Starting phenix.real_space_refine on Tue Aug 26 14:59:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwx_27765/08_2025/8dwx_27765.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwx_27765/08_2025/8dwx_27765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dwx_27765/08_2025/8dwx_27765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwx_27765/08_2025/8dwx_27765.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dwx_27765/08_2025/8dwx_27765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwx_27765/08_2025/8dwx_27765.map" } resolution = 3.27 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= 0.047 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 24116 2.51 5 N 6556 2.21 5 O 7296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38228 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: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "U" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "X" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "W" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "Z" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 993 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Y" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.44, per 1000 atoms: 0.27 Number of scatterers: 38228 At special positions: 0 Unit cell: (186.76, 221.56, 241.28, 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 7296 8.00 N 6556 7.00 C 24116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=72, 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=2.04 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=2.05 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=2.04 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=2.03 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=2.04 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=2.05 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 L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 110 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 97 " distance=2.03 Simple disulfide: pdb=" SG CYS V 105 " - pdb=" SG CYS V 110 " distance=2.03 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 97 " distance=2.03 Simple disulfide: pdb=" SG CYS X 105 " - pdb=" SG CYS X 110 " distance=2.03 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 105 " - pdb=" SG CYS Z 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 116 sheets defined 12.5% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.643A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.852A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.540A pdb=" N THR A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.745A pdb=" N ALA A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.625A pdb=" N VAL A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.612A pdb=" N LYS B 115 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.881A pdb=" N TYR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.699A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.569A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 439 removed outlier: 3.565A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.742A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.091A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.621A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 removed outlier: 3.595A pdb=" N CYS C 259 " --> pdb=" O PRO C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 259' Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.565A pdb=" N ALA C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 439 removed outlier: 3.613A pdb=" N TRP C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 427 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.686A pdb=" N LYS D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.899A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.712A pdb=" N THR D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.597A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.691A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 427 " --> pdb=" O VAL D 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 10 Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 178 through 181 Processing helix chain 'M' and resid 351 through 363 removed outlier: 3.518A pdb=" N ILE M 355 " --> pdb=" O HIS M 351 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE M 356 " --> pdb=" O PRO M 352 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M 357 " --> pdb=" O HIS M 353 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU M 362 " --> pdb=" O TYR M 358 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 398 removed outlier: 3.769A pdb=" N VAL M 368 " --> pdb=" O PRO M 364 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS M 389 " --> pdb=" O ALA M 385 " (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: 3.550A 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: 3.716A pdb=" N LEU N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU N 362 " --> pdb=" O TYR N 358 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 403 removed outlier: 3.606A pdb=" N VAL N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL N 386 " --> pdb=" O VAL N 382 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET N 388 " --> pdb=" O THR N 384 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS N 389 " --> pdb=" O ALA N 385 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG N 395 " --> pdb=" O CYS N 391 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.808A 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: 3.508A 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 361 removed outlier: 3.586A pdb=" N ILE O 355 " --> pdb=" O HIS O 351 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE O 356 " --> pdb=" O PRO O 352 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 398 removed outlier: 3.502A pdb=" N VAL O 368 " --> pdb=" O PRO O 364 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS O 389 " --> pdb=" O ALA O 385 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL O 390 " --> pdb=" O VAL O 386 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS O 391 " --> pdb=" O GLY O 387 " (cutoff:3.500A) Processing helix chain 'O' and resid 399 through 401 No H-bonds generated for 'chain 'O' and resid 399 through 401' Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'P' and resid 6 through 10 removed outlier: 3.523A 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: 3.632A pdb=" N LEU P 357 " --> pdb=" O HIS P 353 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR P 359 " --> pdb=" O ILE P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 403 removed outlier: 3.810A pdb=" N VAL P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL P 369 " --> pdb=" O THR P 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG P 395 " --> pdb=" O CYS P 391 " (cutoff:3.500A) Proline residue: P 399 - end of helix removed outlier: 3.563A pdb=" N LEU P 402 " --> pdb=" O THR P 398 " (cutoff:3.500A) removed outlier: 3.668A 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 146 through 151 removed outlier: 3.950A pdb=" N LYS Q 151 " --> pdb=" O ALA Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 175 removed outlier: 4.944A pdb=" N SER Q 173 " --> pdb=" O HIS Q 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 152 removed outlier: 3.530A pdb=" N LYS R 151 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 175 removed outlier: 4.989A pdb=" N SER R 173 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.724A pdb=" N LYS S 151 " --> pdb=" O ASP S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 175 removed outlier: 3.581A pdb=" N MET S 171 " --> pdb=" O PRO S 168 " (cutoff:3.500A) removed outlier: 5.106A 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 168 through 175 removed outlier: 3.597A pdb=" N MET T 171 " --> pdb=" O PRO T 168 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER T 173 " --> pdb=" O HIS T 170 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.879A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.957A pdb=" N THR H 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 92 removed outlier: 3.894A pdb=" N THR V 92 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.888A pdb=" N PHE U 83 " --> pdb=" O PRO U 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 92 removed outlier: 3.923A pdb=" N THR X 92 " --> pdb=" O ALA X 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 83 removed outlier: 3.882A pdb=" N PHE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 88 through 92 removed outlier: 3.933A pdb=" N THR Z 92 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.867A pdb=" N PHE Y 83 " --> pdb=" O PRO Y 80 " (cutoff:3.500A) 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: 3.854A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 48 removed outlier: 7.181A pdb=" N ALA A 121 " --> pdb=" O ASP A 45 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 120 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.586A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.586A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 79 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 106 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.510A 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 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: 3.654A pdb=" N SER A 300 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.700A 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: 3.615A 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: 3.520A pdb=" N TYR M 297 " --> pdb=" O HIS M 307 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.658A 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: 3.968A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.526A 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: 7.175A pdb=" N ALA B 121 " --> pdb=" O