Starting phenix.real_space_refine on Mon Jul 6 18:12:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_27767.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_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_27767/07_2026/8dwy_27767.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_27767.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_27767.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_27767.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_27767.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dwy_27767/07_2026/8dwy_27767.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 8.75, per 1000 atoms: 0.23 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.88 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: 10.37 Time building geometry restraints manager: 4.10 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: 21296 17.90 - 35.80: 1527 35.80 - 53.70: 340 53.70 - 71.60: 53 71.60 - 89.51: 24 Dihedral angle restraints: 23240 sinusoidal: 9028 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 23237 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: 0.01 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: 4.550 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: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 37.850 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 13.035 89.505 13932 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 are 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/Z covalent geometry : bond 0.00263 / 0.12 (38996) covalent geometry : angle 0.57481 / 0.30 (53140) SS BOND : bond 0.00436 / 0.29 ( 68) SS BOND : angle 1.96010 / 1.54 ( 136) hydrogen bonds : bond 0.33456 / 22.50 ( 1323) hydrogen bonds : angle 8.35154 / 5.71 ( 3513) link_NAG-ASN : bond 0.00723 / 0.33 ( 12) link_NAG-ASN : angle 3.26484 / 2.24 ( 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 : 1.394 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: 0.2495 time to fit residues: 282.3046 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 : 1.328 ------------------------------------------------------------------------------- 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... 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 = 0.142748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108837 restraints weight = 60493.541| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.40 r_work: 0.3155 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 39076 Z= 0.214 Angle : 0.676 12.267 53312 Z= 0.372 Chirality : 0.049 0.414 6028 Planarity : 0.007 0.108 6828 Dihedral : 5.315 52.160 5318 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.69 % Allowed : 12.21 % Favored : 85.10 % 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 are not related in a simple way. whole: -0.66 (0.11), residues: 4880 helix: 1.68 (0.25), residues: 410 sheet: 0.38 (0.13), residues: 1663 loop : -1.34 (0.10), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 134 TYR 0.020 0.002 TYR C 122 PHE 0.018 0.002 PHE A 365 TRP 0.019 0.002 TRP O 330 HIS 0.010 0.002 HIS N 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.21 (38996) covalent geometry : angle 0.66790 / 0.37 (53140) SS BOND : bond 0.00510 / 0.32 ( 68) SS BOND : angle 1.40415 / 0.96 ( 136) hydrogen bonds : bond 0.08982 / 5.99 ( 1323) hydrogen bonds : angle 6.13983 / 4.18 ( 3513) link_NAG-ASN : bond 0.00472 / 0.24 ( 12) link_NAG-ASN : angle 3.26344 / 2.13 ( 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 794 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 682 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8139 (mt) cc_final: 0.7812 (mp) REVERT: A 76 TYR cc_start: 0.8509 (t80) cc_final: 0.8274 (t80) REVERT: A 209 GLU cc_start: 0.7396 (mp0) cc_final: 0.7014 (mp0) REVERT: A 345 GLU cc_start: 0.7506 (tt0) cc_final: 0.7227 (tt0) REVERT: B 284 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7203 (t0) REVERT: B 341 GLU cc_start: 0.7812 (mp0) cc_final: 0.7576 (mp0) REVERT: B 407 MET cc_start: 0.8086 (tpt) cc_final: 0.7701 (tpt) REVERT: B 432 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8416 (mm) REVERT: C 245 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8390 (mtpp) REVERT: C 284 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8112 (t0) REVERT: D 130 SER cc_start: 0.8746 (p) cc_final: 0.8382 (m) REVERT: D 347 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7871 (tm-30) REVERT: M 87 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7039 (t) REVERT: M 107 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7787 (mtmm) REVERT: M 254 LYS cc_start: 0.8817 (ptpt) cc_final: 0.8580 (ptmt) REVERT: M 277 THR cc_start: 0.8387 (t) cc_final: 0.8082 (p) REVERT: M 357 LEU cc_start: 0.8215 (tp) cc_final: 0.7888 (tp) REVERT: P 52 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7355 (pp) REVERT: Q 180 HIS cc_start: 0.8442 (p90) cc_final: 0.8146 (p90) REVERT: Q 194 VAL cc_start: 0.8186 (p) cc_final: 0.7949 (m) REVERT: Q 218 PHE cc_start: 0.7811 (m-80) cc_final: 0.7577 (m-80) REVERT: T 155 LYS cc_start: 0.7518 (mtpp) cc_final: 0.7281 (mtmm) REVERT: V 98 ARG cc_start: 0.5232 (OUTLIER) cc_final: 0.4739 (ptt180) outliers start: 112 outliers final: 67 residues processed: 744 average time/residue: 0.2259 time to fit residues: 271.9946 Evaluate side-chains 718 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 645 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 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 211 THR Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 357 LEU 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 H residue 59 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: 0.7980 chunk 234 optimal weight: 10.0000 chunk 294 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 chunk 313 optimal weight: 7.9990 chunk 374 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 438 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3753 r_free = 0.3753 target = 0.143120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109441 restraints weight = 60744.180| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.41 r_work: 0.3172 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39076 Z= 0.154 Angle : 0.594 10.834 53312 Z= 0.323 Chirality : 0.046 0.355 6028 Planarity : 0.006 0.081 6828 Dihedral : 4.993 43.938 5311 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.84 % Allowed : 13.37 % Favored : 83.80 % 