restraints excluded: chain B residue 4505 LEU Chi-restraints excluded: chain B residue 4572 LEU Chi-restraints excluded: chain B residue 4615 LEU Chi-restraints excluded: chain C residue 880 ARG Chi-restraints excluded: chain C residue 986 ILE Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1720 MET Chi-restraints excluded: chain C residue 1842 ILE Chi-restraints excluded: chain C residue 1953 MET Chi-restraints excluded: chain C residue 1975 MET Chi-restraints excluded: chain C residue 2192 MET Chi-restraints excluded: chain C residue 2355 GLU Chi-restraints excluded: chain C residue 2695 MET Chi-restraints excluded: chain C residue 2734 MET Chi-restraints excluded: chain C residue 2921 PHE Chi-restraints excluded: chain C residue 2935 GLU Chi-restraints excluded: chain C residue 2972 ASP Chi-restraints excluded: chain C residue 3956 MET Chi-restraints excluded: chain C residue 4075 ASN Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain C residue 4283 PHE Chi-restraints excluded: chain C residue 4505 LEU Chi-restraints excluded: chain C residue 4572 LEU Chi-restraints excluded: chain C residue 4615 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 880 ARG Chi-restraints excluded: chain D residue 986 ILE Chi-restraints excluded: chain D residue 1001 GLU Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1953 MET Chi-restraints excluded: chain D residue 1975 MET Chi-restraints excluded: chain D residue 2192 MET Chi-restraints excluded: chain D residue 2355 GLU Chi-restraints excluded: chain D residue 2695 MET Chi-restraints excluded: chain D residue 2734 MET Chi-restraints excluded: chain D residue 2921 PHE Chi-restraints excluded: chain D residue 2935 GLU Chi-restraints excluded: chain D residue 2972 ASP Chi-restraints excluded: chain D residue 3956 MET Chi-restraints excluded: chain D residue 4075 ASN Chi-restraints excluded: chain D residue 4274 MET Chi-restraints excluded: chain D residue 4283 PHE Chi-restraints excluded: chain D residue 4505 LEU Chi-restraints excluded: chain D residue 4572 LEU Chi-restraints excluded: chain D residue 4615 LEU Chi-restraints excluded: chain D residue 4943 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1688 random chunks: chunk 1063 optimal weight: 7.9990 chunk 1426 optimal weight: 0.0870 chunk 410 optimal weight: 10.0000 chunk 1234 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 372 optimal weight: 8.9990 chunk 1341 optimal weight: 5.9990 chunk 561 optimal weight: 3.9990 chunk 1377 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 247 optimal weight: 0.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3774 GLN A3851 ASN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** B1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3774 GLN B3851 ASN C 927 GLN ** C1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2586 GLN ** C2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3077 GLN ** C3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3774 GLN C3851 ASN C3955 GLN C3975 GLN D 927 GLN ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1656 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2586 GLN ** D2612 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3774 GLN D3851 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.045126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.033229 restraints weight = 1436343.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034640 restraints weight = 621251.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.035496 restraints weight = 362013.335| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 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 = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 138292 Z= 0.173 Angle : 0.626 16.264 186864 Z= 0.310 Chirality : 0.040 0.281 20500 Planarity : 0.004 0.136 23992 Dihedral : 5.540 78.635 18576 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.13 % Favored : 96.80 % Rotamer: Outliers : 0.67 % Allowed : 9.32 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % 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: 1.12 (0.07), residues: 16792 helix: 1.76 (0.06), residues: 9000 sheet: -0.30 (0.13), residues: 1584 loop : -0.42 (0.08), residues: 6208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A2732 HIS 0.006 0.001 HIS A 692 PHE 0.021 0.001 PHE A3162 TYR 0.041 0.001 TYR A2760 ARG 0.005 0.000 ARG B1960 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34518.66 seconds wall clock time: 603 minutes 58.64 seconds (36238.64 seconds total)