ASP B 45 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.545A 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: 3.608A pdb=" N ALA B 106 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 77 " --> pdb=" O ALA B 106 " (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: 3.688A pdb=" N SER B 300 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) removed outlier: 3.521A 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 Processing sheet with id=AC6, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.592A pdb=" N TYR N 297 " --> pdb=" O HIS N 307 " (cutoff:3.500A) removed outlier: 3.501A 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: 3.691A 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: 4.178A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.811A 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: 6.602A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (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: 7.049A pdb=" N ALA C 121 " --> pdb=" O ASP C 45 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 119 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER C 120 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.565A 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 Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.629A pdb=" N SER C 104 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 106 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 77 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD6, first strand: chain 'C' and resid 219 through 221 Processing sheet with id=AD7, first strand: chain 'C' and resid 300 through 306 removed outlier: 3.535A pdb=" N SER C 300 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.656A pdb=" N TYR O 297 " --> pdb=" O HIS O 307 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.655A 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: 4.155A pdb=" N GLU D 30 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS D 132 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 36 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER D 130 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU D 38 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N SER D 128 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 15 through 19 Processing sheet with id=AE4, first strand: chain 'D' and resid 42 through 48 removed outlier: 7.109A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 120 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AE6, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.622A pdb=" N SER D 104 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS D 79 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 106 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AE9, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AF1, first strand: chain 'D' and resid 296 through 306 removed outlier: 6.710A pdb=" N THR D 321 " --> pdb=" O THR D 297 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET D 299 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS D 319 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N CYS D 301 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE D 317 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N VAL D 303 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL D 315 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 350 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 343 through 346 removed outlier: 3.524A pdb=" N PHE D 365 " --> pdb=" O CYS D 376 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 337 through 339 Processing sheet with id=AF4, first strand: chain 'D' and resid 387 through 388 removed outlier: 3.685A pdb=" N TYR P 297 " --> pdb=" O HIS P 307 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 17 through 19 removed outlier: 3.639A pdb=" N ALA M 17 " --> pdb=" O SER M 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS M 28 " --> pdb=" O CYS M 19 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 74 through 79 removed outlier: 3.585A pdb=" N THR M 74 " --> pdb=" O ASP M 71 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS M 66 " --> pdb=" O GLY M 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN M 53 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET M 70 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N SER M 51 " --> pdb=" O MET M 70 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS M 99 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N LEU M 52 " --> pdb=" O MET M 97 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N MET M 97 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N ILE M 54 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N GLY M 95 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 16.920A pdb=" N ILE M 56 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 19.818A pdb=" N ILE M 93 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 84 through 86 removed outlier: 4.335A pdb=" N GLU M 109 " --> pdb=" O PHE M 129 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 149 through 156 removed outlier: 3.727A pdb=" N THR M 155 " --> pdb=" O ALA M 262 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 166 through 170 removed outlier: 4.068A pdb=" N GLY M 253 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 175 through 176 removed outlier: 3.629A pdb=" N HIS M 226 " --> pdb=" O LYS M 200 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR M 199 " --> pdb=" O GLY M 209 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY M 209 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 182 through 184 removed outlier: 3.923A pdb=" N VAL M 188 " --> pdb=" O ILE M 217 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS M 215 " --> pdb=" O ILE M 190 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 275 through 279 removed outlier: 3.800A pdb=" N GLN M 282 " --> pdb=" O GLY M 279 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS M 315 " --> pdb=" O LEU M 287 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.563A pdb=" N ALA N 17 " --> pdb=" O SER N 30 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 34 through 38 removed outlier: 8.887A pdb=" N LEU N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER N 51 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN N 49 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 10.724A pdb=" N SER N 51 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET N 70 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN N 53 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS N 66 " --> pdb=" O GLY N 55 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 34 through 38 removed outlier: 8.887A pdb=" N LEU N 34 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER N 51 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ARG N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN N 49 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LEU N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N MET N 97 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 10.161A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.486A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 17.070A pdb=" N ILE N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 19.967A pdb=" N ILE N 93 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.452A pdb=" N GLU N 109 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE N 129 " --> pdb=" O GLU N 109 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 148 through 156 Processing sheet with id=AG9, first strand: chain 'N' and resid 236 through 237 removed outlier: 4.181A pdb=" N GLY N 253 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 175 through 176 removed outlier: 4.148A pdb=" N TYR N 199 " --> pdb=" O GLY N 209 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY N 209 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 181 through 184 removed outlier: 3.580A pdb=" N ASN N 187 " --> pdb=" O GLN N 184 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL N 188 " --> pdb=" O ILE N 217 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS N 215 " --> pdb=" O ILE N 190 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.700A pdb=" N GLN N 282 " --> pdb=" O GLY N 279 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS N 315 " --> pdb=" O LEU N 287 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'O' and resid 17 through 19 removed outlier: 3.542A pdb=" N ALA O 17 " --> pdb=" O SER O 30 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS O 28 " --> pdb=" O CYS O 19 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 34 through 38 removed outlier: 5.266A pdb=" N GLN O 49 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE O 37 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS O 47 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 10.618A pdb=" N SER O 51 " --> pdb=" O MET O 70 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET O 70 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LYS O 66 " --> pdb=" O GLY O 55 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR O 74 " --> pdb=" O ASP O 71 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 34 through 38 removed outlier: 5.266A pdb=" N GLN O 49 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE O 37 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS O 47 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA O 103 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS O 99 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU O 52 " --> pdb=" O MET O 97 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N MET O 97 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N ILE O 54 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.527A pdb=" N GLY O 95 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 17.231A pdb=" N ILE O 