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 are not related in a simple way. whole: -0.68 (0.11), residues: 4880 helix: 1.76 (0.26), residues: 416 sheet: 0.27 (0.13), residues: 1676 loop : -1.31 (0.10), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.013 0.001 TYR C 122 PHE 0.014 0.001 PHE A 365 TRP 0.013 0.001 TRP N 330 HIS 0.017 0.001 HIS N 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (38996) covalent geometry : angle 0.58779 / 0.32 (53140) SS BOND : bond 0.00448 / 0.29 ( 68) SS BOND : angle 1.04355 / 0.71 ( 136) hydrogen bonds : bond 0.07466 / 4.98 ( 1323) hydrogen bonds : angle 5.67416 / 3.86 ( 3513) link_NAG-ASN : bond 0.00510 / 0.25 ( 12) link_NAG-ASN : angle 3.04021 / 1.97 ( 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 782 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 664 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8125 (mt) cc_final: 0.7769 (mp) REVERT: A 209 GLU cc_start: 0.7510 (mp0) cc_final: 0.7125 (mp0) REVERT: B 284 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7274 (t0) REVERT: B 341 GLU cc_start: 0.7818 (mp0) cc_final: 0.7531 (mp0) REVERT: B 407 MET cc_start: 0.7874 (tpt) cc_final: 0.7476 (tpt) REVERT: B 432 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8289 (mm) REVERT: C 160 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8076 (mtpp) REVERT: C 245 LYS cc_start: 0.8620 (ttmt) cc_final: 0.8381 (mtpp) REVERT: C 284 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8093 (t0) REVERT: C 296 VAL cc_start: 0.8490 (m) cc_final: 0.8084 (t) REVERT: C 373 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8523 (mt0) REVERT: D 130 SER cc_start: 0.8771 (p) cc_final: 0.8406 (m) REVERT: D 347 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 430 VAL cc_start: 0.7971 (t) cc_final: 0.7482 (p) REVERT: M 87 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6598 (p) REVERT: M 208 GLU cc_start: 0.7764 (mp0) cc_final: 0.7511 (mp0) REVERT: M 212 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8466 (m) REVERT: M 254 LYS cc_start: 0.8784 (ptpt) cc_final: 0.8539 (ptmt) REVERT: N 13 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8330 (ptt180) REVERT: N 212 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7260 (t) REVERT: P 52 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7235 (pp) REVERT: P 211 THR cc_start: 0.7712 (OUTLIER) cc_final: 0.7507 (t) REVERT: P 291 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7212 (p-80) REVERT: Q 180 HIS cc_start: 0.8401 (p90) cc_final: 0.8179 (p90) REVERT: Q 194 VAL cc_start: 0.8112 (p) cc_final: 0.7891 (m) REVERT: R 124 MET cc_start: 0.6462 (pmm) cc_final: 0.6238 (pmm) REVERT: T 155 LYS cc_start: 0.7490 (mtpp) cc_final: 0.7250 (mtmm) REVERT: T 243 VAL cc_start: 0.8348 (p) cc_final: 0.8037 (t) REVERT: V 98 ARG cc_start: 0.5310 (OUTLIER) cc_final: 0.4806 (ptt180) outliers start: 118 outliers final: 78 residues processed: 734 average time/residue: 0.2305 time to fit residues: 273.8865 Evaluate side-chains 734 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 645 time to evaluate : 1.339 ------------------------------------------------------------------------------- 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 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 163 VAL Chi-restraints excluded: chain B residue 284 ASP 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 67 GLU 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 C residue 433 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 143 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 437 SER 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 386 VAL 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 121 ILE 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 390 VAL Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 285 MET 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 398 THR 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 390 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 244 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 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: 0.9980 chunk 428 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 435 optimal weight: 30.0000 chunk 321 optimal weight: 2.9990 chunk 273 optimal weight: 9.9990 chunk 195 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 439 HIS B 389 ASN C 252 GLN M 131 HIS M 158 GLN M 218 ASN M 245 ASN M 313 HIS N 313 HIS O 218 ASN O 299 ASN P 218 ASN Q 195 GLN R 139 HIS R 170 HIS R 191 HIS T 190 HIS U 33 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106808 restraints weight = 60967.358| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.55 r_work: 0.3121 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 39076 Z= 0.220 Angle : 0.663 10.466 53312 Z= 0.362 Chirality : 0.049 0.432 6028 Planarity : 0.007 0.061 6828 Dihedral : 5.236 44.461 5311 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.56 % Allowed : 14.23 % Favored : 82.21 % 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 are not related in a simple way. whole: -0.96 (0.11), residues: 4880 helix: 1.58 (0.26), residues: 419 sheet: 0.19 (0.13), residues: 1564 loop : -1.52 (0.10), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.020 0.002 TYR A 46 PHE 0.020 0.002 PHE A 365 TRP 0.019 0.002 TRP R 189 HIS 0.029 0.002 HIS R 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.22 (38996) covalent geometry : angle 0.65469 / 0.36 (53140) SS BOND : bond 0.00532 / 0.35 ( 68) SS BOND : angle 1.29165 / 0.88 ( 136) hydrogen bonds : bond 0.07907 / 5.31 ( 1323) hydrogen bonds : angle 5.61962 / 3.82 ( 3513) link_NAG-ASN : bond 0.00654 / 0.31 ( 12) link_NAG-ASN : angle 3.47363 / 2.29 ( 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 803 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 655 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8323 (t) cc_final: 0.8012 (m) REVERT: A 29 LEU cc_start: 0.8067 (mt) cc_final: 0.7708 (mp) REVERT: A 209 GLU cc_start: 0.7601 (mp0) cc_final: 0.7232 (mp0) REVERT: A 345 GLU cc_start: 0.7588 (tt0) cc_final: 0.7309 (tt0) REVERT: B 327 LYS cc_start: 0.8260 (mtpt) cc_final: 0.7861 (mtpt) REVERT: B 343 ASP cc_start: 0.8127 (p0) cc_final: 0.7869 (p0) REVERT: B 407 MET cc_start: 0.7945 (tpt) cc_final: 0.7559 (tpt) REVERT: B 434 VAL cc_start: 0.8673 (p) cc_final: 0.8464 (p) REVERT: C 45 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: C 284 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8125 (t0) REVERT: C 373 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8488 (mt0) REVERT: D 95 PHE cc_start: 0.7858 (t80) cc_final: 0.7650 (t80) REVERT: D 130 SER cc_start: 0.8789 (p) cc_final: 0.8428 (m) REVERT: D 430 VAL cc_start: 0.7962 (t) cc_final: 0.7518 (p) REVERT: M 87 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.6877 (p) REVERT: M 251 ARG cc_start: 0.8344 (mtp180) cc_final: 0.8065 (ttp80) REVERT: M 277 THR cc_start: 0.8385 (t) cc_final: 0.8027 (p) REVERT: N 13 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8392 (ptt180) REVERT: N 286 LEU cc_start: 0.8563 (tt) cc_final: 0.8336 (tp) REVERT: N 394 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7817 (mtm-85) REVERT: O 394 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8667 (ttp80) REVERT: P 52 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7309 (pp) REVERT: P 291 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7323 (p-80) REVERT: Q 194 VAL cc_start: 0.8150 (p) cc_final: 0.7902 (m) REVERT: T 155 LYS cc_start: 0.7599 (mtpp) cc_final: 0.7374 (mtpp) REVERT: T 243 VAL cc_start: 0.8399 (p) cc_final: 0.8096 (t) REVERT: V 98 ARG cc_start: 0.5427 (OUTLIER) cc_final: 0.5145 (ptm160) outliers start: 148 outliers final: 113 residues processed: 751 average time/residue: 0.2292 time to fit residues: 277.7543 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 : 1.208 ------------------------------------------------------------------------------- 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 133 LEU 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 357 SER Chi-restraints excluded: chain A residue 402 ILE 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 47 ILE Chi-restraints excluded: chain B residue 63 CYS 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 33 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 143 THR 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 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 265 THR Chi-restraints excluded: chain M residue 293 THR 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 13 ARG Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 121 ILE 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 313 HIS 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 390 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 255 ILE Chi-restraints excluded: chain O residue 285 MET 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 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 398 THR 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 S residue 169 VAL Chi-restraints excluded: chain S residue 225 VAL 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 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: 0.8980 chunk 69 optimal weight: 3.9990 chunk 475 optimal weight: 50.0000 chunk 262 optimal weight: 0.8980 chunk 388 optimal weight: 4.9990 chunk 415 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 436 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 chunk 414 optimal weight: 30.0000 chunk 443 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 GLN C 252 GLN M 158 GLN M 218 ASN N 245 ASN N 313 HIS O 193 ASN O 218 ASN O 299 ASN P 62 HIS P 218 ASN S 139 HIS T 139 HIS H 84 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.141609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107516 restraints weight = 60663.195| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.35 r_work: 0.3133 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 39076 Z= 0.202 Angle : 0.645 12.089 53312 Z= 0.350 Chirality : 0.048 0.446 6028 Planarity : 0.006 0.060 6828 Dihedral : 5.214 44.869 5311 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.97 % Allowed : 14.74 % Favored : 81.30 % 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 are not related in a simple way. whole: -1.05 (0.11), residues: 4880 helix: 1.60 (0.26), residues: 413 sheet: 0.11 (0.13), residues: 1533 loop : -1.56 (0.10), residues: 2934 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 0.002 PHE A 365 TRP 0.020 0.002 TRP Y 37 HIS 0.010 0.002 HIS N 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 (38996) covalent geometry : angle 0.63519 / 0.35 (53140) SS BOND : bond 0.00590 / 0.38 ( 68) SS BOND : angle 1.56126 / 1.07 ( 136) hydrogen bonds : bond 0.07537 / 5.05 ( 1323) hydrogen bonds : angle 5.52265 / 3.75 ( 3513) link_NAG-ASN : bond 0.00576 / 0.28 ( 12) link_NAG-ASN : angle 3.48296 / 2.29 ( 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 816 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 651 time to evaluate : 1.600 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: 0.8415 (t) cc_final: 0.8124 (m) REVERT: A 209 GLU cc_start: 0.7460 (mp0) cc_final: 0.7126 (mp0) REVERT: A 345 GLU cc_start: 0.7464 (tt0) cc_final: 0.7195 (tt0) REVERT: B 282 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7999 (mt) REVERT: B 407 MET cc_start: 0.8003 (tpt) cc_final: 0.7623 (tpt) REVERT: C 284 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8221 (t0) REVERT: C 373 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8517 (mt0) REVERT: D 130 SER cc_start: 0.8746 (p) cc_final: 0.8397 (m) REVERT: D 430 VAL cc_start: 0.7978 (t) cc_final: 0.7576 (p) REVERT: M 87 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.6888 (p) REVERT: M 212 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8571 (m) REVERT: M 251 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8034 (ttp80) REVERT: M 277 THR cc_start: 0.8367 (t) cc_final: 0.8023 (p) REVERT: N 13 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8395 (ptt180) REVERT: N 394 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7726 (mtm-85) REVERT: O 394 ARG cc_start: 0.8933 (ttp80) cc_final: 0.8669 (ttp80) REVERT: P 52 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7363 (pp) REVERT: P 74 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8045 (p) REVERT: P 254 LYS cc_start: 0.8731 (ptpt) cc_final: 0.8395 (mtpt) REVERT: P 291 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7387 (p-80) REVERT: Q 194 VAL cc_start: 0.8186 (p) cc_final: 0.7921 (m) REVERT: T 243 VAL cc_start: 0.8336 (p) cc_final: 0.8037 (t) REVERT: V 34 MET cc_start: 0.7056 (mmm) cc_final: 0.6128 (tmm) outliers start: 165 outliers final: 122 residues processed: 756 average time/residue: 0.2424 time to fit residues: 296.6046 Evaluate side-chains 789 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 659 