Starting phenix.real_space_refine on Tue Aug 26 14:30:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwy_27767/08_2025/8dwy_27767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwy_27767/08_2025/8dwy_27767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dwy_27767/08_2025/8dwy_27767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwy_27767/08_2025/8dwy_27767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dwy_27767/08_2025/8dwy_27767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwy_27767/08_2025/8dwy_27767.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 sd= 0.049 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: 4 Type Number sf(0) Gaussians S 260 5.16 5 C 24016 2.51 5 N 6528 2.21 5 O 7244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38048 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "C" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3318 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "M" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "N" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "O" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "P" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3240 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "Q" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "R" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "S" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "T" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1157 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "H" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "V" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "U" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "X" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "W" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "Z" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 936 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "Y" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.98, per 1000 atoms: 0.21 Number of scatterers: 38048 At special positions: 0 Unit cell: (169.36, 245.92, 238.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 260 16.00 O 7244 8.00 N 6528 7.00 C 24016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 125 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 28 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 105 " distance=2.03 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 266 " distance=2.06 Simple disulfide: pdb=" SG CYS M 201 " - pdb=" SG CYS M 225 " distance=2.03 Simple disulfide: pdb=" SG CYS M 203 " - pdb=" SG CYS M 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 396 " - pdb=" SG CYS M 417 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 28 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 105 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 266 " distance=2.04 Simple disulfide: pdb=" SG CYS N 201 " - pdb=" SG CYS N 225 " distance=2.03 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 396 " - pdb=" SG CYS N 417 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 125 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 28 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.03 Simple disulfide: pdb=" SG CYS O 153 " - pdb=" SG CYS O 266 " distance=2.04 Simple disulfide: pdb=" SG CYS O 201 " - pdb=" SG CYS O 225 " distance=2.03 Simple disulfide: pdb=" SG CYS O 203 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS O 396 " - pdb=" SG CYS O 417 " distance=2.04 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 125 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 28 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 105 " distance=2.03 Simple disulfide: pdb=" SG CYS P 153 " - pdb=" SG CYS P 266 " distance=2.04 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 225 " distance=2.03 Simple disulfide: pdb=" SG CYS P 203 " - pdb=" SG CYS P 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 396 " - pdb=" SG CYS P 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 90 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 90 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 141 " " NAG B 501 " - " ASN B 141 " " NAG C 501 " - " ASN C 141 " " NAG D 501 " - " ASN D 141 " " NAG M 501 " - " ASN M 263 " " NAG M 502 " - " ASN M 345 " " NAG N 501 " - " ASN N 263 " " NAG N 502 " - " ASN N 345 " " NAG O 501 " - " ASN O 263 " " NAG O 502 " - " ASN O 345 " " NAG P 501 " - " ASN P 263 " " NAG P 502 " - " ASN P 345 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.4 microseconds 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9104 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 111 sheets defined 13.3% alpha, 40.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.658A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.850A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.760A pdb=" N ALA A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 287 " --> pdb=" O ASP A 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 283 through 287' Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.569A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.517A pdb=" N LYS B 115 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.904A pdb=" N TYR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.680A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 283 through 287' Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 403 through 439 removed outlier: 3.660A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.720A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 removed outlier: 4.179A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.501A pdb=" N HIS C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.242A pdb=" N GLY C 258 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.602A pdb=" N ALA C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE C 287 " --> pdb=" O ASP C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 287' Processing helix chain 'C' and resid 403 through 439 removed outlier: 3.633A pdb=" N TRP C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.700A pdb=" N LYS D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.997A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.712A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE D 287 " --> pdb=" O ASP D 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 283 through 287' Processing helix chain 'D' and resid 403 through 439 removed outlier: 3.626A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 427 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 10 removed outlier: 3.591A pdb=" N LYS M 10 " --> pdb=" O ASN M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 363 removed outlier: 3.576A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU M 357 " --> pdb=" O HIS M 353 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU M 362 " --> pdb=" O TYR M 358 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 398 removed outlier: 3.800A pdb=" N VAL M 368 " --> pdb=" O PRO M 364 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL M 369 " --> pdb=" O THR M 365 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG M 394 " --> pdb=" O VAL M 390 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG M 395 " --> pdb=" O CYS M 391 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 402 Processing helix chain 'M' and resid 409 through 415 Processing helix chain 'N' and resid 6 through 10 removed outlier: 3.540A pdb=" N LYS N 10 " --> pdb=" O ASN N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.537A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU N 362 " --> pdb=" O TYR N 358 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 403 removed outlier: 3.621A pdb=" N VAL N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA N 385 " --> pdb=" O MET N 381 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS N 389 " --> pdb=" O ALA N 385 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG N 394 " --> pdb=" O VAL N 390 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG N 395 " --> pdb=" O CYS N 391 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 4.022A pdb=" N THR N 403 " --> pdb=" O PRO N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 Processing helix chain 'O' and resid 6 through 10 removed outlier: 3.632A pdb=" N LYS O 10 " --> pdb=" O ASN O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing helix chain 'O' and resid 351 through 363 removed outlier: 3.615A pdb=" N ILE O 355 " --> pdb=" O HIS O 351 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU O 361 " --> pdb=" O LEU O 357 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU O 362 " --> pdb=" O TYR O 358 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 398 removed outlier: 3.617A pdb=" N VAL O 368 " --> pdb=" O PRO O 364 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL O 369 " --> pdb=" O THR O 365 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG O 395 " --> pdb=" O CYS O 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 403 removed outlier: 3.549A pdb=" N LEU O 402 " --> pdb=" O THR O 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR O 403 " --> pdb=" O PRO O 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 398 through 403' Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'P' and resid 6 through 10 removed outlier: 3.603A pdb=" N LYS P 10 " --> pdb=" O ASN P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 83 No H-bonds generated for 'chain 'P' and resid 81 through 83' Processing helix chain 'P' and resid 351 through 361 removed outlier: 3.754A pdb=" N LEU P 357 " --> pdb=" O HIS P 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR P 358 " --> pdb=" O GLU P 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR P 359 " --> pdb=" O ILE P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 403 removed outlier: 3.910A pdb=" N VAL P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL P 369 " --> pdb=" O THR P 365 " (cutoff:3.500A) Proline residue: P 399 - end of helix removed outlier: 3.629A pdb=" N LEU P 402 " --> pdb=" O THR P 398 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR P 403 " --> pdb=" O PRO P 399 " (cutoff:3.500A) Processing helix chain 'P' and resid 409 through 415 Processing helix chain 'Q' and resid 148 through 152 Processing helix chain 'Q' and resid 168 through 175 removed outlier: 3.577A pdb=" N MET Q 171 " --> pdb=" O PRO Q 168 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER Q 173 " --> pdb=" O HIS Q 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 152 Processing helix chain 'R' and resid 168 through 175 removed outlier: 4.909A pdb=" N SER R 173 " --> pdb=" O HIS R 170 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP R 174 " --> pdb=" O MET R 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.774A pdb=" N LYS S 151 " --> pdb=" O ASP S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 175 removed outlier: 3.661A pdb=" N MET S 171 " --> pdb=" O PRO S 168 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER S 173 " --> pdb=" O HIS S 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 148 through 152 Processing helix chain 'T' and resid 171 through 175 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.533A pdb=" N GLU H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.674A pdb=" N LYS H 65 " --> pdb=" O GLU H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.888A pdb=" N THR H 91 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'V' and resid 28 through 32 removed outlier: 3.553A pdb=" N GLU V 31 " --> pdb=" O THR V 28 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR V 32 " --> pdb=" O PHE V 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 28 through 32' Processing helix chain 'V' and resid 62 through 65 removed outlier: 3.580A pdb=" N LYS V 65 " --> pdb=" O GLU V 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 62 through 65' Processing helix chain 'V' and resid 87 through 91 removed outlier: 3.956A pdb=" N THR V 91 " --> pdb=" O ASN V 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 34 removed outlier: 3.961A pdb=" N CYS U 34 " --> pdb=" O SER U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 85 Processing helix chain 'X' and resid 28 through 32 removed outlier: 3.542A pdb=" N GLU X 31 " --> pdb=" O THR X 28 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR X 32 " --> pdb=" O PHE X 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 28 through 32' Processing helix chain 'X' and resid 62 through 65 removed outlier: 3.656A pdb=" N LYS X 65 " --> pdb=" O GLU X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 65' Processing helix chain 'X' and resid 87 through 91 removed outlier: 3.976A pdb=" N THR X 91 " --> pdb=" O ASN X 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 85 Processing helix chain 'Z' and resid 28 through 32 removed outlier: 3.549A pdb=" N GLU Z 31 " --> pdb=" O THR Z 28 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR Z 32 " --> pdb=" O PHE Z 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 28 through 32' Processing helix chain 'Z' and resid 62 through 65 removed outlier: 3.605A pdb=" N LYS Z 65 " --> pdb=" O GLU Z 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 62 through 65' Processing helix chain 'Z' and resid 87 through 91 removed outlier: 3.977A pdb=" N THR Z 91 " --> pdb=" O ASN Z 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 34 removed outlier: 4.039A pdb=" N CYS Y 34 " --> pdb=" O SER Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 4.005A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 146 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.506A pdb=" N ALA A 262 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 48 removed outlier: 7.232A pdb=" N ALA A 121 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 177 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.618A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.618A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 104 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 79 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 106 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 77 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.507A pdb=" N GLY A 91 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AB1, first strand: chain 'A' and resid 300 through 306 removed outlier: 3.702A pdb=" N SER A 300 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 356 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.518A pdb=" N VAL A 346 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.730A pdb=" N TYR M 297 " --> pdb=" O HIS M 307 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS M 307 " --> pdb=" O TYR M 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.707A pdb=" N LYS B 160 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 19 removed outlier: 4.124A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 15 through 19 Processing sheet with id=AB7, first strand: chain 'B' and resid 42 through 48 removed outlier: 7.125A pdb=" N ALA B 121 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 177 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.505A pdb=" N TYR B 59 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.511A pdb=" N LYS B 79 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 106 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AC3, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AC4, first strand: chain 'B' and resid 300 through 306 removed outlier: 3.651A pdb=" N SER B 300 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 356 " --> pdb=" O GLY B 314 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 350 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 343 through 346 removed outlier: 3.606A pdb=" N GLY B 326 " --> pdb=" O VAL B 346 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.576A pdb=" N TYR N 297 " --> pdb=" O HIS N 307 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS N 307 " --> pdb=" O TYR N 297 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.705A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 19 removed outlier: 4.263A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 146 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AD1, first strand: chain 'C' and resid 42 through 48 removed outlier: 7.106A pdb=" N ALA C 121 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA C 119 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 177 " --> pdb=" O TYR C 122 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.642A pdb=" N LYS C 52 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.642A pdb=" N LYS C 52 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 104 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 106 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 77 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD5, first strand: chain 'C' and resid 219 through 221 Processing sheet with id=AD6, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.589A pdb=" N SER C 300 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS C 319 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.523A pdb=" N GLY C 326 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.720A pdb=" N TYR O 297 " --> pdb=" O HIS O 307 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS O 307 " --> pdb=" O TYR O 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.724A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 15 through 19 removed outlier: 9.689A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 120 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 177 " --> pdb=" O TYR D 122 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.775A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.666A pdb=" N LYS D 52 " --> pdb=" O GLU D 109 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.666A pdb=" N LYS D 52 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 104 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D 79 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA D 106 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER D 77 " --> pdb=" O ALA D 106 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AE7, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AE8, first strand: chain 'D' and resid 296 through 306 removed outlier: 6.600A pdb=" N THR D 321 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N MET D 299 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS D 319 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N CYS D 301 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE D 317 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL D 303 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL D 315 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 350 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.606A pdb=" N GLY D 326 " --> pdb=" O VAL D 346 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AF2, first strand: chain 'D' and resid 387 through 388 removed outlier: 3.717A pdb=" N TYR P 297 " --> pdb=" O HIS P 307 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 17 through 19 removed outlier: 3.708A pdb=" N ALA M 17 " --> pdb=" O SER M 30 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 34 through 38 removed outlier: 5.095A pdb=" N GLN M 49 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE M 37 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS M 47 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 27.130A pdb=" N LYS M 47 " --> pdb=" O ASP M 71 " (cutoff:3.500A) removed outlier: 23.791A pdb=" N ASP M 71 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 17.636A pdb=" N GLN M 49 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 14.624A pdb=" N TYR M 69 " --> pdb=" O GLN M 49 " (cutoff:3.500A) removed outlier: 12.589A pdb=" N SER M 51 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 11.892A pdb=" N LEU M 67 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 12.203A pdb=" N GLN M 53 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR M 65 " --> pdb=" O GLN M 53 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY M 55 " --> pdb=" O ASP M 63 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR M 74 " --> pdb=" O ASP M 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 34 through 38 removed outlier: 5.095A pdb=" N GLN M 49 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE M 37 " --> pdb=" O LYS M 47 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS M 47 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA M 103 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS M 99 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N LEU M 52 " --> pdb=" O MET M 97 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N MET M 97 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N ILE M 54 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.242A