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 20.047A pdb=" N ILE O 93 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 84 through 86 removed outlier: 4.353A pdb=" N GLU O 109 " --> pdb=" O PHE O 129 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 149 through 156 Processing sheet with id=AH9, first strand: chain 'O' and resid 236 through 237 removed outlier: 4.234A pdb=" N GLY O 253 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 175 through 176 removed outlier: 3.855A pdb=" N TYR O 199 " --> pdb=" O GLY O 209 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY O 209 " --> pdb=" O TYR O 199 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'O' and resid 181 through 184 removed outlier: 3.629A pdb=" N ASN O 187 " --> pdb=" O GLN O 184 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL O 188 " --> pdb=" O ILE O 217 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS O 215 " --> pdb=" O ILE O 190 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 275 through 279 removed outlier: 3.584A pdb=" N GLN O 282 " --> pdb=" O GLY O 279 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS O 315 " --> pdb=" O LEU O 287 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 17 through 19 removed outlier: 3.707A pdb=" N CYS P 28 " --> pdb=" O CYS P 19 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'P' and resid 74 through 79 removed outlier: 3.579A pdb=" N THR P 74 " --> pdb=" O ASP P 71 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS P 66 " --> pdb=" O GLY P 55 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN P 53 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET P 70 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 10.700A pdb=" N SER P 51 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N HIS P 99 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N LEU P 52 " --> pdb=" O MET P 97 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N MET P 97 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N ILE P 54 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N GLY P 95 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 17.066A pdb=" N ILE P 56 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 19.906A pdb=" N ILE P 93 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'P' and resid 84 through 86 removed outlier: 4.336A pdb=" N GLU P 109 " --> pdb=" O PHE P 129 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'P' and resid 149 through 156 removed outlier: 3.602A pdb=" N THR P 155 " --> pdb=" O ALA P 262 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'P' and resid 236 through 237 removed outlier: 4.038A pdb=" N GLY P 253 " --> pdb=" O VAL P 169 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'P' and resid 175 through 176 removed outlier: 3.521A pdb=" N THR P 175 " --> pdb=" O VAL P 229 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'P' and resid 181 through 184 removed outlier: 3.907A pdb=" N VAL P 188 " --> pdb=" O ILE P 217 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE P 217 " --> pdb=" O VAL P 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE P 190 " --> pdb=" O LYS P 215 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS P 215 " --> pdb=" O ILE P 190 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'P' and resid 197 through 200 removed outlier: 3.840A pdb=" N TYR P 199 " --> pdb=" O GLY P 209 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY P 209 " --> pdb=" O TYR P 199 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 275 through 279 removed outlier: 3.641A pdb=" N GLN P 282 " --> pdb=" O GLY P 279 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS P 315 " --> pdb=" O LEU P 287 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Q' and resid 143 through 144 removed outlier: 6.834A pdb=" N PHE Q 115 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR Q 126 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL Q 117 " --> pdb=" O MET Q 124 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR Q 126 " --> pdb=" O PRO Q 137 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU Q 162 " --> pdb=" O SER Q 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER Q 157 " --> pdb=" O LEU Q 162 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS Q 164 " --> pdb=" O LYS Q 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS Q 155 " --> pdb=" O CYS Q 164 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Q' and resid 249 through 253 removed outlier: 6.916A pdb=" N ALA Q 239 " --> pdb=" O GLY Q 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY Q 231 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER Q 241 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TRP Q 245 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL Q 225 " --> pdb=" O TRP Q 245 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA Q 226 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY Q 185 " --> pdb=" O TYR Q 196 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N ALA Q 193 " --> pdb=" O PRO Q 204 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER Q 197 " --> pdb=" O ARG Q 200 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG Q 200 " --> pdb=" O SER Q 197 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N PHE Q 201 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 240 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 143 through 144 removed outlier: 4.103A pdb=" N GLY R 125 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS R 119 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL R 123 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TYR R 126 " --> pdb=" O PRO R 137 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU R 162 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER R 157 " --> pdb=" O LEU R 162 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS R 164 " --> pdb=" O LYS R 155 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 249 through 253 removed outlier: 3.604A pdb=" N ILE R 249 " --> pdb=" O ASN R 246 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA R 239 " --> pdb=" O GLY R 231 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY R 231 " --> pdb=" O ALA R 239 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER R 241 " --> pdb=" O LEU R 229 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP R 245 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL R 225 " --> pdb=" O TRP R 245 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE R 217 " --> pdb=" O VAL R 225 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY R 185 " --> pdb=" O TYR R 196 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N ALA R 193 " --> pdb=" O PRO R 204 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE R 201 " --> pdb=" O LEU R 240 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'S' and resid 143 through 144 removed outlier: 6.929A pdb=" N PHE S 115 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR S 126 " --> pdb=" O PHE S 115 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL S 117 " --> pdb=" O MET S 124 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR S 126 " --> pdb=" O PRO S 137 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU S 162 " --> pdb=" O SER S 157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER S 157 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N CYS S 164 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS S 155 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'S' and resid 249 through 253 removed outlier: 3.566A pdb=" N THR S 251 " --> pdb=" O THR S 244 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 241 " --> pdb=" O GLY S 230 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY S 230 " --> pdb=" O SER S 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL S 243 " --> pdb=" O VAL S 228 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL S 228 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N TRP S 245 " --> pdb=" O ALA S 226 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA S 226 " --> pdb=" O TRP S 245 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE S 217 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN S 188 " --> pdb=" O PHE S 218 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY S 185 " --> pdb=" O TYR S 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR S 196 " --> pdb=" O GLY S 185 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N ALA S 193 " --> pdb=" O PRO S 204 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE S 201 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'T' and resid 143 through 144 removed outlier: 6.666A pdb=" N PHE T 115 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR T 126 " --> pdb=" O PHE T 115 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL T 117 " --> pdb=" O MET T 124 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N TYR T 126 " --> pdb=" O PRO T 137 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU T 162 " --> pdb=" O SER T 157 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER T 157 " --> pdb=" O LEU T 162 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'T' and resid 250 through 253 removed outlier: 4.309A pdb=" N GLY T 230 " --> pdb=" O SER T 241 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL T 243 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL T 228 " --> pdb=" O VAL T 243 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TRP T 245 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ALA T 226 " --> pdb=" O TRP T 245 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE T 217 " --> pdb=" O VAL T 225 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE T 218 " --> pdb=" O ASN T 188 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN T 188 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ALA T 193 " --> pdb=" O PRO T 204 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE T 201 " --> pdb=" O LEU T 240 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE T 203 " --> pdb=" O THR T 238 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.328A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AK6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AK7, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.617A pdb=" N TYR H 60 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA H 100 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 117 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.617A pdb=" N TYR H 60 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP H 38 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR H 52 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA H 100 " --> pdb=" O TYR H 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 122 " --> pdb=" O TYR H 95 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'V' and resid 3 through 7 Processing sheet with id=AL1, first strand: chain 'V' and resid 11 through 12 Processing sheet with id=AL2, first strand: chain 'V' and resid 59 through 61 removed outlier: 3.502A pdb=" N TYR V 60 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP V 38 " --> pdb=" O ILE V 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR V 52 " --> pdb=" O TRP V 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP V 36 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA V 100 " --> pdb=" O TYR V 35 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER V 117 " --> pdb=" O ARG V 99 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'V' and resid 59 through 61 removed outlier: 3.502A pdb=" N TYR V 60 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP V 38 " --> pdb=" O ILE V 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR V 52 " --> pdb=" O TRP V 36 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP V 36 " --> pdb=" O TYR V 52 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA V 100 " --> pdb=" O TYR V 35 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR V 122 " --> pdb=" O TYR V 95 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'U' and resid 4 through 7 removed outlier: 3.834A pdb=" N VAL U 19 " --> pdb=" O ILE U 75 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP U 70 " --> pdb=" O SER U 67 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'U' and resid 10 through 13 removed outlier: 6.326A pdb=" N VAL U 11 " --> pdb=" O GLU U 105 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU U 33 " --> pdb=" O TYR U 49 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N TYR U 49 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP U 35 " --> pdb=" O LEU U 47 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'X' and resid 3 through 7 removed outlier: 3.605A pdb=" N PHE X 80 " --> pdb=" O CYS X 22 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'X' and resid 11 through 12 Processing sheet with id=AL8, first strand: chain 'X' and resid 59 through 61 removed outlier: 3.672A pdb=" N TYR X 60 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP X 38 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR X 52 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP X 36 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA X 100 " --> pdb=" O TYR X 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER X 117 " --> pdb=" O ARG X 99 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'X' and resid 59 through 61 removed outlier: 3.672A pdb=" N TYR X 60 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP X 38 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR X 52 " --> pdb=" O TRP X 36 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP X 36 " --> pdb=" O TYR X 52 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA X 100 " --> pdb=" O TYR X 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR X 122 " --> pdb=" O TYR X 95 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'W' and resid 4 through 7 removed outlier: 3.827A pdb=" N VAL W 19 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'W' and resid 10 through 13 removed outlier: 7.277A pdb=" N LEU W 33 " --> pdb=" O TYR W 49 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR W 49 " --> pdb=" O LEU W 33 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'Z' and resid 3 through 7 removed outlier: 3.636A pdb=" N PHE Z 80 " --> pdb=" O CYS Z 22 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER Z 81 " --> pdb=" O SER Z 72 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'Z' and resid 11 through 12 Processing sheet with id=AM5, first strand: chain 'Z' and resid 59 through 61 removed outlier: 3.699A pdb=" N TYR Z 60 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR Z 52 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP Z 38 " --> pdb=" O ILE Z 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR Z 52 " --> pdb=" O TRP Z 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP Z 36 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA Z 100 " --> pdb=" O TYR Z 35 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER Z 117 " --> pdb=" O ARG Z 99 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'Z' and resid 59 through 61 removed outlier: 3.699A pdb=" N TYR Z 60 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR Z 52 " --> pdb=" O TYR Z 60 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TRP Z 38 " --> pdb=" O ILE Z 50 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR Z 52 " --> pdb=" O TRP Z 36 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP Z 36 " --> pdb=" O TYR Z 52 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA Z 100 " --> pdb=" O TYR Z 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR Z 122 " --> pdb=" O TYR Z 95 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.792A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP Y 70 " --> pdb=" O SER Y 67 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.535A pdb=" N ALA Y 13 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) 1407 hydrogen bonds defined for protein. 3606 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.28 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 12383 1.35 - 1.47: 10043 1.47 - 1.60: 16422 1.60 - 1.73: 0 1.73 - 1.85: 348 Bond restraints: 39196 Sorted by residual: bond pdb=" CB PRO R 255 " pdb=" CG PRO R 255 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.33e+00 bond pdb=" CB CYS B 94 " pdb=" SG CYS B 94 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.29e+00 bond pdb=" CB PRO Q 204 " pdb=" CG PRO Q 204 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.26e+00 bond pdb=" CB CYS B 62 " pdb=" SG CYS B 62 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.13e+00 bond pdb=" C1 NAG N 501 " pdb=" O5 NAG N 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.33e+00 ... (remaining 39191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 52977 2.58 - 5.17: 373 5.17 - 7.75: 40 7.75 - 10.34: 11 10.34 - 12.92: 3 Bond angle restraints: 53404 Sorted by residual: angle pdb=" CA CYS M 153 " pdb=" CB CYS M 153 " pdb=" SG CYS M 153 " ideal model delta sigma weight residual 114.40 124.85 -10.45 2.30e+00 1.89e-01 2.07e+01 angle pdb=" CA CYS P 153 " pdb=" CB CYS P 153 " pdb=" SG CYS P 153 " ideal model delta sigma weight residual 114.40 124.67 -10.27 2.30e+00 1.89e-01 1.99e+01 angle pdb=" CA CYS A 63 " pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " ideal model delta sigma weight residual 114.40 124.32 -9.92 2.30e+00 1.89e-01 1.86e+01 angle pdb=" CA PRO Q 204 " pdb=" N PRO Q 204 " pdb=" CD PRO Q 204 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA ASP D 97 " pdb=" CB ASP D 97 " pdb=" CG ASP D 97 " ideal model delta sigma weight residual 112.60 116.71 -4.11 1.00e+00 1.00e+00 1.69e+01 ... (remaining 53399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 21805 18.04 - 36.09: 1400 36.09 - 54.13: 369 54.13 - 72.18: 73 72.18 - 90.22: 33 Dihedral angle restraints: 23680 sinusoidal: 9352 harmonic: 14328 Sorted by residual: 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 -173.04 87.04 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS B 62 " pdb=" SG CYS B 62 " pdb=" SG CYS B 94 " pdb=" CB CYS B 94 " ideal model delta sinusoidal sigma weight residual -86.00 -141.48 55.48 1 1.00e+01 1.00e-02 4.16e+01 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 93.00 148.23 -55.23 1 1.00e+01 1.00e-02 4.12e+01 ... (remaining 23677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5276 0.072 - 0.144: 731 0.144 - 0.215: 21 0.215 - 0.287: 3 0.287 - 0.359: 5 Chirality restraints: 6036 Sorted by residual: 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 -2.04 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1 NAG O 501 " pdb=" ND2 ASN O 263 " pdb=" C2 NAG O 501 " pdb=" O5 NAG O 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+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 -2.05 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 6033 not shown) Planarity restraints: 6860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS S 136 " -0.087 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO S 137 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO S 137 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO S 137 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 203 " -0.085 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO Q 204 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO Q 204 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO Q 204 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL O 321 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO O 322 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO O 322 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO O 322 " -0.059 5.00e-02 4.00e+02 ... (remaining 6857 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 514 2.67 - 