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 133 LEU 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 254 THR 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 374 VAL Chi-restraints excluded: chain A residue 402 ILE 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 80 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 210 SER 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 396 THR 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 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 143 THR 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 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 212 THR Chi-restraints excluded: chain M residue 293 THR 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 13 ARG Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 121 ILE 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 261 LEU 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 390 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 193 ASN Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET 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 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 74 THR 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 291 HIS Chi-restraints excluded: chain P residue 370 ILE 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 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 S residue 130 VAL Chi-restraints excluded: chain S 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 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: 5.9990 chunk 183 optimal weight: 2.9990 chunk 373 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 423 optimal weight: 30.0000 chunk 205 optimal weight: 0.0010 chunk 272 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 360 optimal weight: 0.7980 chunk 332 optimal weight: 0.6980 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 GLN C 252 GLN M 218 ASN M 245 ASN N 245 ASN N 313 HIS O 218 ASN O 299 ASN P 62 HIS P 218 ASN S 139 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109073 restraints weight = 61028.929| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.36 r_work: 0.3161 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39076 Z= 0.151 Angle : 0.594 11.703 53312 Z= 0.320 Chirality : 0.046 0.393 6028 Planarity : 0.006 0.056 6828 Dihedral : 4.998 44.761 5311 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.80 % Allowed : 15.38 % Favored : 80.82 % 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 are not related in a simple way. whole: -1.02 (0.11), residues: 4880 helix: 1.71 (0.26), residues: 418 sheet: 0.07 (0.13), residues: 1586 loop : -1.56 (0.10), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 156 TYR 0.017 0.001 TYR S 160 PHE 0.013 0.001 PHE A 365 TRP 0.015 0.001 TRP M 235 HIS 0.017 0.001 HIS S 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (38996) covalent geometry : angle 0.58600 / 0.32 (53140) SS BOND : bond 0.00464 / 0.30 ( 68) SS BOND : angle 1.15677 / 0.81 ( 136) hydrogen bonds : bond 0.06676 / 4.46 ( 1323) hydrogen bonds : angle 5.33682 / 3.63 ( 3513) link_NAG-ASN : bond 0.00573 / 0.27 ( 12) link_NAG-ASN : angle 3.20191 / 2.11 ( 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 824 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 666 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8380 (t) cc_final: 0.8065 (m) REVERT: A 209 GLU cc_start: 0.7435 (mp0) cc_final: 0.7101 (mp0) REVERT: A 427 ILE cc_start: 0.8923 (mm) cc_final: 0.8623 (tt) REVERT: B 407 MET cc_start: 0.7844 (tpt) cc_final: 0.7493 (tpt) REVERT: C 13 VAL cc_start: 0.8280 (OUTLIER) cc_final: 0.8073 (m) REVERT: C 133 LEU cc_start: 0.8475 (mt) cc_final: 0.8225 (mt) REVERT: C 187 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (mtp) REVERT: C 284 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8190 (t0) REVERT: C 296 VAL cc_start: 0.8495 (m) cc_final: 0.8115 (t) REVERT: C 373 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8515 (mt0) REVERT: D 130 SER cc_start: 0.8749 (p) cc_final: 0.8403 (m) REVERT: D 430 VAL cc_start: 0.7971 (t) cc_final: 0.7525 (p) REVERT: M 87 THR cc_start: 0.7522 (OUTLIER) cc_final: 0.6842 (p) REVERT: M 212 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8562 (m) REVERT: M 251 ARG cc_start: 0.8356 (mtp180) cc_final: 0.8066 (ttp80) REVERT: N 13 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8360 (ptt180) REVERT: N 212 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.7245 (t) REVERT: N 286 LEU cc_start: 0.8543 (tt) cc_final: 0.8311 (tp) REVERT: N 293 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8190 (m) REVERT: O 373 VAL cc_start: 0.8344 (t) cc_final: 0.7976 (m) REVERT: O 394 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8584 (ttp80) REVERT: P 52 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7307 (pp) REVERT: P 74 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8075 (p) REVERT: P 117 ASP cc_start: 0.7500 (t0) cc_final: 0.7251 (t0) REVERT: P 244 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (mtm-85) REVERT: P 254 LYS cc_start: 0.8722 (ptpt) cc_final: 0.8393 (mtpt) REVERT: P 291 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7414 (p-80) REVERT: P 408 VAL cc_start: 0.8168 (t) cc_final: 0.7786 (m) REVERT: Q 194 VAL cc_start: 0.8126 (p) cc_final: 0.7899 (m) REVERT: T 243 VAL cc_start: 0.8333 (p) cc_final: 0.8030 (t) REVERT: H 53 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8053 (p) REVERT: V 34 MET cc_start: 0.7086 (mmm) cc_final: 0.5991 (tmm) outliers start: 158 outliers final: 114 residues processed: 769 average time/residue: 0.2225 time to fit residues: 278.1010 Evaluate side-chains 781 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 654 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 133 LEU 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 357 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 414 THR 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 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 321 THR Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 370 CYS 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 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 187 MET 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 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 143 THR 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 374 VAL Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 399 