pdb=" N GLY M 95 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 16.815A pdb=" N ILE M 56 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 19.656A pdb=" N ILE M 93 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 84 through 86 removed outlier: 4.345A pdb=" N GLU M 109 " --> pdb=" O PHE M 129 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 149 through 156 removed outlier: 3.650A pdb=" N CYS M 153 " --> pdb=" O VAL M 264 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR M 155 " --> pdb=" O ALA M 262 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA M 262 " --> pdb=" O THR M 155 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 236 through 237 removed outlier: 3.889A pdb=" N GLY M 253 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 181 through 184 removed outlier: 3.813A pdb=" N LYS M 189 " --> pdb=" O THR M 182 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS M 215 " --> pdb=" O ILE M 190 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 207 through 211 removed outlier: 3.886A pdb=" N GLY M 209 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR M 199 " --> pdb=" O GLY M 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL M 197 " --> pdb=" O THR M 211 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 275 through 279 removed outlier: 3.852A pdb=" N GLN M 282 " --> pdb=" O GLY M 279 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS M 315 " --> pdb=" O LEU M 287 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.598A pdb=" N ALA N 17 " --> pdb=" O SER N 30 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 37 through 38 removed outlier: 3.564A pdb=" N LYS N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 17.588A pdb=" N GLN N 49 " --> pdb=" O TYR N 69 " (cutoff:3.500A) removed outlier: 14.576A pdb=" N TYR N 69 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N SER N 51 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU N 67 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N GLN N 53 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N THR N 65 " --> pdb=" O GLN N 53 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY N 55 " --> pdb=" O ASP N 63 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 37 through 38 removed outlier: 3.564A pdb=" N LYS N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N LEU N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N MET N 97 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 10.056A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 16.958A pdb=" N ILE N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 19.798A pdb=" N ILE N 93 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.405A pdb=" N GLU N 109 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE N 129 " --> pdb=" O GLU N 109 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 149 through 156 Processing sheet with id=AG8, first strand: chain 'N' and resid 236 through 237 removed outlier: 3.509A pdb=" N VAL N 169 " --> pdb=" O GLY N 253 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY N 253 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 175 through 176 removed outlier: 3.765A pdb=" N GLY N 209 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN N 207 " --> pdb=" O CYS N 201 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 182 through 184 removed outlier: 3.523A pdb=" N ASN N 187 " --> pdb=" O GLN N 184 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS N 215 " --> pdb=" O ILE N 190 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.780A pdb=" N GLN N 282 " --> pdb=" O GLY N 279 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS N 315 " --> pdb=" O LEU N 287 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 17 through 19 removed outlier: 3.647A pdb=" N ALA O 17 " --> pdb=" O SER O 30 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 34 through 38 removed outlier: 8.892A pdb=" N LEU O 34 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER O 51 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG O 36 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN O 49 " --> pdb=" O ARG O 36 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N SER O 51 " --> pdb=" O MET O 70 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET O 70 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS O 66 " --> pdb=" O GLY O 55 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 34 through 38 removed outlier: 8.892A pdb=" N LEU O 34 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER O 51 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ARG O 36 " --> pdb=" O GLN O 49 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN O 49 " --> pdb=" O ARG O 36 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA O 103 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS O 99 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.460A pdb=" N LEU O 52 " --> pdb=" O MET O 97 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N MET O 97 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N ILE O 54 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N GLY O 95 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 17.322A pdb=" N ILE O 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 19.994A pdb=" N ILE O 93 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 84 through 86 removed outlier: 3.535A pdb=" N GLY O 114 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU O 109 " --> pdb=" O PHE O 129 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 149 through 156 removed outlier: 3.651A pdb=" N THR O 155 " --> pdb=" O ALA O 262 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA O 262 " --> pdb=" O THR O 155 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 236 through 237 removed outlier: 4.178A pdb=" N GLY O 253 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 175 through 176 removed outlier: 3.699A pdb=" N GLY O 209 " --> pdb=" O TYR O 199 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN O 207 " --> pdb=" O CYS O 201 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 181 through 184 removed outlier: 3.569A pdb=" N ASN O 187 " --> pdb=" O GLN O 184 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS O 215 " --> pdb=" O ILE O 190 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 275 through 279 removed outlier: 3.865A pdb=" N LYS O 315 " --> pdb=" O LEU O 287 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 17 through 19 removed outlier: 3.639A pdb=" N CYS P 28 " --> pdb=" O CYS P 19 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 74 through 79 removed outlier: 3.607A pdb=" N THR P 74 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY P 55 " --> pdb=" O ASP P 63 " (cutoff:3.500A) removed outlier: 9.781A pdb=" N THR P 65 " --> pdb=" O GLN P 53 " (cutoff:3.500A) removed outlier: 12.017A pdb=" N GLN P 53 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N LEU P 67 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 12.272A pdb=" N SER P 51 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 14.479A pdb=" N TYR P 69 " --> pdb=" O GLN P 49 " (cutoff:3.500A) removed outlier: 17.643A pdb=" N GLN P 49 " --> pdb=" O TYR P 69 " (cutoff:3.500A) removed outlier: 23.972A pdb=" N ASP P 71 " --> pdb=" O LYS P 47 " (cutoff:3.500A) removed outlier: 27.267A pdb=" N LYS P 47 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N HIS P 99 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU P 52 " --> pdb=" O MET P 97 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N MET P 97 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N ILE P 54 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.373A pdb=" N GLY P 95 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 17.200A pdb=" N ILE P 56 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 19.984A pdb=" N ILE P 93 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 84 through 86 removed outlier: 4.261A pdb=" N GLU P 109 " --> pdb=" O PHE P 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE P 115 " --> pdb=" O HIS P 123 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 149 through 156 removed outlier: 3.640A pdb=" N VAL P 264 " --> pdb=" O CYS P 153 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR P 155 " --> pdb=" O ALA P 262 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 236 through 237 removed outlier: 3.957A pdb=" N GLY P 253 " --> pdb=" O VAL P 169 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 175 through 176 removed outlier: 3.531A pdb=" N THR P 175 " --> pdb=" O VAL P 229 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR P 199 " --> pdb=" O GLY P 209 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY P 209 " --> pdb=" O TYR P 199 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 181 through 184 removed outlier: 3.871A pdb=" N LYS P 215 " --> pdb=" O ILE P 190 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 275 through 279 removed outlier: 3.734A pdb=" N GLN P 282 " --> pdb=" O GLY P 279 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS P 315 " --> pdb=" O LEU P 287 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 143 through 144 removed outlier: 6.539A pdb=" N PHE Q 115 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR Q 126 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL Q 117 " --> pdb=" O MET Q 124 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N TYR Q 126 " --> pdb=" O PRO Q 137 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU Q 162 " --> pdb=" O SER Q 157 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER Q 157 " --> pdb=" O LEU Q 162 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS Q 164 " --> pdb=" O LYS Q 155 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS Q 155 " --> pdb=" O CYS Q 164 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Q' and resid 249 through 253 removed outlier: 3.883A pdb=" N ILE Q 249 " --> pdb=" O ASN Q 246 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN Q 246 " --> pdb=" O ILE Q 249 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA Q 239 " --> pdb=" O GLY Q 231 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY Q 231 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER Q 241 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP Q 245 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N VAL Q 225 " --> pdb=" O TRP Q 245 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE Q 217 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY Q 185 " --> pdb=" O TYR Q 196 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR Q 196 " --> pdb=" O GLY Q 185 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ALA Q 193 " --> pdb=" O PRO Q 204 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG Q 200 " --> pdb=" O SER Q 197 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE Q 201 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU Q 240 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 143 through 144 removed outlier: 4.159A pdb=" N GLY R 125 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N HIS R 119 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL R 123 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N TYR R 126 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA R 165 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU R 162 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS R 164 " --> pdb=" O LYS R 155 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 177 through 178 removed outlier: 7.119A pdb=" N LYS R 177 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA R 226 " --> pdb=" O LYS R 177 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE R 217 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY R 185 " --> pdb=" O TYR R 196 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY R 192 " --> pdb=" O TRP R 189 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA R 193 " --> pdb=" O PRO R 204 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N PHE R 201 " --> pdb=" O LEU R 240 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE R 249 " --> pdb=" O ASN R 246 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 177 through 178 removed outlier: 7.119A pdb=" N LYS R 177 " --> pdb=" O VAL R 224 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA R 226 " --> pdb=" O LYS R 177 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N VAL R 225 " --> pdb=" O TRP R 245 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP R 245 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER R 241 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY R 231 " --> pdb=" O ALA R 239 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA R 239 " --> pdb=" O GLY R 231 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE R 249 " --> pdb=" O ASN R 246 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'S' and resid 143 through 144 removed outlier: 6.910A pdb=" N PHE S 115 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR S 126 " --> pdb=" O PHE S 115 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL S 117 " --> pdb=" O MET S 124 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR S 126 " --> pdb=" O PRO S 137 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU S 162 " --> pdb=" O SER S 157 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER S 157 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS S 164 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS S 155 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 249 through 253 removed outlier: 3.523A pdb=" N ILE S 249 " --> pdb=" O ASN S 246 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER S 241 " --> pdb=" O GLY S 230 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY S 230 " --> pdb=" O SER S 241 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL S 243 " --> pdb=" O VAL S 228 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL S 228 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N TRP S 245 " --> pdb=" O ALA S 226 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA S 226 " --> pdb=" O TRP S 245 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE S 217 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY S 185 " --> pdb=" O TYR S 196 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR S 196 " --> pdb=" O GLY S 185 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ALA S 193 " --> pdb=" O PRO S 204 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE S 201 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'T' and resid 143 through 144 removed outlier: 6.837A pdb=" N PHE T 115 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR T 126 " --> pdb=" O PHE T 115 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL T 117 " --> pdb=" O MET T 124 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N TYR T 126 " --> pdb=" O PRO T 137 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS T 128 " --> pdb=" O MET T 135 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU T 162 " --> pdb=" O SER T 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER T 157 " --> pdb=" O LEU T 162 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS T 164 " --> pdb=" O LYS T 155 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 250 through 253 removed outlier: 4.395A pdb=" N GLY T 230 " --> pdb=" O SER T 241 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL T 243 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL T 228 " --> pdb=" O VAL T 243 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TRP T 245 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA T 226 " --> pdb=" O TRP T 245 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE T 217 " --> pdb=" O VAL T 225 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN T 188 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ALA T 193 " --> pdb=" O PRO T 204 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N PHE T 201 " --> pdb=" O LEU T 240 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.726A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.775A pdb=" N GLU H 10 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 114 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.633A pdb=" N ARG L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.686A pdb=" N ILE L 87 " --> pdb=" O GLU L 40 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AK7, first strand: chain 'V' and resid 3 through 6 removed outlier: 3.603A pdb=" N SER V 71 " --> pdb=" O TYR V 80 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'V' and resid 10 through 12 removed outlier: 3.656A pdb=" N GLU V 10 " --> pdb=" O THR V 112 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET V 34 " --> pdb=" O LEU V 50 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TRP V 36 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET V 48 " --> pdb=" O TRP V 36 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'U' and resid 4 through 6 removed outlier: 3.530A pdb=" N ARG U 23 " --> pdb=" O THR U 5 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'U' and resid 9 through 12 removed outlier: 3.609A pdb=" N ILE U 87 " --> pdb=" O GLU U 40 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP U 37 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'U' and resid 9 through 12 Processing sheet with id=AL3, first strand: chain 'X' and resid 3 through 6 removed outlier: 3.720A pdb=" N SER X 71 " --> pdb=" O TYR X 80 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.587A pdb=" N GLU X 10 " --> pdb=" O THR X 112 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N MET X 34 " --> pdb=" O LEU X 50 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N TRP X 36 " --> pdb=" O MET X 48 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET X 48 " --> pdb=" O TRP X 36 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'W' and resid 4 through 6 Processing sheet with id=AL6, first strand: chain 'W' and resid 9 through 12 removed outlier: 3.689A pdb=" N ILE W 87 " --> pdb=" O GLU W 40 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP W 37 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE W 45 " --> pdb=" O LYS W 41 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'W' and resid 9 through 12 Processing sheet with id=AL8, first strand: chain 'Z' and resid 3 through 6 removed outlier: 3.697A pdb=" N SER Z 71 " --> pdb=" O TYR Z 80 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'Z' and resid 10 through 12 removed outlier: 3.581A pdb=" N GLU Z 10 " --> pdb=" O THR Z 112 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N MET Z 34 " --> pdb=" O LEU Z 50 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N TRP Z 36 " --> pdb=" O MET Z 48 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET Z 48 " --> pdb=" O TRP Z 36 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Y' and resid 4 through 6 Processing sheet with id=AM2, first strand: chain 'Y' and resid 9 through 12 removed outlier: 3.625A pdb=" N ILE Y 87 " --> pdb=" O GLU Y 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP Y 37 " --> pdb=" O LEU Y 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE Y 45 " --> pdb=" O LYS Y 41 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'Y' and resid 9 through 12 1387 hydrogen bonds defined for protein. 3513 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: 11.90 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12444 1.35 - 1.48: 9895 1.48 - 1.61: 16305 1.61 - 1.74: 0 1.74 - 1.86: 352 Bond restraints: 38996 Sorted by residual: bond pdb=" CB CYS O 266 " pdb=" SG CYS O 266 " ideal model delta sigma weight residual 1.808 1.863 -0.055 3.30e-02 9.18e+02 2.73e+00 bond pdb=" CB PRO P 240 " pdb=" CG PRO P 240 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.33e+00 bond pdb=" CB CYS M 266 " pdb=" SG CYS M 266 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" C1 NAG N 501 " pdb=" O5 NAG N 501 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C1 NAG N 502 " pdb=" O5 NAG N 502 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 ... (remaining 38991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 52963 2.99 - 5.99: 154 5.99 - 8.98: 14 8.98 - 11.98: 7 11.98 - 14.97: 2 Bond angle restraints: 53140 Sorted by residual: angle pdb=" CA PRO P 240 " pdb=" N PRO P 240 " pdb=" CD PRO P 240 " ideal model delta sigma weight residual 112.00 103.27 8.73 1.40e+00 5.10e-01 3.89e+01 angle pdb=" C CYS M 266 " pdb=" CA CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sigma weight residual 109.79 119.85 -10.06 2.05e+00 2.38e-01 2.41e+01 angle pdb=" CA GLU N 401 " pdb=" CB GLU N 401 " pdb=" CG GLU N 401 " ideal model delta sigma weight residual 114.10 123.20 -9.10 2.00e+00 2.50e-01 2.07e+01 angle pdb=" N CYS M 266 " pdb=" CA CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sigma weight residual 111.55 104.47 7.08 1.74e+00 3.30e-01 