3.23: 31748 3.23 - 3.79: 50884 3.79 - 4.34: 64764 4.34 - 4.90: 114690 Nonbonded interactions: 262600 Sorted by model distance: nonbonded pdb=" OD1 ASP O 117 " pdb=" N SER O 118 " model vdw 2.116 3.120 nonbonded pdb=" OD1 ASP M 117 " pdb=" N SER M 118 " model vdw 2.163 3.120 nonbonded pdb=" OG SER A 57 " pdb=" O VAL M 242 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 10 " pdb=" OH TYR A 15 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR N 69 " pdb=" OD1 ASP N 117 " model vdw 2.213 3.040 ... (remaining 262595 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: 2.760 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 40.670 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.091 39280 Z= 0.139 Angle : 0.626 12.921 53584 Z= 0.330 Chirality : 0.047 0.359 6036 Planarity : 0.007 0.131 6848 Dihedral : 13.244 90.223 14296 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.10 % Allowed : 11.53 % Favored : 88.38 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.11), residues: 4916 helix: 1.48 (0.24), residues: 409 sheet: 0.25 (0.12), residues: 1734 loop : -0.70 (0.10), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 267 TYR 0.020 0.001 TYR D 59 PHE 0.027 0.002 PHE B 95 TRP 0.018 0.001 TRP Q 189 HIS 0.008 0.001 HIS Q 170 Details of bonding type rmsd covalent geometry : bond 0.00306 (39196) covalent geometry : angle 0.61790 (53404) SS BOND : bond 0.00493 ( 72) SS BOND : angle 1.47368 ( 144) hydrogen bonds : bond 0.32140 ( 1322) hydrogen bonds : angle 8.54848 ( 3606) link_NAG-ASN : bond 0.00503 ( 12) link_NAG-ASN : angle 2.87432 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 716 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 28 CYS cc_start: 0.7127 (p) cc_final: 0.6655 (p) REVERT: O 24 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7138 (mm-30) REVERT: P 24 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7171 (mm-30) REVERT: P 200 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8162 (ttmm) REVERT: P 223 ASP cc_start: 0.7334 (t0) cc_final: 0.6950 (t0) REVERT: Q 132 ASP cc_start: 0.6823 (p0) cc_final: 0.6516 (p0) REVERT: S 172 LYS cc_start: 0.7813 (tttt) cc_final: 0.7570 (tttt) outliers start: 4 outliers final: 2 residues processed: 719 average time/residue: 0.2564 time to fit residues: 293.6811 Evaluate side-chains 677 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 675 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain O residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.3980 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 186 ASN A 222 GLN A 389 ASN C 252 GLN C 439 HIS D 230 HIS M 158 GLN M 184 GLN M 234 ASN M 273 ASN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN N 53 GLN N 184 GLN N 226 HIS N 234 ASN N 273 ASN O 53 GLN O 193 ASN P 183 GLN P 184 GLN P 193 ASN P 273 ASN P 299 ASN P 302 GLN ** Q 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS R 139 HIS S 190 HIS S 220 ASN T 190 HIS L 92 ASN Y 92 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116374 restraints weight = 61991.889| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.26 r_work: 0.3238 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 39280 Z= 0.196 Angle : 0.653 9.948 53584 Z= 0.360 Chirality : 0.048 0.321 6036 Planarity : 0.007 0.086 6848 Dihedral : 5.541 53.539 5606 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.14 % Allowed : 11.17 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.11), residues: 4916 helix: 1.32 (0.24), residues: 460 sheet: 0.27 (0.12), residues: 1728 loop : -0.99 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 223 TYR 0.017 0.002 TYR D 122 PHE 0.024 0.002 PHE R 201 TRP 0.019 0.002 TRP O 330 HIS 0.011 0.002 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00446 (39196) covalent geometry : angle 0.64634 (53404) SS BOND : bond 0.00426 ( 72) SS BOND : angle 1.16557 ( 144) hydrogen bonds : bond 0.08973 ( 1322) hydrogen bonds : angle 6.28148 ( 3606) link_NAG-ASN : bond 0.00502 ( 12) link_NAG-ASN : angle 2.94866 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 666 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7761 (ttm-80) REVERT: M 147 HIS cc_start: 0.7561 (t-170) cc_final: 0.7003 (t-90) REVERT: M 223 ASP cc_start: 0.7382 (t0) cc_final: 0.6896 (t0) REVERT: M 324 GLU cc_start: 0.8026 (mp0) cc_final: 0.7624 (mp0) REVERT: N 188 VAL cc_start: 0.8043 (m) cc_final: 0.7775 (m) REVERT: N 344 THR cc_start: 0.8719 (t) cc_final: 0.8403 (p) REVERT: N 357 LEU cc_start: 0.8222 (tp) cc_final: 0.8013 (tp) REVERT: N 375 SER cc_start: 0.8379 (t) cc_final: 0.8080 (m) REVERT: N 379 LEU cc_start: 0.8273 (mm) cc_final: 0.8042 (mt) REVERT: N 382 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8382 (p) REVERT: O 24 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7297 (mm-30) REVERT: O 64 TRP cc_start: 0.7231 (p-90) cc_final: 0.6563 (p-90) REVERT: O 87 THR cc_start: 0.7498 (p) cc_final: 0.7175 (t) REVERT: O 181 MET cc_start: 0.8474 (mtm) cc_final: 0.8248 (mtt) REVERT: O 199 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.8084 (p90) REVERT: O 366 MET cc_start: 0.7264 (mpp) cc_final: 0.6996 (mpp) REVERT: O 394 ARG cc_start: 0.8807 (ttm110) cc_final: 0.8583 (ttm-80) REVERT: P 223 ASP cc_start: 0.7515 (t0) cc_final: 0.7146 (t0) REVERT: Q 118 LYS cc_start: 0.6345 (mttt) cc_final: 0.6139 (tttt) REVERT: Q 132 ASP cc_start: 0.6985 (p0) cc_final: 0.6738 (p0) REVERT: R 172 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8198 (mttp) REVERT: T 171 MET cc_start: 0.8567 (mtp) cc_final: 0.8356 (mtp) REVERT: T 194 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7437 (m) outliers start: 90 outliers final: 56 residues processed: 708 average time/residue: 0.2527 time to fit residues: 286.5773 Evaluate side-chains 716 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 657 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 390 VAL Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 199 TYR Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 380 SER Chi-restraints excluded: chain O residue 381 MET Chi-restraints excluded: chain O residue 386 VAL Chi-restraints excluded: chain O residue 411 LEU Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 199 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 242 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain T residue 194 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 162 optimal weight: 4.9990 chunk 470 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 409 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 196 optimal weight: 7.9990 chunk 319 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 131 HIS O 184 GLN O 193 ASN P 131 HIS P 193 ASN R 170 HIS Z 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.115940 restraints weight = 62144.887| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.26 r_work: 0.3225 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 39280 Z= 0.199 Angle : 0.641 7.983 53584 Z= 0.351 Chirality : 0.048 0.337 6036 Planarity : 0.007 0.072 6848 Dihedral : 5.566 53.421 5605 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.40 % Allowed : 12.64 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.11), residues: 4916 helix: 1.19 (0.25), residues: 460 sheet: 0.21 (0.13), residues: 1674 loop : -1.21 (0.10), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 223 TYR 0.018 0.002 TYR D 51 PHE 0.026 0.002 PHE R 201 TRP 0.018 0.002 TRP O 330 HIS 0.027 0.002 HIS R 139 Details of bonding type rmsd covalent geometry : bond 0.00468 (39196) covalent geometry : angle 0.63408 (53404) SS BOND : bond 0.00541 ( 72) SS BOND : angle 1.22675 ( 144) hydrogen bonds : bond 0.08120 ( 1322) hydrogen bonds : angle 5.80356 ( 3606) link_NAG-ASN : bond 0.00453 ( 12) link_NAG-ASN : angle 3.06526 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 675 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 155 THR cc_start: 0.8364 (p) cc_final: 0.8025 (m) REVERT: C 123 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7822 (ttm-80) REVERT: C 210 SER cc_start: 0.8473 (m) cc_final: 0.8189 (m) REVERT: C 303 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7956 (p) REVERT: D 95 PHE cc_start: 0.7982 (t80) cc_final: 0.7766 (t80) REVERT: D 130 SER cc_start: 0.8726 (p) cc_final: 0.8282 (m) REVERT: D 188 ASP cc_start: 0.8152 (t0) cc_final: 0.7902 (t0) REVERT: D 362 SER cc_start: 0.8576 (t) cc_final: 0.8323 (p) REVERT: M 223 ASP cc_start: 0.7393 (t0) cc_final: 0.6921 (t0) REVERT: M 324 GLU cc_start: 0.8063 (mp0) cc_final: 0.7672 (mp0) REVERT: N 24 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7501 (mp0) REVERT: N 188 VAL cc_start: 0.8020 (m) cc_final: 0.7751 (m) REVERT: N 291 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7066 (p-80) REVERT: N 344 THR cc_start: 0.8756 (t) cc_final: 0.8389 (p) REVERT: N 357 LEU cc_start: 0.8155 (tp) cc_final: 0.7938 (tp) REVERT: N 375 SER cc_start: 0.8353 (t) cc_final: 0.8095 (m) REVERT: N 382 VAL cc_start: 0.8507 (p) cc_final: 0.8295 (p) REVERT: O 24 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7489 (mm-30) REVERT: O 64 TRP cc_start: 0.7242 (p-90) cc_final: 0.6607 (p-90) REVERT: O 87 THR cc_start: 0.7533 (p) cc_final: 0.7166 (t) REVERT: O 181 MET cc_start: 0.8517 (mtm) cc_final: 0.8290 (mtt) REVERT: O 195 GLN cc_start: 0.7996 (mt0) cc_final: 0.7719 (mt0) REVERT: O 199 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7990 (p90) REVERT: O 394 ARG cc_start: 0.8802 (ttm110) cc_final: 0.8592 (ttm170) REVERT: O 401 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7628 (tt0) REVERT: O 412 LEU cc_start: 0.7190 (mm) cc_final: 0.6906 (mp) REVERT: P 24 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7546 (mt-10) REVERT: P 52 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7573 (pp) REVERT: P 223 ASP cc_start: 0.7425 (t0) cc_final: 0.7092 (t0) REVERT: P 418 VAL cc_start: 0.6200 (t) cc_final: 0.5976 (p) REVERT: Q 156 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7746 (ptm-80) REVERT: Q 171 MET cc_start: 0.8056 (mpp) cc_final: 0.7815 (mmt) REVERT: R 172 LYS cc_start: 0.8463 (mtmm) cc_final: 0.7965 (mttp) REVERT: T 171 MET cc_start: 0.8534 (mtp) cc_final: 0.8329 (mtp) outliers start: 101 outliers final: 72 residues processed: 727 average time/residue: 0.2474 time to fit residues: 290.2272 Evaluate side-chains 720 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 644 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 347 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 181 MET Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 390 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 199 TYR Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 36 ARG 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 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 251 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 438 optimal weight: 0.0170 chunk 209 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 440 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 310 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 412 optimal weight: 6.