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 220 CYS 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 398 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG 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 236 GLN 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 166 GLU Chi-restraints excluded: chain O residue 255 ILE Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET 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 O residue 397 ILE 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 74 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 112 THR 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 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 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 244 THR Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain S residue 130 VAL 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 S residue 244 THR 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 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=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: 1.9990 chunk 317 optimal weight: 1.9990 chunk 124 optimal weight: 0.0970 chunk 434 optimal weight: 9.9990 chunk 403 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 252 GLN M 127 HIS M 218 ASN O 218 ASN O 299 ASN P 62 HIS P 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.142113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108153 restraints weight = 60790.925| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.35 r_work: 0.3151 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 39076 Z= 0.181 Angle : 0.621 11.887 53312 Z= 0.335 Chirality : 0.048 0.380 6028 Planarity : 0.006 0.060 6828 Dihedral : 5.056 44.965 5311 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.99 % Allowed : 15.77 % Favored : 80.24 % 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 are not related in a simple way. whole: -1.08 (0.11), residues: 4880 helix: 1.65 (0.26), residues: 419 sheet: 0.10 (0.13), residues: 1573 loop : -1.62 (0.10), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 156 TYR 0.017 0.002 TYR S 160 PHE 0.016 0.001 PHE A 365 TRP 0.014 0.002 TRP R 189 HIS 0.008 0.001 HIS N 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (38996) covalent geometry : angle 0.61355 / 0.33 (53140) SS BOND : bond 0.00528 / 0.34 ( 68) SS BOND : angle 1.12228 / 0.77 ( 136) hydrogen bonds : bond 0.07000 / 4.70 ( 1323) hydrogen bonds : angle 5.33160 / 3.63 ( 3513) link_NAG-ASN : bond 0.00547 / 0.28 ( 12) link_NAG-ASN : angle 3.31171 / 2.16 ( 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 829 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 663 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8410 (t) cc_final: 0.8091 (m) REVERT: A 209 GLU cc_start: 0.7447 (mp0) cc_final: 0.7128 (mp0) REVERT: A 427 ILE cc_start: 0.8912 (mm) cc_final: 0.8620 (tt) REVERT: B 407 MET cc_start: 0.7895 (tpt) cc_final: 0.7550 (tpt) REVERT: C 133 LEU cc_start: 0.8512 (mt) cc_final: 0.8252 (mt) REVERT: C 187 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: C 284 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8241 (t0) REVERT: C 373 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8535 (mt0) REVERT: D 130 SER cc_start: 0.8741 (p) cc_final: 0.8397 (m) REVERT: D 430 VAL cc_start: 0.7992 (t) cc_final: 0.7538 (p) REVERT: M 87 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7197 (t) REVERT: M 212 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8576 (m) REVERT: M 251 ARG cc_start: 0.8372 (mtp180) cc_final: 0.8162 (ttp80) REVERT: M 277 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8038 (p) REVERT: N 13 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8385 (ptt180) REVERT: N 212 THR cc_start: 0.7540 (OUTLIER) cc_final: 0.7266 (t) REVERT: N 286 LEU cc_start: 0.8569 (tt) cc_final: 0.8336 (tp) REVERT: N 293 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8237 (m) REVERT: O 373 VAL cc_start: 0.8326 (t) cc_final: 0.7963 (m) REVERT: O 394 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8595 (ttp80) REVERT: P 52 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7348 (pp) REVERT: P 74 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8073 (p) REVERT: P 117 ASP cc_start: 0.7552 (t0) cc_final: 0.7340 (t0) REVERT: P 244 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7858 (mtm-85) REVERT: P 254 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8422 (mtpt) REVERT: P 291 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7383 (p-80) REVERT: P 408 VAL cc_start: 0.8163 (t) cc_final: 0.7810 (m) REVERT: Q 194 VAL cc_start: 0.8011 (p) cc_final: 0.7779 (m) REVERT: T 243 VAL cc_start: 0.8344 (p) cc_final: 0.8057 (t) REVERT: H 53 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8074 (p) REVERT: V 34 MET cc_start: 0.7078 (mmm) cc_final: 0.6024 (tmm) outliers start: 166 outliers final: 131 residues processed: 779 average time/residue: 0.2414 time to fit residues: 303.4907 Evaluate side-chains 801 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 657 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 133 LEU 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 246 GLU 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 374 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 321 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 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 187 MET 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 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 143 THR 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 374 VAL Chi-restraints excluded: chain D residue 388 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 208 GLU Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 220 CYS Chi-restraints excluded: chain M residue 277 THR 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 398 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG 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 236 GLN 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 386 VAL Chi-restraints excluded: chain N residue 389 CYS Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 52 LEU 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 265 THR Chi-restraints excluded: chain O residue 285 MET 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 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 74 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 112 THR 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 