1.66e+01 angle pdb=" CA LEU Q 229 " pdb=" CB LEU Q 229 " pdb=" CG LEU Q 229 " ideal model delta sigma weight residual 116.30 130.21 -13.91 3.50e+00 8.16e-02 1.58e+01 ... (remaining 53135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21524 17.90 - 35.80: 1535 35.80 - 53.70: 352 53.70 - 71.60: 57 71.60 - 89.51: 24 Dihedral angle restraints: 23492 sinusoidal: 9280 harmonic: 14212 Sorted by residual: dihedral pdb=" CB CYS M 153 " pdb=" SG CYS M 153 " pdb=" SG CYS M 266 " pdb=" CB CYS M 266 " ideal model delta sinusoidal sigma weight residual 93.00 165.58 -72.58 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CB CYS N 153 " pdb=" SG CYS N 153 " pdb=" SG CYS N 266 " pdb=" CB CYS N 266 " ideal model delta sinusoidal sigma weight residual -86.00 -153.90 67.90 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CB CYS D 68 " pdb=" SG CYS D 68 " pdb=" SG CYS D 78 " pdb=" CB CYS D 78 " ideal model delta sinusoidal sigma weight residual -86.00 -146.53 60.53 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 23489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5788 0.109 - 0.217: 231 0.217 - 0.326: 6 0.326 - 0.434: 2 0.434 - 0.543: 1 Chirality restraints: 6028 Sorted by residual: chirality pdb=" C1 NAG P 501 " pdb=" ND2 ASN P 263 " pdb=" C2 NAG P 501 " pdb=" O5 NAG P 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C1 NAG N 501 " pdb=" ND2 ASN N 263 " pdb=" C2 NAG N 501 " pdb=" O5 NAG N 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C1 NAG M 501 " pdb=" ND2 ASN M 263 " pdb=" C2 NAG M 501 " pdb=" O5 NAG M 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 6025 not shown) Planarity restraints: 6840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER P 239 " -0.125 5.00e-02 4.00e+02 1.84e-01 5.43e+01 pdb=" N PRO P 240 " 0.318 5.00e-02 4.00e+02 pdb=" CA PRO P 240 " -0.105 5.00e-02 4.00e+02 pdb=" CD PRO P 240 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 254 " 0.080 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO R 255 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO R 255 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO R 255 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS S 182 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO S 183 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO S 183 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 183 " -0.047 5.00e-02 4.00e+02 ... (remaining 6837 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 561 2.68 - 3.24: 31532 3.24 - 3.79: 49893 3.79 - 4.35: 63329 4.35 - 4.90: 113381 Nonbonded interactions: 258696 Sorted by model distance: nonbonded pdb=" O LEU S 229 " pdb=" OG SER S 241 " model vdw 2.126 3.040 nonbonded pdb=" OD1 ASP N 117 " pdb=" N SER N 118 " model vdw 2.133 3.120 nonbonded pdb=" NH1 ARG B 21 " pdb=" OD1 ASP B 284 " model vdw 2.181 3.120 nonbonded pdb=" O LEU T 229 " pdb=" OG SER T 241 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN T 246 " pdb=" N LYS T 247 " model vdw 2.208 3.120 ... (remaining 258691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'L' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 39.050 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 39076 Z= 0.120 Angle : 0.589 14.970 53312 Z= 0.308 Chirality : 0.046 0.543 6028 Planarity : 0.007 0.184 6828 Dihedral : 13.058 89.505 14184 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.48 % Allowed : 12.55 % Favored : 86.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.11), residues: 4880 helix: 0.65 (0.24), residues: 377 sheet: 0.45 (0.13), residues: 1733 loop : -1.06 (0.11), residues: 2770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 267 TYR 0.021 0.001 TYR N 199 PHE 0.026 0.001 PHE D 436 TRP 0.017 0.001 TRP B 89 HIS 0.005 0.001 HIS O 170 Details of bonding type rmsd covalent geometry : bond 0.00263 (38996) covalent geometry : angle 0.57481 (53140) SS BOND : bond 0.00436 ( 68) SS BOND : angle 1.96010 ( 136) hydrogen bonds : bond 0.33456 ( 1323) hydrogen bonds : angle 8.35154 ( 3513) link_NAG-ASN : bond 0.00723 ( 12) link_NAG-ASN : angle 3.26484 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 690 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 257 PHE cc_start: 0.8301 (m-80) cc_final: 0.7712 (m-80) REVERT: D 50 GLU cc_start: 0.7886 (tt0) cc_final: 0.7656 (tt0) REVERT: P 12 THR cc_start: 0.8182 (p) cc_final: 0.7910 (p) REVERT: P 52 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7415 (pp) REVERT: P 199 TYR cc_start: 0.8234 (p90) cc_final: 0.7954 (p90) REVERT: P 266 CYS cc_start: 0.6890 (m) cc_final: 0.6515 (m) REVERT: Q 180 HIS cc_start: 0.8305 (p-80) cc_final: 0.8080 (p90) REVERT: R 254 THR cc_start: 0.8528 (t) cc_final: 0.8310 (p) REVERT: S 155 LYS cc_start: 0.7372 (mtmm) cc_final: 0.7078 (mtmm) REVERT: T 155 LYS cc_start: 0.7699 (mtpp) cc_final: 0.7469 (mtmm) REVERT: T 243 VAL cc_start: 0.8523 (p) cc_final: 0.8200 (t) REVERT: V 34 MET cc_start: 0.6587 (mmm) cc_final: 0.6307 (mmm) outliers start: 20 outliers final: 8 residues processed: 705 average time/residue: 0.2083 time to fit residues: 234.9496 Evaluate side-chains 671 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 662 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain S residue 128 CYS Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 40.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 222 GLN C 175 ASN C 252 GLN C 389 ASN M 147 HIS M 158 GLN M 218 ASN M 224 GLN M 234 ASN M 245 ASN M 273 ASN N 53 GLN N 130 HIS N 224 GLN N 234 ASN N 273 ASN N 313 HIS N 341 GLN O 53 GLN O 131 HIS O 170 HIS O 193 ASN O 218 ASN O 224 GLN O 299 ASN P 62 HIS P 127 HIS P 218 ASN P 224 GLN P 273 ASN P 299 ASN P 302 GLN Q 180 HIS Q 190 HIS Q 191 HIS R 139 HIS R 190 HIS S 139 HIS S 220 ASN L 55 ASN U 33 ASN U 55 ASN W 55 ASN Y 33 ASN Y 55 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108804 restraints weight = 60487.437| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.39 r_work: 0.3155 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 39076 Z= 0.213 Angle : 0.673 13.126 53312 Z= 0.369 Chirality : 0.049 0.438 6028 Planarity : 0.007 0.109 6828 Dihedral : 5.934 54.950 5570 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.74 % Allowed : 12.19 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.11), residues: 4880 helix: 1.67 (0.25), residues: 410 sheet: 0.41 (0.13), residues: 1627 loop : -1.35 (0.10), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 267 TYR 0.020 0.002 TYR C 122 PHE 0.018 0.002 PHE A 365 TRP 0.020 0.002 TRP O 330 HIS 0.010 0.002 HIS N 99 Details of bonding type rmsd covalent geometry : bond 0.00496 (38996) covalent geometry : angle 0.66471 (53140) SS BOND : bond 0.00569 ( 68) SS BOND : angle 1.43392 ( 136) hydrogen bonds : bond 0.09170 ( 1323) hydrogen bonds : angle 6.11991 ( 3513) link_NAG-ASN : bond 0.00475 ( 12) link_NAG-ASN : angle 3.27892 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 678 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8507 (t80) cc_final: 0.8273 (t80) REVERT: A 209 GLU cc_start: 0.7390 (mp0) cc_final: 0.7009 (mp0) REVERT: A 345 GLU cc_start: 0.7501 (tt0) cc_final: 0.7223 (tt0) REVERT: B 284 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7198 (t0) REVERT: B 341 GLU cc_start: 0.7807 (mp0) cc_final: 0.7568 (mp0) REVERT: B 407 MET cc_start: 0.8084 (tpt) cc_final: 0.7698 (tpt) REVERT: B 432 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8419 (mm) REVERT: C 245 LYS cc_start: 0.8613 (ttmt) cc_final: 0.8388 (mtpp) REVERT: C 284 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8108 (t0) REVERT: D 130 SER cc_start: 0.8745 (p) cc_final: 0.8381 (m) REVERT: D 347 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7874 (tm-30) REVERT: M 87 THR cc_start: 0.7268 (OUTLIER) cc_final: 0.6913 (t) REVERT: M 107 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7782 (mtmm) REVERT: M 254 LYS cc_start: 0.8815 (ptpt) cc_final: 0.8580 (ptmt) REVERT: M 277 THR cc_start: 0.8387 (t) cc_final: 0.8080 (p) REVERT: P 52 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7353 (pp) REVERT: Q 180 HIS cc_start: 0.8443 (p90) cc_final: 0.8143 (p90) REVERT: Q 194 VAL cc_start: 0.8164 (p) cc_final: 0.7926 (m) REVERT: Q 218 PHE cc_start: 0.7815 (m-80) cc_final: 0.7584 (m-80) REVERT: T 155 LYS cc_start: 0.7511 (mtpp) cc_final: 0.7274 (mtmm) REVERT: V 98 ARG cc_start: 0.5245 (OUTLIER) cc_final: 0.4750 (ptt180) outliers start: 114 outliers final: 68 residues processed: 742 average time/residue: 0.2012 time to fit residues: 240.8946 Evaluate side-chains 716 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 642 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 384 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain N residue 121 ILE Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 313 HIS Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 193 ASN Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 357 LEU Chi-restraints excluded: chain P residue 370 ILE Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain P residue 398 THR Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 146 ASN Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 98 ARG Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 362 optimal weight: 0.3980 chunk 234 optimal weight: 9.9990 chunk 294 optimal weight: 0.0050 chunk 231 optimal weight: 1.9990 chunk 313 optimal weight: 8.9990 chunk 374 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 chunk 438 optimal weight: 5.9990 chunk 33 optimal weight: 0.0470 overall best weight: 0.6694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 HIS C 252 GLN M 158 GLN M 218 ASN M 302 GLN N 313 HIS O 299 ASN P 62 HIS P 218 ASN R 139 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112875 restraints weight = 60568.608| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.40 r_work: 0.3215 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39076 Z= 0.118 Angle : 0.545 11.288 53312 Z= 0.293 Chirality : 0.045 0.345 6028 Planarity : 0.005 0.077 6828 Dihedral : 5.390 52.653 5563 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.31 % Allowed : 13.77 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.12), residues: 4880 helix: 1.81 (0.26), residues: 421 sheet: 0.30 (0.12), residues: 1786 loop : -1.19 (0.11), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.012 0.001 TYR O 363 PHE 0.010 0.001 PHE O 115 TRP 0.011 0.001 TRP B 89 HIS 0.025 0.001 HIS N 313 Details of bonding type rmsd covalent geometry : bond 