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN N 183 GLN O 53 GLN O 183 GLN P 193 ASN R 139 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.118086 restraints weight = 62344.720| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.29 r_work: 0.3265 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39280 Z= 0.133 Angle : 0.558 9.006 53584 Z= 0.300 Chirality : 0.045 0.332 6036 Planarity : 0.006 0.062 6848 Dihedral : 5.242 52.815 5605 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.42 % Allowed : 13.71 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.11), residues: 4916 helix: 1.32 (0.25), residues: 462 sheet: 0.19 (0.12), residues: 1790 loop : -1.26 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 223 TYR 0.011 0.001 TYR A 242 PHE 0.015 0.001 PHE S 201 TRP 0.014 0.001 TRP H 49 HIS 0.006 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00284 (39196) covalent geometry : angle 0.55233 (53404) SS BOND : bond 0.00373 ( 72) SS BOND : angle 0.88323 ( 144) hydrogen bonds : bond 0.06395 ( 1322) hydrogen bonds : angle 5.32330 ( 3606) link_NAG-ASN : bond 0.00596 ( 12) link_NAG-ASN : angle 2.89182 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 659 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8198 (t0) cc_final: 0.7803 (t0) REVERT: B 35 SER cc_start: 0.8469 (p) cc_final: 0.8162 (m) REVERT: B 155 THR cc_start: 0.8314 (p) cc_final: 0.8009 (m) REVERT: C 210 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8198 (m) REVERT: C 303 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7882 (p) REVERT: D 130 SER cc_start: 0.8730 (p) cc_final: 0.8288 (m) REVERT: D 428 LEU cc_start: 0.8624 (tp) cc_final: 0.8416 (tt) REVERT: M 223 ASP cc_start: 0.7380 (t0) cc_final: 0.6940 (t0) REVERT: M 324 GLU cc_start: 0.8018 (mp0) cc_final: 0.7665 (mp0) REVERT: M 384 THR cc_start: 0.8701 (m) cc_final: 0.8495 (t) REVERT: M 394 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7989 (ttm-80) REVERT: N 24 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7489 (mp0) REVERT: N 188 VAL cc_start: 0.8018 (m) cc_final: 0.7718 (m) REVERT: N 291 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.6933 (p-80) REVERT: N 357 LEU cc_start: 0.8182 (tp) cc_final: 0.7966 (tp) REVERT: N 382 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8129 (p) REVERT: O 24 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7506 (mm-30) REVERT: O 64 TRP cc_start: 0.7218 (p-90) cc_final: 0.6578 (p-90) REVERT: O 181 MET cc_start: 0.8530 (mtm) cc_final: 0.8313 (mtt) REVERT: O 195 GLN cc_start: 0.7914 (mt0) cc_final: 0.7639 (mt0) REVERT: O 223 ASP cc_start: 0.8163 (t0) cc_final: 0.7842 (t0) REVERT: O 382 VAL cc_start: 0.8618 (t) cc_final: 0.8344 (p) REVERT: O 394 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8524 (ttm170) REVERT: O 401 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7721 (tt0) REVERT: P 24 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7544 (mt-10) REVERT: P 158 GLN cc_start: 0.8246 (mt0) cc_final: 0.8026 (mt0) REVERT: P 181 MET cc_start: 0.7756 (mtt) cc_final: 0.7530 (mtt) REVERT: P 223 ASP cc_start: 0.7380 (t0) cc_final: 0.7068 (t0) REVERT: P 265 THR cc_start: 0.8702 (p) cc_final: 0.8455 (m) REVERT: P 305 ASN cc_start: 0.8047 (m-40) cc_final: 0.7774 (t0) REVERT: P 418 VAL cc_start: 0.5988 (t) cc_final: 0.5721 (p) REVERT: Q 156 ARG cc_start: 0.8120 (ptm-80) cc_final: 0.7812 (ptm-80) REVERT: Q 171 MET cc_start: 0.7976 (mpp) cc_final: 0.7773 (mmt) REVERT: R 172 LYS cc_start: 0.8339 (mtmm) cc_final: 0.7834 (mttp) REVERT: T 171 MET cc_start: 0.8500 (mtp) cc_final: 0.8291 (mtp) outliers start: 102 outliers final: 71 residues processed: 713 average time/residue: 0.2499 time to fit residues: 287.4454 Evaluate side-chains 730 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 655 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 228 THR 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 M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 182 THR Chi-restraints excluded: chain O residue 198 ARG Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 136 ILE Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 391 CYS Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 248 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 407 optimal weight: 0.0060 chunk 412 optimal weight: 5.9990 chunk 459 optimal weight: 50.0000 chunk 52 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 384 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 184 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN P 127 HIS P 193 ASN P 302 GLN R 119 HIS R 139 HIS S 191 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113899 restraints weight = 62775.161| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.41 r_work: 0.3187 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 39280 Z= 0.240 Angle : 0.676 11.484 53584 Z= 0.368 Chirality : 0.050 0.397 6036 Planarity : 0.007 0.070 6848 Dihedral : 5.670 53.911 5605 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.23 % Allowed : 14.31 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.11), residues: 4916 helix: 1.04 (0.25), residues: 462 sheet: 0.21 (0.13), residues: 1663 loop : -1.55 (0.10), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 223 TYR 0.024 0.002 TYR D 51 PHE 0.036 0.002 PHE R 201 TRP 0.018 0.002 TRP O 330 HIS 0.032 0.002 HIS R 139 Details of bonding type rmsd covalent geometry : bond 0.00587 (39196) covalent geometry : angle 0.66918 (53404) SS BOND : bond 0.00495 ( 72) SS BOND : angle 1.26111 ( 144) hydrogen bonds : bond 0.07953 ( 1322) hydrogen bonds : angle 5.47595 ( 3606) link_NAG-ASN : bond 0.00423 ( 12) link_NAG-ASN : angle 3.20745 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 691 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 THR cc_start: 0.7178 (m) cc_final: 0.5559 (t) REVERT: B 155 THR cc_start: 0.8361 (p) cc_final: 0.8093 (m) REVERT: B 290 VAL cc_start: 0.8345 (p) cc_final: 0.8119 (t) REVERT: C 210 SER cc_start: 0.8434 (m) cc_final: 0.8175 (m) REVERT: C 303 VAL cc_start: 0.8145 (OUTLIER) cc_final: 0.7925 (p) REVERT: D 130 SER cc_start: 0.8726 (p) cc_final: 0.8310 (m) REVERT: D 188 ASP cc_start: 0.8192 (t0) cc_final: 0.7910 (t0) REVERT: M 223 ASP cc_start: 0.7475 (t0) cc_final: 0.7043 (t0) REVERT: M 290 ASP cc_start: 0.7259 (m-30) cc_final: 0.6925 (m-30) REVERT: M 394 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.8023 (ttm-80) REVERT: N 24 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7644 (mp0) REVERT: N 43 ASP cc_start: 0.7902 (m-30) cc_final: 0.7425 (p0) REVERT: N 188 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7690 (m) REVERT: N 291 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7312 (p-80) REVERT: N 344 THR cc_start: 0.8713 (t) cc_final: 0.8348 (p) REVERT: N 357 LEU cc_start: 0.8060 (tp) cc_final: 0.7852 (tp) REVERT: N 382 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8289 (p) REVERT: O 24 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7640 (mm-30) REVERT: O 64 TRP cc_start: 0.7304 (p-90) cc_final: 0.6637 (p-90) REVERT: O 87 THR cc_start: 0.7552 (p) cc_final: 0.7141 (t) REVERT: O 181 MET cc_start: 0.8474 (mtm) cc_final: 0.8233 (mtt) REVERT: O 195 GLN cc_start: 0.8099 (mt0) cc_final: 0.7827 (mt0) REVERT: O 223 ASP cc_start: 0.8235 (t0) cc_final: 0.7937 (t0) REVERT: O 393 ARG cc_start: 0.8175 (ttt90) cc_final: 0.7724 (ttt180) REVERT: P 181 MET cc_start: 0.7720 (mtt) cc_final: 0.7454 (mtt) REVERT: P 223 ASP cc_start: 0.7490 (t0) cc_final: 0.7176 (t0) REVERT: P 265 THR cc_start: 0.8731 (p) cc_final: 0.8359 (m) REVERT: P 305 ASN cc_start: 0.8139 (m-40) cc_final: 0.7824 (t0) REVERT: Q 156 ARG cc_start: 0.8124 (ptm-80) cc_final: 0.7842 (ptm-80) REVERT: R 172 LYS cc_start: 0.8473 (mtmm) cc_final: 0.7972 (mttp) outliers start: 136 outliers final: 107 residues processed: 771 average time/residue: 0.2459 time to fit residues: 306.8491 Evaluate side-chains 765 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 654 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR 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 175 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 94 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 280 ILE 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 413 ILE Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 179 THR Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain M residue 411 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 111 LEU Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 390 VAL Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 182 THR Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 36 ARG Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 