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 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 244 THR Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 167 ILE 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 S residue 244 THR 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 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 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: 3.9990 chunk 465 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 319 optimal weight: 0.6980 chunk 290 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 366 optimal weight: 0.9980 chunk 411 optimal weight: 20.0000 chunk 401 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 252 GLN M 127 HIS M 218 ASN N 193 ASN O 218 ASN O 299 ASN P 62 HIS P 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.110961 restraints weight = 59811.390| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.39 r_work: 0.3184 rms_B_bonded: 2.54 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: 0.8028 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39076 Z= 0.128 Angle : 0.569 11.499 53312 Z= 0.303 Chirality : 0.046 0.493 6028 Planarity : 0.006 0.056 6828 Dihedral : 4.808 44.685 5311 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.44 % Allowed : 16.49 % Favored : 80.07 % 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 are not related in a simple way. whole: -0.96 (0.12), residues: 4880 helix: 1.75 (0.26), residues: 421 sheet: 0.18 (0.13), residues: 1597 loop : -1.57 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 156 TYR 0.016 0.001 TYR S 160 PHE 0.011 0.001 PHE A 365 TRP 0.012 0.001 TRP Y 98 HIS 0.012 0.001 HIS M 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (38996) covalent geometry : angle 0.56230 / 0.30 (53140) SS BOND : bond 0.00380 / 0.24 ( 68) SS BOND : angle 0.99989 / 0.69 ( 136) hydrogen bonds : bond 0.05993 / 4.00 ( 1323) hydrogen bonds : angle 5.12982 / 3.49 ( 3513) link_NAG-ASN : bond 0.00707 / 0.33 ( 12) link_NAG-ASN : angle 2.96210 / 1.89 ( 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 809 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 666 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 VAL cc_start: 0.8375 (t) cc_final: 0.8053 (m) REVERT: A 209 GLU cc_start: 0.7451 (mp0) cc_final: 0.7134 (mp0) REVERT: A 402 ILE cc_start: 0.8677 (pt) cc_final: 0.8340 (mt) REVERT: A 427 ILE cc_start: 0.8907 (mm) cc_final: 0.8602 (tt) REVERT: B 407 MET cc_start: 0.7645 (tpt) cc_final: 0.7327 (tpt) REVERT: C 13 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.8014 (m) REVERT: C 133 LEU cc_start: 0.8480 (mt) cc_final: 0.8219 (mt) REVERT: C 187 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8561 (mtp) REVERT: C 284 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (t0) REVERT: C 296 VAL cc_start: 0.8505 (m) cc_final: 0.8057 (t) REVERT: C 373 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8533 (mt0) REVERT: D 130 SER cc_start: 0.8744 (p) cc_final: 0.8394 (m) REVERT: D 402 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7639 (tt) REVERT: D 430 VAL cc_start: 0.7947 (t) cc_final: 0.7480 (p) REVERT: M 87 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.6818 (p) REVERT: M 212 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8462 (m) REVERT: N 13 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8353 (ptt180) REVERT: N 212 THR cc_start: 0.7459 (OUTLIER) cc_final: 0.7224 (t) REVERT: N 293 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8196 (m) REVERT: O 373 VAL cc_start: 0.8194 (t) cc_final: 0.7816 (m) REVERT: O 394 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8601 (ttp80) REVERT: O 398 THR cc_start: 0.7332 (m) cc_final: 0.6927 (m) REVERT: P 52 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7253 (pp) REVERT: P 70 MET cc_start: 0.8357 (tpp) cc_final: 0.7507 (ttm) REVERT: P 74 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8095 (p) REVERT: P 244 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7866 (mtm-85) REVERT: P 254 LYS cc_start: 0.8710 (ptpt) cc_final: 0.8368 (mtpt) REVERT: P 291 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7329 (p-80) REVERT: P 408 VAL cc_start: 0.8111 (t) cc_final: 0.7772 (m) REVERT: Q 194 VAL cc_start: 0.8013 (p) cc_final: 0.7790 (m) REVERT: H 53 THR cc_start: 0.8382 (p) cc_final: 0.8045 (p) REVERT: V 34 MET cc_start: 0.7083 (mmm) cc_final: 0.5945 (tmm) outliers start: 143 outliers final: 110 residues processed: 761 average time/residue: 0.2433 time to fit residues: 299.6891 Evaluate side-chains 781 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 657 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 246 GLU Chi-restraints excluded: chain A residue 303 VAL 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 143 THR 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 309 SER Chi-restraints excluded: chain B residue 321 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 429 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 67 GLU Chi-restraints excluded: chain C residue 187 MET 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 373 GLN 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 42 LEU 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 325 LYS Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 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 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 111 LEU 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 220 CYS 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 37 ILE Chi-restraints excluded: chain N residue 52 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 193 ASN Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 236 GLN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 389 CYS 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 285 MET 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 O residue 397 ILE Chi-restraints excluded: chain O residue 401 GLU 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 74 THR 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 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 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 S residue 244 THR Chi-restraints excluded: chain T residue 179 THR 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 T residue 253 ILE Chi-restraints excluded: chain H residue 48 MET 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: 30.0000 chunk 