0.00225 (38996) covalent geometry : angle 0.53944 (53140) SS BOND : bond 0.00378 ( 68) SS BOND : angle 0.82382 ( 136) hydrogen bonds : bond 0.06515 ( 1323) hydrogen bonds : angle 5.49879 ( 3513) link_NAG-ASN : bond 0.00529 ( 12) link_NAG-ASN : angle 2.78220 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 680 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8104 (mt) cc_final: 0.7717 (mp) REVERT: A 209 GLU cc_start: 0.7350 (mp0) cc_final: 0.6996 (mp0) REVERT: B 257 PHE cc_start: 0.8237 (m-80) cc_final: 0.7850 (m-80) REVERT: B 284 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7209 (t0) REVERT: B 341 GLU cc_start: 0.7702 (mp0) cc_final: 0.7438 (mp0) REVERT: B 432 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8273 (mm) REVERT: C 160 LYS cc_start: 0.8361 (mtmt) cc_final: 0.8101 (mtpp) REVERT: C 284 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8046 (t0) REVERT: C 296 VAL cc_start: 0.8465 (m) cc_final: 0.8027 (t) REVERT: C 417 VAL cc_start: 0.8111 (t) cc_final: 0.7895 (t) REVERT: D 130 SER cc_start: 0.8738 (p) cc_final: 0.8357 (m) REVERT: D 320 TYR cc_start: 0.8493 (p90) cc_final: 0.8276 (p90) REVERT: D 347 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7814 (tm-30) REVERT: M 87 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6509 (p) REVERT: M 212 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8473 (m) REVERT: M 251 ARG cc_start: 0.8222 (mtp180) cc_final: 0.7859 (ttp80) REVERT: M 254 LYS cc_start: 0.8746 (ptpt) cc_final: 0.8523 (ptmt) REVERT: M 357 LEU cc_start: 0.8283 (tp) cc_final: 0.8012 (tp) REVERT: N 13 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (ptt180) REVERT: N 212 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7300 (t) REVERT: O 394 ARG cc_start: 0.8917 (ttp80) cc_final: 0.8460 (ttp80) REVERT: O 398 THR cc_start: 0.7658 (OUTLIER) cc_final: 0.7212 (m) REVERT: P 12 THR cc_start: 0.8142 (p) cc_final: 0.7870 (p) REVERT: P 52 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7184 (pp) REVERT: P 263 ASN cc_start: 0.7770 (m-40) cc_final: 0.7507 (m110) REVERT: P 291 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7015 (p-80) REVERT: V 34 MET cc_start: 0.7011 (mmm) cc_final: 0.6271 (tmm) REVERT: V 98 ARG cc_start: 0.5169 (OUTLIER) cc_final: 0.4730 (ptt180) outliers start: 96 outliers final: 55 residues processed: 738 average time/residue: 0.2056 time to fit residues: 245.8896 Evaluate side-chains 727 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 661 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 247 LYS Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 98 ARG Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 219 optimal weight: 4.9990 chunk 425 optimal weight: 30.0000 chunk 55 optimal weight: 0.0270 chunk 428 optimal weight: 30.0000 chunk 125 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 435 optimal weight: 50.0000 chunk 321 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 195 optimal weight: 0.7980 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS B 389 ASN C 252 GLN M 131 HIS M 218 ASN M 313 HIS N 313 HIS O 218 ASN P 62 HIS P 218 ASN Q 195 GLN R 170 HIS R 191 HIS S 139 HIS H 84 ASN L 54 ASN U 33 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.142341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108448 restraints weight = 60108.894| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.40 r_work: 0.3144 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 39076 Z= 0.203 Angle : 0.643 11.664 53312 Z= 0.351 Chirality : 0.048 0.354 6028 Planarity : 0.006 0.056 6828 Dihedral : 5.677 54.651 5561 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.27 % Allowed : 13.87 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.11), residues: 4880 helix: 1.71 (0.26), residues: 419 sheet: 0.26 (0.13), residues: 1571 loop : -1.41 (0.10), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 178 TYR 0.019 0.002 TYR A 46 PHE 0.019 0.002 PHE A 365 TRP 0.018 0.002 TRP R 189 HIS 0.010 0.002 HIS N 99 Details of bonding type rmsd covalent geometry : bond 0.00487 (38996) covalent geometry : angle 0.63553 (53140) SS BOND : bond 0.00471 ( 68) SS BOND : angle 1.26177 ( 136) hydrogen bonds : bond 0.07573 ( 1323) hydrogen bonds : angle 5.52264 ( 3513) link_NAG-ASN : bond 0.00459 ( 12) link_NAG-ASN : angle 3.17538 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 660 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8388 (t) cc_final: 0.8074 (m) REVERT: A 29 LEU cc_start: 0.8143 (mt) cc_final: 0.7789 (mp) REVERT: A 209 GLU cc_start: 0.7409 (mp0) cc_final: 0.7070 (mp0) REVERT: A 345 GLU cc_start: 0.7503 (tt0) cc_final: 0.7261 (tt0) REVERT: B 327 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7836 (mtpp) REVERT: B 343 ASP cc_start: 0.8048 (p0) cc_final: 0.7841 (p0) REVERT: C 45 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: C 284 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8123 (t0) REVERT: C 373 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8509 (mt0) REVERT: D 130 SER cc_start: 0.8753 (p) cc_final: 0.8394 (m) REVERT: D 430 VAL cc_start: 0.7979 (t) cc_final: 0.7627 (p) REVERT: M 87 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.6930 (p) REVERT: M 251 ARG cc_start: 0.8312 (mtp180) cc_final: 0.8044 (ttp80) REVERT: M 408 VAL cc_start: 0.8858 (t) cc_final: 0.8569 (p) REVERT: N 394 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7823 (mtm-85) REVERT: O 394 ARG cc_start: 0.8913 (ttp80) cc_final: 0.8539 (ttp80) REVERT: P 52 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7382 (pp) REVERT: P 117 ASP cc_start: 0.7407 (t0) cc_final: 0.7150 (t0) REVERT: P 291 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7357 (p-80) REVERT: R 124 MET cc_start: 0.6468 (pmm) cc_final: 0.6256 (pmm) REVERT: T 155 LYS cc_start: 0.7559 (mtpp) cc_final: 0.7350 (mtpp) REVERT: V 34 MET cc_start: 0.7125 (mmm) cc_final: 0.6204 (tmm) REVERT: V 98 ARG cc_start: 0.5418 (OUTLIER) cc_final: 0.5159 (ptm160) outliers start: 136 outliers final: 103 residues processed: 745 average time/residue: 0.2003 time to fit residues: 242.7890 Evaluate side-chains 752 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 643 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 313 HIS Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 255 ILE Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 264 VAL Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 98 ARG Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 261 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 475 optimal weight: 50.0000 chunk 262 optimal weight: 1.9990 chunk 388 optimal weight: 0.1980 chunk 415 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 436 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 chunk 414 optimal weight: 40.0000 chunk 443 optimal weight: 10.0000 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 158 GLN M 218 ASN N 245 ASN N 313 HIS O 218 ASN P 218 ASN S 139 HIS T 139 HIS T 190 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108490 restraints weight = 60824.436| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.36 r_work: 0.3152 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 39076 Z= 0.181 Angle : 0.619 11.892 53312 Z= 0.335 Chirality : 0.048 0.556 6028 Planarity : 0.006 0.056 6828 Dihedral : 5.661 56.429 5561 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.68 % Allowed : 14.42 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.11), residues: 4880 helix: 1.70 (0.26), residues: 419 sheet: 0.17 (0.13), residues: 1550 loop : -1.46 (0.10), residues: 2911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 156 TYR 0.021 0.002 TYR S 160 PHE 0.017 0.001 PHE A 365 TRP 0.019 0.002 TRP Y 37 HIS 0.016 0.001 HIS M 313 Details of bonding type rmsd covalent geometry : bond 0.00426 (38996) covalent geometry : angle 0.61029 (53140) SS BOND : bond 0.00468 ( 68) SS BOND : angle 1.35126 ( 136) hydrogen bonds : bond 0.07125 ( 1323) hydrogen bonds : angle 5.41330 ( 3513) link_NAG-ASN : bond 0.00767 ( 12) link_NAG-ASN : angle 3.33862 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 649 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8402 (t) cc_final: 0.8081 (m) REVERT: A 29 LEU cc_start: 0.8141 (mt) cc_final: 0.7781 (mp) REVERT: A 209 GLU cc_start: 0.7446 (mp0) cc_final: 0.7107 (mp0) REVERT: A 345 GLU cc_start: 0.7462 (tt0) cc_final: 0.7194 (tt0) REVERT: A 427 ILE cc_start: 0.8914 (mm) cc_final: 0.8621 (tt) REVERT: B 282 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7980 (mt) REVERT: B 327 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7816 (mtpp) REVERT: B 343 ASP cc_start: 0.8055 (p0) cc_final: 0.7816 (p0) REVERT: C 187 MET cc_start: 0.8701 (ttp) cc_final: 0.8436 (mtp) REVERT: C 284 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8154 (t0) REVERT: D 130 SER cc_start: 0.8748 (p) cc_final: 0.8387 (m) REVERT: D 430 VAL cc_start: 0.7983 (t) cc_final: 0.7587 (p) REVERT: M 87 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.6876 (p) REVERT: M 212 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8549 (m) REVERT: M 251 ARG cc_start: 0.8337 (mtp180) cc_final: 0.8065 (ttp80) REVERT: M 291 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7065 (p-80) REVERT: N 212 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7237 (t) REVERT: N 286 LEU cc_start: 0.8548 (tt) cc_final: 0.8320 (tp) REVERT: N 293 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8235 (m) REVERT: N 366 MET cc_start: 0.7719 (mmm) cc_final: 0.7321 (mmt) REVERT: N 394 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7772 (mtm-85) REVERT: O 394 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8586 (ttp80) REVERT: P 52 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7309 (pp) REVERT: P 254 LYS cc_start: 0.8703 (ptpt) cc_final: 0.8346 (mtpt) REVERT: P 291 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7366 (p-80) REVERT: V 34 MET cc_start: 0.7222 (mmm) cc_final: 0.6248 (tmm) outliers start: 153 outliers final: 115 residues processed: 743 average time/residue: 0.1995 time to fit residues: 240.6802 Evaluate side-chains 771 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 647 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 265 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 388 MET Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 381 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain O residue 398 THR Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 