127 HIS Chi-restraints excluded: chain P residue 160 THR Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 199 TYR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 382 VAL Chi-restraints excluded: chain P residue 391 CYS Chi-restraints excluded: chain P residue 401 GLU Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 164 CYS Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 250 VAL Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 79 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 223 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 307 optimal weight: 0.0170 chunk 264 optimal weight: 0.0010 chunk 147 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 336 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 127 HIS M 184 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN N 341 GLN P 193 ASN Q 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120738 restraints weight = 62928.218| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.31 r_work: 0.3287 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 39280 Z= 0.109 Angle : 0.532 9.927 53584 Z= 0.280 Chirality : 0.044 0.310 6036 Planarity : 0.005 0.058 6848 Dihedral : 5.077 52.718 5605 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.28 % Allowed : 15.38 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.11), residues: 4916 helix: 1.48 (0.26), residues: 460 sheet: 0.23 (0.12), residues: 1775 loop : -1.35 (0.11), residues: 2681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 223 TYR 0.010 0.001 TYR O 9 PHE 0.013 0.001 PHE O 115 TRP 0.013 0.001 TRP H 49 HIS 0.028 0.001 HIS P 127 Details of bonding type rmsd covalent geometry : bond 0.00209 (39196) covalent geometry : angle 0.52522 (53404) SS BOND : bond 0.00352 ( 72) SS BOND : angle 1.00191 ( 144) hydrogen bonds : bond 0.05361 ( 1322) hydrogen bonds : angle 4.99927 ( 3606) link_NAG-ASN : bond 0.00530 ( 12) link_NAG-ASN : angle 2.82143 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 656 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8254 (t0) cc_final: 0.7808 (t0) REVERT: B 155 THR cc_start: 0.8255 (p) cc_final: 0.8010 (m) REVERT: B 290 VAL cc_start: 0.8305 (p) cc_final: 0.8066 (t) REVERT: C 210 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8193 (m) REVERT: C 303 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7807 (p) REVERT: M 24 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7758 (mt-10) REVERT: M 223 ASP cc_start: 0.7292 (t0) cc_final: 0.6910 (t0) REVERT: N 24 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7582 (mp0) REVERT: N 149 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7141 (ttpp) REVERT: N 188 VAL cc_start: 0.7994 (OUTLIER) cc_final: 0.7706 (m) REVERT: N 291 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6974 (p-80) REVERT: N 344 THR cc_start: 0.8689 (t) cc_final: 0.8306 (p) REVERT: N 357 LEU cc_start: 0.8132 (tp) cc_final: 0.7920 (tp) REVERT: O 24 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7485 (mm-30) REVERT: O 64 TRP cc_start: 0.7209 (p-90) cc_final: 0.6588 (p-90) REVERT: O 181 MET cc_start: 0.8497 (mtm) cc_final: 0.8278 (mtt) REVERT: O 195 GLN cc_start: 0.7917 (mt0) cc_final: 0.7629 (mt0) REVERT: O 223 ASP cc_start: 0.8177 (t0) cc_final: 0.7911 (t0) REVERT: O 373 VAL cc_start: 0.8384 (t) cc_final: 0.7964 (m) REVERT: O 382 VAL cc_start: 0.8542 (t) cc_final: 0.8219 (p) REVERT: O 393 ARG cc_start: 0.8262 (ttt90) cc_final: 0.7771 (ttt90) REVERT: O 401 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7841 (tt0) REVERT: P 52 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7438 (pp) REVERT: P 181 MET cc_start: 0.7764 (mtt) cc_final: 0.7523 (mtt) REVERT: P 223 ASP cc_start: 0.7291 (t0) cc_final: 0.7007 (t0) REVERT: P 265 THR cc_start: 0.8734 (p) cc_final: 0.8385 (m) REVERT: P 305 ASN cc_start: 0.7892 (m-40) cc_final: 0.7625 (t0) REVERT: R 172 LYS cc_start: 0.8247 (mtmm) cc_final: 0.7846 (mtmm) REVERT: T 171 MET cc_start: 0.8367 (mtp) cc_final: 0.8165 (mtp) outliers start: 96 outliers final: 62 residues processed: 714 average time/residue: 0.2061 time to fit residues: 239.8065 Evaluate side-chains 720 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 652 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 402 LEU Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 198 ARG Chi-restraints excluded: chain O residue 236 GLN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS 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 127 HIS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 111 ASN Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 139 HIS Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 117 optimal weight: 1.9990 chunk 351 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 430 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 200 optimal weight: 3.9990 chunk 343 optimal weight: 0.0070 chunk 222 optimal weight: 4.9990 chunk 317 optimal weight: 8.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 184 GLN M 307 HIS N 183 GLN P 193 ASN Q 111 ASN R 190 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.120824 restraints weight = 62708.839| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.28 r_work: 0.3291 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 39280 Z= 0.108 Angle : 0.530 13.261 53584 Z= 0.276 Chirality : 0.044 0.307 6036 Planarity : 0.005 0.055 6848 Dihedral : 4.898 52.639 5605 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 15.71 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.12), residues: 4916 helix: 1.63 (0.26), residues: 460 sheet: 0.35 (0.12), residues: 1786 loop : -1.32 (0.11), residues: 2670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 223 TYR 0.014 0.001 TYR S 160 PHE 0.014 0.001 PHE S 115 TRP 0.013 0.001 TRP H 49 HIS 0.013 0.001 HIS P 127 Details of bonding type rmsd covalent geometry : bond 0.00220 (39196) covalent geometry : angle 0.52442 (53404) SS BOND : bond 0.00369 ( 72) SS BOND : angle 0.87369 ( 144) hydrogen bonds : bond 0.05165 ( 1322) hydrogen bonds : angle 4.81090 ( 3606) link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.51824 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 661 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8250 (t0) cc_final: 0.7821 (t0) REVERT: B 155 THR cc_start: 0.8257 (p) cc_final: 0.8038 (m) REVERT: C 210 SER cc_start: 0.8451 (m) cc_final: 0.8196 (m) REVERT: C 303 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7802 (p) REVERT: D 426 LEU cc_start: 0.8769 (tp) cc_final: 0.8565 (tt) REVERT: M 223 ASP cc_start: 0.7256 (t0) cc_final: 0.6871 (t0) REVERT: N 24 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7572 (mp0) REVERT: N 149 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7175 (ttpp) REVERT: N 188 VAL cc_start: 0.7986 (OUTLIER) cc_final: 0.7679 (m) REVERT: N 291 HIS cc_start: 0.7608 (OUTLIER) cc_final: 0.7162 (p-80) REVERT: N 293 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8171 (m) REVERT: N 357 LEU cc_start: 0.8114 (tp) cc_final: 0.7892 (tp) REVERT: O 24 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7423 (mm-30) REVERT: O 64 TRP cc_start: 0.7200 (p-90) cc_final: 0.6576 (p-90) REVERT: O 87 THR cc_start: 0.7435 (p) cc_final: 0.7158 (t) REVERT: O 181 MET cc_start: 0.8534 (mtm) cc_final: 0.8326 (mtt) REVERT: O 195 GLN cc_start: 0.7907 (mt0) cc_final: 0.7635 (mt0) REVERT: O 223 ASP cc_start: 0.8163 (t0) cc_final: 0.7918 (t0) REVERT: O 231 ASN cc_start: 0.7808 (t0) cc_final: 0.7559 (m-40) REVERT: O 366 MET cc_start: 0.6526 (mpp) cc_final: 0.6321 (mpp) REVERT: O 393 ARG cc_start: 0.8234 (ttt90) cc_final: 0.7745 (ttt180) REVERT: P 181 MET cc_start: 0.7798 (mtt) cc_final: 0.7591 (mtt) REVERT: P 223 ASP cc_start: 0.7232 (t0) cc_final: 0.6964 (t0) REVERT: P 265 THR cc_start: 0.8804 (p) cc_final: 0.8462 (m) REVERT: P 330 TRP cc_start: 0.8612 (t-100) cc_final: 0.8360 (t-100) REVERT: R 172 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7880 (mttp) REVERT: T 171 MET cc_start: 0.8372 (mtp) cc_final: 0.8162 (mtp) outliers start: 97 outliers final: 70 residues processed: 719 average time/residue: 0.2093 time to fit residues: 242.6807 Evaluate side-chains 720 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 645 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain M residue 418 VAL Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 59 ASP Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 236 GLN Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 278 optimal weight: 5.9990 chunk 408 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 461 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 427 optimal weight: 6.9990 chunk 423 optimal weight: 20.0000 chunk 224 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 325 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 HIS C 375 HIS ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN N 302 GLN P 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114776 restraints weight = 63229.705| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.38 r_work: 0.3197 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 39280 Z= 0.219 Angle : 0.655 11.232 53584 Z= 0.351 Chirality : 0.049 0.417 6036 Planarity : 0.006 0.063 6848 Dihedral : 5.438 54.398 5605 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.57 % Allowed : 15.83 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.11), residues: 4916 helix: 1.25 (0.25), residues: 462 sheet: 0.25 (0.13), residues: 1671 loop : -1.62 (0.10), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 156 TYR 0.022 0.002 TYR D 51 PHE 0.031 0.002 PHE R 201 TRP 0.015 0.002 TRP N 339 HIS 0.009 0.002 HIS M 18 Details of bonding type rmsd covalent geometry : bond 0.00533 (39196) covalent geometry : angle 0.64801 (53404) SS BOND : bond 0.00509 ( 72) SS BOND : angle 1.25958 ( 144) hydrogen bonds : bond 0.07209 ( 1322) hydrogen bonds : angle 5.16665 ( 