477 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 333 optimal weight: 0.9990 chunk 334 optimal weight: 1.9990 chunk 303 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 426 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 252 GLN M 127 HIS M 218 ASN N 193 ASN O 218 ASN O 299 ASN P 62 HIS P 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.143217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109461 restraints weight = 60936.266| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.36 r_work: 0.3164 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2481 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= 0.153 Angle : 0.594 11.282 53312 Z= 0.317 Chirality : 0.046 0.450 6028 Planarity : 0.006 0.061 6828 Dihedral : 4.838 44.617 5311 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.49 % Allowed : 16.66 % Favored : 79.86 % 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 are not related in a simple way. whole: -0.99 (0.12), residues: 4880 helix: 1.75 (0.26), residues: 419 sheet: 0.14 (0.13), residues: 1612 loop : -1.59 (0.10), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 156 TYR 0.015 0.001 TYR S 160 PHE 0.014 0.001 PHE A 365 TRP 0.013 0.001 TRP Y 98 HIS 0.008 0.001 HIS P 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (38996) covalent geometry : angle 0.58750 / 0.32 (53140) SS BOND : bond 0.00439 / 0.29 ( 68) SS BOND : angle 1.06305 / 0.73 ( 136) hydrogen bonds : bond 0.06301 / 4.23 ( 1323) hydrogen bonds : angle 5.11796 / 3.48 ( 3513) link_NAG-ASN : bond 0.00565 / 0.28 ( 12) link_NAG-ASN : angle 2.91863 / 1.90 ( 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 801 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 656 time to evaluate : 1.495 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: 0.8419 (t) cc_final: 0.8082 (m) REVERT: A 29 LEU cc_start: 0.8150 (mt) cc_final: 0.7781 (mp) REVERT: A 209 GLU cc_start: 0.7451 (mp0) cc_final: 0.7124 (mp0) REVERT: A 402 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 427 ILE cc_start: 0.8931 (mm) cc_final: 0.8618 (tt) REVERT: B 166 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7700 (mtm) REVERT: B 407 MET cc_start: 0.7686 (tpt) cc_final: 0.7299 (tpt) REVERT: C 133 LEU cc_start: 0.8486 (mt) cc_final: 0.8204 (mt) REVERT: C 187 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8580 (mtp) REVERT: C 284 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8222 (t0) REVERT: C 296 VAL cc_start: 0.8513 (m) cc_final: 0.8083 (t) REVERT: C 373 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: D 130 SER cc_start: 0.8747 (p) cc_final: 0.8398 (m) REVERT: D 402 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7707 (tt) REVERT: D 430 VAL cc_start: 0.7994 (t) cc_final: 0.7543 (p) REVERT: M 87 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7047 (p) REVERT: M 212 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (m) REVERT: M 251 ARG cc_start: 0.8334 (ttp80) cc_final: 0.8042 (ttp80) REVERT: N 13 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8358 (ptt180) REVERT: N 212 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.7245 (t) REVERT: N 293 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8210 (m) REVERT: O 373 VAL cc_start: 0.8240 (t) cc_final: 0.7887 (m) REVERT: O 394 ARG cc_start: 0.8813 (ttp80) cc_final: 0.8600 (ttp80) REVERT: O 398 THR cc_start: 0.7385 (OUTLIER) cc_final: 0.7008 (m) REVERT: P 52 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7286 (pp) REVERT: P 70 MET cc_start: 0.8367 (tpp) cc_final: 0.7497 (ttm) REVERT: P 74 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8089 (p) REVERT: P 244 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7861 (mtm-85) REVERT: P 254 LYS cc_start: 0.8713 (ptpt) cc_final: 0.8384 (mtpt) REVERT: P 291 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7390 (p-80) REVERT: P 408 VAL cc_start: 0.8106 (t) cc_final: 0.7762 (m) REVERT: Q 194 VAL cc_start: 0.8049 (p) cc_final: 0.7819 (m) REVERT: H 53 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8060 (p) REVERT: V 34 MET cc_start: 0.7080 (mmm) cc_final: 0.5949 (tmm) outliers start: 145 outliers final: 113 residues processed: 752 average time/residue: 0.2435 time to fit residues: 295.9831 Evaluate side-chains 792 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 662 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 80 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 321 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 429 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 187 MET 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 373 GLN 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 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 374 VAL Chi-restraints excluded: chain D residue 388 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 85 VAL Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 111 LEU 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 220 CYS Chi-restraints excluded: chain M residue 293 THR Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 13 ARG 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 236 GLN 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 402 LEU Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 192 VAL Chi-restraints excluded: chain O residue 263 ASN Chi-restraints excluded: chain O residue 285 MET 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 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 74 THR 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 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 S residue 130 VAL Chi-restraints excluded: chain S residue 167 ILE 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 S residue 244 THR Chi-restraints excluded: chain T residue 179 THR 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 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 97 VAL Chi-restraints excluded: chain H residue 104 LEU 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 X residue 91 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: 1.9990 chunk 200 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 0.0570 chunk 222 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 349 optimal weight: 5.9990 chunk 331 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 373 GLN C 252 GLN M 127 HIS M 218 ASN O 218 ASN O 299 ASN P 62 HIS P 218 ASN L 33 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114394 restraints weight = 60303.414| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.41 r_work: 0.3226 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 39076 Z= 0.102 Angle : 0.530 10.951 53312 Z= 0.277 Chirality : 0.045 0.611 6028 Planarity : 0.005 0.102 6828 Dihedral : 4.440 43.608 5310 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.69 % Allowed : 17.33 % Favored : 79.98 % 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 are not related in a simple way. whole: -0.81 (0.12), residues: 4880 helix: 1.78 (0.27), residues: 427 sheet: 0.25 (0.13), residues: 1649 loop : -1.46 (0.11), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 156 TYR 0.012 0.001 TYR O 363 PHE 0.009 0.001 PHE N 115 TRP 0.016 0.001 TRP U 98 HIS 0.006 0.001 HIS P 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (38996) covalent geometry : angle 0.52227 / 0.28 (53140) SS BOND : bond 0.00299 / 0.20 ( 68) SS BOND : angle 0.87224 / 0.61 ( 136) hydrogen bonds : bond 0.04779 / 3.18 ( 1323) hydrogen bonds : angle 4.81148 / 3.27 ( 3513) link_NAG-ASN : bond 0.00844 / 0.38 ( 12) link_NAG-ASN : angle 3.17830 / 2.12 ( 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 761 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 649 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LEU cc_start: 0.8109 (mt) cc_final: 0.7704 (mp) REVERT: A 209 GLU cc_start: 0.7377 (mp0) cc_final: 0.7069 (mp0) REVERT: A 402 ILE cc_start: 0.8561 (pt) cc_final: 0.8297 (mt) REVERT: B 166 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7697 (mtm) REVERT: B 432 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8141 (mm) REVERT: C 133 LEU cc_start: 0.8457 (mt) cc_final: 0.8188 (mt) REVERT: C 187 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8491 (mtp) REVERT: C 284 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8233 (t0) REVERT: C 417 VAL cc_start: 0.8056 (t) cc_final: 0.7812 (t) REVERT: D 130 SER cc_start: 0.8730 (p) cc_final: 0.8361 (m) REVERT: D 402 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7538 (tt) REVERT: M 87 THR cc_start: 0.7384 (OUTLIER) cc_final: 0.6673 (p) REVERT: M 251 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8073 (ttp80) REVERT: N 181 MET cc_start: 0.7639 (mtp) cc_final: 0.7436 (mtp) REVERT: N 293 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8111 (m) REVERT: N 397 ILE cc_start: 0.7713 (mt) cc_final: 0.7419 (tt) REVERT: O 16 LEU cc_start: 0.8245 (mt) cc_final: 0.8041 (mp) REVERT: O 373 VAL cc_start: 0.7951 (t) cc_final: 0.7582 (m) REVERT: P 52 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7166 (pp) REVERT: P 70 MET cc_start: 0.8106 (tpp) cc_final: 0.7346 (ttm) REVERT: P 254 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8323 (mtpt) REVERT: P 408 VAL cc_start: 0.8070 (t) cc_final: 0.7701 (m) REVERT: Q 194 VAL cc_start: 0.8136 (p) cc_final: 0.7928 (m) REVERT: S 167 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6722 (mt) REVERT: H 53 THR cc_start: 0.8343 (p) cc_final: 0.7997 (p) REVERT: V 34 MET cc_start: 0.7089 (mmm) cc_final: 0.5981 (tmm) outliers start: 112 outliers final: 81 residues processed: 720 average time/residue: 0.2226 time to fit residues: 261.8124 Evaluate side-chains 715 residues out of total 4160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 625 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 374 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 166 MET 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 309 SER 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 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 187 MET 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 D residue 109 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 VAL Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 402 ILE 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 185 SER Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain M residue 220 CYS 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 302 GLN Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 192 VAL 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 O residue 397 ILE Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 43 ASP Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 52 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 Q residue 241 SER Chi-restraints excluded: chain R residue 205 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 167 ILE 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 T residue 179 THR 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 T residue 253 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 104 LEU 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 X residue 91 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: 0.2980 chunk 205 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 477 optimal weight: 50.0000 chunk 452 optimal weight: 6.9990 chunk 424 optimal weight: 30.0000 chunk 121 optimal weight: 0.7980 chunk 140 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 389 ASN C 252 GLN M 127 HIS M 218 ASN M 313 HIS O 147 HIS O 218 ASN O 299 ASN R 170 HIS L 33 ASN U 33 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.147914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115173 restraints weight = 60537.659| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.41 r_work: 0.3236 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 39076 Z= 0.102 Angle : 0.527 10.716 53312 Z= 0.274 Chirality : 0.044 0.492 6028 Planarity : 0.005 0.055 6828 Dihedral : 4.278 42.611 5310 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.26 % Allowed : 17.84 % Favored : 79.90 % 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 are not related in a simple way. whole: -0.69 (0.12), residues: 4880 helix: 1.85 (0.27), residues: 427 sheet: 0.31 (0.13), residues: 1658 loop : -1.37 (0.11), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 394 TYR 0.015 0.001 TYR M 199 PHE 0.009 0.001 PHE O 115 TRP 0.014 0.001 TRP U 98 HIS 0.007 0.001 HIS O 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (38996) covalent geometry : angle 0.51937 / 0.27 (53140) SS BOND : bond 0.00301 / 0.20 ( 68) SS BOND : angle 0.82408 / 0.56 ( 136) hydrogen bonds : bond 0.04531 / 3.03 ( 1323) hydrogen bonds : angle 4.67882 / 3.18 ( 3513) link_NAG-ASN : bond 0.00650 / 0.30 ( 12) link_NAG-ASN : angle 3.14611 / 2.10 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13297.98 seconds wall clock time: 226 minutes 52.47 seconds (13612.47 seconds total)