27 SER Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 119 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 373 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 423 optimal weight: 0.0270 chunk 205 optimal weight: 0.0770 chunk 272 optimal weight: 0.6980 chunk 264 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 360 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 158 GLN M 218 ASN N 245 ASN N 313 HIS O 193 ASN O 218 ASN P 218 ASN U 33 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113821 restraints weight = 60757.369| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.41 r_work: 0.3227 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 39076 Z= 0.105 Angle : 0.524 10.726 53312 Z= 0.278 Chirality : 0.045 0.438 6028 Planarity : 0.005 0.053 6828 Dihedral : 5.192 52.517 5561 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.67 % Allowed : 15.48 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.12), residues: 4880 helix: 1.95 (0.26), residues: 421 sheet: 0.26 (0.13), residues: 1672 loop : -1.35 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 178 TYR 0.012 0.001 TYR S 160 PHE 0.009 0.001 PHE O 115 TRP 0.013 0.001 TRP Y 37 HIS 0.005 0.001 HIS N 313 Details of bonding type rmsd covalent geometry : bond 0.00207 (38996) covalent geometry : angle 0.51664 (53140) SS BOND : bond 0.00377 ( 68) SS BOND : angle 1.06903 ( 136) hydrogen bonds : bond 0.05160 ( 1323) hydrogen bonds : angle 5.00167 ( 3513) link_NAG-ASN : bond 0.00628 ( 12) link_NAG-ASN : angle 2.92636 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 658 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8105 (mt) cc_final: 0.7695 (mp) REVERT: A 209 GLU cc_start: 0.7399 (mp0) cc_final: 0.7081 (mp0) REVERT: B 257 PHE cc_start: 0.8221 (m-80) cc_final: 0.7931 (m-80) REVERT: B 432 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8158 (mm) REVERT: C 13 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7920 (m) REVERT: C 133 LEU cc_start: 0.8442 (mt) cc_final: 0.8187 (mt) REVERT: C 187 MET cc_start: 0.8659 (ttp) cc_final: 0.8428 (mtp) REVERT: C 284 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.8107 (t0) REVERT: C 296 VAL cc_start: 0.8466 (m) cc_final: 0.8021 (t) REVERT: C 417 VAL cc_start: 0.8094 (t) cc_final: 0.7850 (t) REVERT: D 130 SER cc_start: 0.8740 (p) cc_final: 0.8366 (m) REVERT: D 402 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7569 (tt) REVERT: D 430 VAL cc_start: 0.7937 (t) cc_final: 0.7485 (p) REVERT: M 87 THR cc_start: 0.7335 (OUTLIER) cc_final: 0.6690 (p) REVERT: M 212 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8487 (m) REVERT: M 251 ARG cc_start: 0.8329 (mtp180) cc_final: 0.8114 (ttp80) REVERT: M 291 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6651 (p-80) REVERT: N 286 LEU cc_start: 0.8566 (tt) cc_final: 0.8293 (tp) REVERT: N 293 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8146 (m) REVERT: N 375 SER cc_start: 0.8325 (t) cc_final: 0.7970 (p) REVERT: P 12 THR cc_start: 0.8171 (p) cc_final: 0.7957 (p) REVERT: P 52 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7160 (pp) REVERT: P 70 MET cc_start: 0.8211 (tpp) cc_final: 0.7429 (ttm) REVERT: P 408 VAL cc_start: 0.8089 (t) cc_final: 0.7673 (m) REVERT: H 53 THR cc_start: 0.8328 (p) cc_final: 0.7964 (p) REVERT: V 34 MET cc_start: 0.7237 (mmm) cc_final: 0.6190 (tmm) outliers start: 111 outliers final: 74 residues processed: 730 average time/residue: 0.1893 time to fit residues: 226.6170 Evaluate side-chains 728 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 645 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 193 ASN Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain Q residue 135 MET Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 136 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 26 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 317 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 434 optimal weight: 9.9990 chunk 403 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 242 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 138 GLN C 252 GLN M 218 ASN O 218 ASN P 218 ASN Q 195 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110829 restraints weight = 60265.595| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.41 r_work: 0.3178 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39076 Z= 0.153 Angle : 0.578 10.063 53312 Z= 0.310 Chirality : 0.046 0.436 6028 Planarity : 0.006 0.055 6828 Dihedral : 5.318 52.838 5561 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.72 % Allowed : 16.30 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.12), residues: 4880 helix: 1.91 (0.26), residues: 421 sheet: 0.26 (0.13), residues: 1615 loop : -1.38 (0.10), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 178 TYR 0.016 0.001 TYR S 160 PHE 0.016 0.001 PHE A 365 TRP 0.013 0.001 TRP R 189 HIS 0.007 0.001 HIS N 99 Details of bonding type rmsd covalent geometry : bond 0.00351 (38996) covalent geometry : angle 0.57173 (53140) SS BOND : bond 0.00485 ( 68) SS BOND : angle 1.01863 ( 136) hydrogen bonds : bond 0.06104 ( 1323) hydrogen bonds : angle 5.07982 ( 3513) link_NAG-ASN : bond 0.00551 ( 12) link_NAG-ASN : angle 2.97999 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 651 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8447 (t) cc_final: 0.8112 (m) REVERT: A 29 LEU cc_start: 0.8124 (mt) cc_final: 0.7739 (mp) REVERT: A 209 GLU cc_start: 0.7392 (mp0) cc_final: 0.7066 (mp0) REVERT: C 13 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.8012 (m) REVERT: C 133 LEU cc_start: 0.8466 (mt) cc_final: 0.8217 (mt) REVERT: C 187 MET cc_start: 0.8700 (ttp) cc_final: 0.8462 (mtp) REVERT: C 284 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8146 (t0) REVERT: C 296 VAL cc_start: 0.8480 (m) cc_final: 0.8036 (t) REVERT: D 130 SER cc_start: 0.8749 (p) cc_final: 0.8375 (m) REVERT: D 402 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7666 (tt) REVERT: D 430 VAL cc_start: 0.7958 (t) cc_final: 0.7527 (p) REVERT: M 87 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.6840 (p) REVERT: M 212 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8529 (m) REVERT: M 291 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6854 (p-80) REVERT: N 293 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8209 (m) REVERT: N 375 SER cc_start: 0.8373 (t) cc_final: 0.7998 (p) REVERT: N 397 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7618 (tt) REVERT: P 52 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7229 (pp) REVERT: P 244 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7874 (mtm-85) REVERT: P 254 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8340 (mtpt) REVERT: P 291 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7369 (p-80) REVERT: P 408 VAL cc_start: 0.8157 (t) cc_final: 0.7757 (m) REVERT: T 135 MET cc_start: 0.8874 (mtp) cc_final: 0.8653 (mtm) REVERT: H 53 THR cc_start: 0.8370 (p) cc_final: 0.8026 (p) REVERT: V 34 MET cc_start: 0.7083 (mmm) cc_final: 0.5954 (tmm) outliers start: 113 outliers final: 87 residues processed: 725 average time/residue: 0.2018 time to fit residues: 239.6916 Evaluate side-chains 745 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 647 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 261 LEU Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 302 GLN Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 244 ARG Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 121 optimal weight: 0.6980 chunk 465 optimal weight: 50.0000 chunk 85 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 366 optimal weight: 0.9990 chunk 411 optimal weight: 0.8980 chunk 401 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 GLN M 218 ASN N 245 ASN N 313 HIS O 218 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.145351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112072 restraints weight = 59999.168| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.39 r_work: 0.3199 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39076 Z= 0.125 Angle : 0.550 9.998 53312 Z= 0.293 Chirality : 0.045 0.410 6028 Planarity : 0.005 0.052 6828 Dihedral : 5.224 52.685 5561 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.88 % Allowed : 16.27 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.12), residues: 4880 helix: 1.98 (0.27), residues: 421 sheet: 0.28 (0.13), residues: 1622 loop : -1.36 (0.11), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 156 TYR 0.014 0.001 TYR S 160 PHE 0.012 0.001 PHE A 365 TRP 0.012 0.001 TRP Y 98 HIS 0.005 0.001 HIS O 147 Details of bonding type rmsd covalent geometry : bond 0.00272 (38996) covalent geometry : angle 0.54383 (53140) SS BOND : bond 0.00402 ( 68) SS BOND : angle 0.97584 ( 136) hydrogen bonds : bond 0.05572 ( 1323) hydrogen bonds : angle 4.95285 ( 3513) link_NAG-ASN : bond 0.00571 ( 12) link_NAG-ASN : angle 2.89064 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 642 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8517 (t) cc_final: 0.8181 (m) REVERT: A 29 LEU cc_start: 0.8123 (mt) cc_final: 0.7738 (mp) REVERT: A 209 GLU cc_start: 0.7406 (mp0) cc_final: 0.7085 (mp0) REVERT: B 67 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 13 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7992 (m) REVERT: C 133 LEU cc_start: 0.8461 (mt) cc_final: 0.8218 (mt) REVERT: C 187 MET cc_start: 0.8698 (ttp) cc_final: 0.8460 (mtp) REVERT: C 284 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8156 (t0) REVERT: C 296 VAL cc_start: 0.8468 (m) cc_final: 0.8012 (t) REVERT: D 130 SER cc_start: 0.8756 (p) cc_final: 0.8381 (m) REVERT: D 402 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7670 (tt) REVERT: D 430 VAL cc_start: 0.7956 (t) cc_final: 0.7523 (p) REVERT: M 87 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.6822 (p) REVERT: M 251 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8093 (ttp80) REVERT: M 291 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6763 (p-80) REVERT: N 293 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8181 (m) REVERT: N 397 ILE cc_start: 0.7791 (tt) cc_final: 0.7584 (tt) REVERT: P 52 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7229 (pp) REVERT: P 70 MET cc_start: 0.8262 (tpp) cc_final: 0.7463 (ttm) REVERT: P 254 LYS cc_start: 0.8666 (ptpt) cc_final: 0.8322 (mtpt) REVERT: P 291 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7302 (p-80) REVERT: P 408 VAL cc_start: 0.8120 (t) cc_final: 0.7737 (m) REVERT: H 53 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8030 (p) REVERT: V 34 MET cc_start: 0.7140 (mmm) cc_final: 0.6013 (tmm) outliers start: 120 outliers final: 98 residues processed: 723 average time/residue: 0.2124 time to fit residues: 251.6908 Evaluate side-chains 747 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 640 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain Q residue 135 MET Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 170 optimal weight: 7.9990 chunk 425 optimal weight: 20.0000 chunk 477 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 234 optimal weight: 2.9990 chunk 333 optimal weight: 0.8980 chunk 334 optimal weight: 0.9980 chunk 303 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 426 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 GLN M 218 ASN N 313 HIS O 218 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.145365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112066 restraints weight = 60446.890| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.40 r_work: 0.3197 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39076 Z= 0.127 Angle : 0.554 9.890 53312 Z= 0.294 Chirality : 0.045 0.395 6028 Planarity : 0.005 0.053 6828 Dihedral : 5.181 52.736 5561 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.91 % Allowed : 16.49 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.12), residues: 4880 helix: 1.97 (0.27), residues: 421 sheet: 0.31 (0.13), residues: 1620 loop : -1.37 (0.11), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 156 TYR 0.014 0.001 TYR S 160 PHE 0.012 0.001 PHE A 365 TRP 0.012 0.001 TRP Y 98 HIS 0.005 0.001 HIS O 147 Details of bonding type rmsd covalent geometry : bond 0.00279 (38996) covalent geometry : angle 0.54828 (53140) SS BOND : bond 0.00399 ( 68) SS BOND : angle 0.96502 ( 136) hydrogen bonds : bond 0.05523 ( 1323) hydrogen bonds : angle 4.91532 ( 3513) link_NAG-ASN : bond 0.00556 ( 12) link_NAG-ASN : angle 2.83941 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 643 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8534 (t) cc_final: 0.8200 (m) REVERT: A 29 LEU cc_start: 0.8137 (mt) cc_final: 0.7769 (mp) REVERT: A 209 GLU cc_start: 0.7408 (mp0) cc_final: 0.7087 (mp0) REVERT: A 402 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8333 (mt) REVERT: B 67 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 13 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7981 (m) REVERT: C 133 LEU cc_start: 0.8461 (mt) cc_final: 0.8219 (mt) REVERT: C 187 MET cc_start: 0.8699 (ttp) cc_final: 0.8462 (mtp) REVERT: C 284 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8210 (t0) REVERT: C 296 VAL cc_start: 0.8464 (m) cc_final: 0.8008 (t) REVERT: D 130 SER cc_start: 0.8761 (p) cc_final: 0.8384 (m) REVERT: D 402 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7639 (tt) REVERT: D 430 VAL cc_start: 0.7963 (t) cc_final: 0.7533 (p) REVERT: M 87 THR cc_start: 0.7516 (OUTLIER) cc_final: 0.6813 (p) REVERT: M 251 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8158 (ttp80) REVERT: M 291 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6771 (p-80) REVERT: N 286 LEU cc_start: 0.8555 (tt) cc_final: 0.8285 (tp) REVERT: N 293 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8193 (m) REVERT: P 52 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7227 (pp) REVERT: P 70 MET cc_start: 0.8267 (tpp) cc_final: 0.7490 (ttm) REVERT: P 254 LYS cc_start: 0.8663 (ptpt) cc_final: 0.8316 (mtpt) REVERT: P 291 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7306 (p-80) REVERT: P 408 VAL cc_start: 0.8097 (t) cc_final: 0.7690 (m) REVERT: H 53 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8025 (p) REVERT: V 34 MET cc_start: 0.7153 (mmm) cc_final: 0.5990 (tmm) outliers start: 121 outliers final: 102 residues processed: 724 average time/residue: 0.2201 time to fit residues: 259.9744 Evaluate side-chains 750 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 638 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 185 SER Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 302 GLN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 255 ILE Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 379 LEU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 271 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 382 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 349 optimal weight: 3.9990 chunk 331 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 252 GLN M 218 ASN M 313 HIS N 193 ASN N 313 HIS O 218 ASN L 33 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114199 restraints weight = 60432.556| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.41 r_work: 0.3231 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39076 Z= 0.104 Angle : 0.524 9.878 53312 Z= 0.275 Chirality : 0.044 0.374 6028 Planarity : 0.005 0.054 6828 Dihedral : 4.993 52.511 5561 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.88 % Allowed : 16.54 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.12), residues: 4880 helix: 1.96 (0.27), residues: 427 sheet: 0.30 (0.13), residues: 1709 loop : -1.29 (0.11), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 178 TYR 0.013 0.001 TYR S 160 PHE 0.009 0.001 PHE A 365 TRP 0.012 0.001 TRP B 89 HIS 0.006 0.001 HIS O 147 Details of bonding type rmsd covalent geometry : bond 0.00218 (38996) covalent geometry : angle 0.51806 (53140) SS BOND : bond 0.00332 ( 68) SS BOND : angle 0.83922 ( 136) hydrogen bonds : bond 0.04738 ( 1323) hydrogen bonds : angle 4.74103 ( 3513) link_NAG-ASN : bond 0.00578 ( 12) link_NAG-ASN : angle 2.69545 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 644 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8520 (t) cc_final: 0.8178 (m) REVERT: A 29 LEU cc_start: 0.8123 (mt) cc_final: 0.7724 (mp) REVERT: A 209 GLU cc_start: 0.7425 (mp0) cc_final: 0.7095 (mp0) REVERT: A 402 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (mt) REVERT: B 67 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 432 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8114 (mm) REVERT: C 13 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7946 (m) REVERT: C 133 LEU cc_start: 0.8464 (mt) cc_final: 0.8196 (mt) REVERT: C 187 MET cc_start: 0.8683 (ttp) cc_final: 0.8475 (mtp) REVERT: C 284 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8190 (t0) REVERT: C 417 VAL cc_start: 0.8133 (t) cc_final: 0.7901 (t) REVERT: D 130 SER cc_start: 0.8763 (p) cc_final: 0.8376 (m) REVERT: D 430 VAL cc_start: 0.7960 (t) cc_final: 0.7542 (p) REVERT: M 87 THR cc_start: 0.7408 (OUTLIER) cc_final: 0.6711 (p) REVERT: M 251 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8173 (ttp80) REVERT: M 291 HIS cc_start: 0.7296 (OUTLIER) cc_final: 0.6779 (p90) REVERT: N 286 LEU cc_start: 0.8546 (tt) cc_final: 0.8281 (tp) REVERT: N 293 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8176 (m) REVERT: O 16 LEU cc_start: 0.8356 (mt) cc_final: 0.8122 (mp) REVERT: P 52 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7192 (pp) REVERT: P 70 MET cc_start: 0.8219 (tpp) cc_final: 0.7414 (ttm) REVERT: P 254 LYS cc_start: 0.8642 (ptpt) cc_final: 0.8289 (mtpt) REVERT: P 408 VAL cc_start: 0.8051 (t) cc_final: 0.7662 (m) REVERT: H 53 THR cc_start: 0.8333 (p) cc_final: 0.7991 (p) REVERT: V 34 MET cc_start: 0.7068 (mmm) cc_final: 0.5981 (tmm) outliers start: 120 outliers final: 97 residues processed: 728 average time/residue: 0.1894 time to fit residues: 225.4142 Evaluate side-chains 738 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 633 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 437 SER Chi-restraints excluded: chain M residue 32 ILE Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 61 SER Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 127 HIS Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 291 HIS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 313 HIS Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 181 MET Chi-restraints excluded: chain N residue 193 ASN Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 302 GLN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 255 ILE Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 402 LEU Chi-restraints excluded: chain Q residue 135 MET Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 251 THR Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 188 ASN Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain T residue 213 SER Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain V residue 28 THR Chi-restraints excluded: chain V residue 93 THR Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain Z residue 60 TYR Chi-restraints excluded: chain Z residue 97 VAL Chi-restraints excluded: chain Y residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 186 optimal weight: 0.4980 chunk 205 optimal weight: 1.9990 chunk 277 optimal weight: 0.0060 chunk 24 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 477 optimal weight: 50.0000 chunk 452 optimal weight: 0.9980 chunk 424 optimal weight: 30.0000 chunk 121 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN C 252 GLN M 218 ASN M 313 HIS N 193 ASN O 147 HIS O 218 ASN R 170 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114838 restraints weight = 60543.865| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.41 r_work: 0.3242 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39076 Z= 0.101 Angle : 0.521 9.956 53312 Z= 0.273 Chirality : 0.044 0.504 6028 Planarity : 0.005 0.054 6828 Dihedral : 4.926 52.402 5561 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.48 % Allowed : 17.24 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.12), residues: 4880 helix: 2.10 (0.27), residues: 421 sheet: 0.41 (0.13), residues: 1631 loop : -1.27 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 237 TYR 0.013 0.001 TYR M 199 PHE 0.008 0.001 PHE O 115 TRP 0.012 0.001 TRP Y 98 HIS 0.010 0.001 HIS M 313 Details of bonding type rmsd covalent geometry : bond 0.00208 (38996) covalent geometry : angle 0.51493 (53140) SS BOND : bond 0.00320 ( 68) SS BOND : angle 0.81527 ( 136) hydrogen bonds : bond 0.04556 ( 1323) hydrogen bonds : angle 4.68121 ( 3513) link_NAG-ASN : bond 0.00772 ( 12) link_NAG-ASN : angle 2.80822 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11561.49 seconds wall clock time: 197 minutes 22.16 seconds (11842.16 seconds total)