3606) link_NAG-ASN : bond 0.00432 ( 12) link_NAG-ASN : angle 3.05632 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 661 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 ASP cc_start: 0.7551 (m-30) cc_final: 0.6893 (p0) REVERT: A 370 CYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6913 (m) REVERT: A 405 THR cc_start: 0.6920 (m) cc_final: 0.5272 (t) REVERT: B 167 SER cc_start: 0.8692 (p) cc_final: 0.8417 (t) REVERT: B 290 VAL cc_start: 0.8221 (p) cc_final: 0.8011 (t) REVERT: C 210 SER cc_start: 0.8430 (OUTLIER) cc_final: 0.8154 (m) REVERT: C 303 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7785 (p) REVERT: C 434 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8066 (p) REVERT: D 130 SER cc_start: 0.8720 (p) cc_final: 0.8303 (m) REVERT: D 188 ASP cc_start: 0.8142 (t0) cc_final: 0.7843 (t0) REVERT: M 24 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7832 (mt-10) REVERT: M 223 ASP cc_start: 0.7355 (t0) cc_final: 0.6951 (t0) REVERT: M 290 ASP cc_start: 0.7221 (m-30) cc_final: 0.6832 (m-30) REVERT: M 394 ARG cc_start: 0.8066 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: N 24 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7613 (mp0) REVERT: N 149 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7330 (ttpp) REVERT: N 188 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7703 (m) REVERT: N 344 THR cc_start: 0.8712 (t) cc_final: 0.8336 (p) REVERT: N 357 LEU cc_start: 0.7914 (tp) cc_final: 0.7710 (tp) REVERT: O 24 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7627 (mm-30) REVERT: O 64 TRP cc_start: 0.7252 (p-90) cc_final: 0.6577 (p-90) REVERT: O 87 THR cc_start: 0.7557 (p) cc_final: 0.7077 (t) REVERT: O 179 THR cc_start: 0.8563 (m) cc_final: 0.8231 (p) REVERT: O 181 MET cc_start: 0.8429 (mtm) cc_final: 0.7908 (mtt) REVERT: O 195 GLN cc_start: 0.8122 (mt0) cc_final: 0.7830 (mt0) REVERT: O 223 ASP cc_start: 0.8262 (t0) cc_final: 0.7984 (t0) REVERT: O 393 ARG cc_start: 0.8123 (ttt90) cc_final: 0.7652 (ttt180) REVERT: P 181 MET cc_start: 0.7639 (mtt) cc_final: 0.7412 (mtt) REVERT: P 223 ASP cc_start: 0.7470 (t0) cc_final: 0.7240 (t0) REVERT: P 265 THR cc_start: 0.8674 (p) cc_final: 0.8284 (m) REVERT: P 305 ASN cc_start: 0.8157 (m-40) cc_final: 0.7833 (t0) REVERT: R 172 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7937 (mttp) outliers start: 108 outliers final: 87 residues processed: 725 average time/residue: 0.2115 time to fit residues: 248.4055 Evaluate side-chains 754 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 661 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 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 370 CYS Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 414 THR Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 236 GLN Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 153 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 236 GLN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 305 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 441 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 296 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS C 375 HIS ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN P 193 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119243 restraints weight = 62296.010| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.26 r_work: 0.3265 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39280 Z= 0.121 Angle : 0.557 11.096 53584 Z= 0.291 Chirality : 0.045 0.360 6036 Planarity : 0.005 0.054 6848 Dihedral : 5.112 53.107 5605 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.42 % Allowed : 16.21 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.11), residues: 4916 helix: 1.51 (0.26), residues: 460 sheet: 0.27 (0.12), residues: 1709 loop : -1.52 (0.11), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 223 TYR 0.022 0.001 TYR S 160 PHE 0.022 0.001 PHE R 178 TRP 0.012 0.001 TRP O 330 HIS 0.006 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00260 (39196) covalent geometry : angle 0.55142 (53404) SS BOND : bond 0.00353 ( 72) SS BOND : angle 0.94307 ( 144) hydrogen bonds : bond 0.05624 ( 1322) hydrogen bonds : angle 4.90606 ( 3606) link_NAG-ASN : bond 0.00498 ( 12) link_NAG-ASN : angle 2.77803 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 654 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8293 (t0) cc_final: 0.7851 (t0) REVERT: A 212 ASP cc_start: 0.7339 (m-30) cc_final: 0.6788 (p0) REVERT: A 370 CYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6797 (m) REVERT: B 167 SER cc_start: 0.8626 (p) cc_final: 0.8307 (t) REVERT: B 290 VAL cc_start: 0.8311 (p) cc_final: 0.8094 (t) REVERT: C 210 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.8183 (m) REVERT: C 303 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7770 (p) REVERT: C 319 LYS cc_start: 0.7816 (mttt) cc_final: 0.7582 (mttm) REVERT: D 130 SER cc_start: 0.8712 (p) cc_final: 0.8290 (m) REVERT: D 188 ASP cc_start: 0.8106 (t0) cc_final: 0.7791 (t0) REVERT: D 211 LYS cc_start: 0.8576 (mmtt) cc_final: 0.8365 (mmtt) REVERT: M 24 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7699 (mt-10) REVERT: M 223 ASP cc_start: 0.7101 (t0) cc_final: 0.6800 (t0) REVERT: N 24 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7609 (mp0) REVERT: N 149 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7225 (ttpp) REVERT: N 188 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7724 (m) REVERT: N 293 THR cc_start: 0.8492 (OUTLIER) cc_final: 0.8163 (m) REVERT: N 344 THR cc_start: 0.8712 (t) cc_final: 0.8320 (p) REVERT: N 357 LEU cc_start: 0.8147 (tp) cc_final: 0.7946 (tp) REVERT: O 24 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7503 (mm-30) REVERT: O 64 TRP cc_start: 0.7247 (p-90) cc_final: 0.6607 (p-90) REVERT: O 87 THR cc_start: 0.7517 (p) cc_final: 0.7026 (t) REVERT: O 179 THR cc_start: 0.8696 (m) cc_final: 0.8410 (p) REVERT: O 181 MET cc_start: 0.8519 (mtm) cc_final: 0.8296 (mtt) REVERT: O 195 GLN cc_start: 0.7988 (mt0) cc_final: 0.7705 (mt0) REVERT: O 223 ASP cc_start: 0.8159 (t0) cc_final: 0.7919 (t0) REVERT: P 181 MET cc_start: 0.7718 (mtt) cc_final: 0.7475 (mtt) REVERT: P 223 ASP cc_start: 0.7250 (t0) cc_final: 0.6997 (t0) REVERT: P 265 THR cc_start: 0.8796 (p) cc_final: 0.8427 (m) REVERT: P 305 ASN cc_start: 0.7970 (m-40) cc_final: 0.7704 (t0) REVERT: R 172 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7881 (mttp) outliers start: 102 outliers final: 84 residues processed: 717 average time/residue: 0.2080 time to fit residues: 241.4604 Evaluate side-chains 747 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 657 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 236 GLN Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 236 GLN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 166 GLU Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 141 LYS Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 227 ILE Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 299 optimal weight: 0.8980 chunk 334 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 462 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 HIS ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN P 193 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.154349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119454 restraints weight = 63317.233| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.40 r_work: 0.3260 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39280 Z= 0.116 Angle : 0.559 13.439 53584 Z= 0.289 Chirality : 0.045 0.332 6036 Planarity : 0.005 0.053 6848 Dihedral : 5.001 53.175 5605 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.19 % Allowed : 16.56 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.12), residues: 4916 helix: 1.63 (0.26), residues: 460 sheet: 0.36 (0.13), residues: 1705 loop : -1.43 (0.11), residues: 2751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 156 TYR 0.012 0.001 TYR N 237 PHE 0.024 0.001 PHE R 178 TRP 0.012 0.001 TRP H 49 HIS 0.007 0.001 HIS C 375 Details of bonding type rmsd covalent geometry : bond 0.00245 (39196) covalent geometry : angle 0.55160 (53404) SS BOND : bond 0.00367 ( 72) SS BOND : angle 1.28458 ( 144) hydrogen bonds : bond 0.05334 ( 1322) hydrogen bonds : angle 4.79626 ( 3606) link_NAG-ASN : bond 0.00459 ( 12) link_NAG-ASN : angle 2.58273 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9832 Ramachandran restraints generated. 4916 Oldfield, 0 Emsley, 4916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 663 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASN cc_start: 0.8285 (t0) cc_final: 0.7799 (t0) REVERT: A 212 ASP cc_start: 0.7511 (m-30) cc_final: 0.6844 (p0) REVERT: B 45 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7624 (t0) REVERT: B 167 SER cc_start: 0.8643 (p) cc_final: 0.8368 (t) REVERT: B 290 VAL cc_start: 0.8139 (p) cc_final: 0.7904 (t) REVERT: B 429 ILE cc_start: 0.8218 (mm) cc_final: 0.7912 (tt) REVERT: C 210 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8095 (m) REVERT: C 303 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7686 (p) REVERT: C 434 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7988 (p) REVERT: D 188 ASP cc_start: 0.8082 (t0) cc_final: 0.7777 (t0) REVERT: D 211 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8348 (mmtt) REVERT: M 24 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7803 (mt-10) REVERT: M 223 ASP cc_start: 0.7254 (t0) cc_final: 0.6918 (t0) REVERT: M 225 CYS cc_start: 0.6809 (m) cc_final: 0.6386 (m) REVERT: N 24 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7523 (mp0) REVERT: N 149 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7130 (ttpp) REVERT: N 188 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7655 (m) REVERT: N 293 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8115 (m) REVERT: N 344 THR cc_start: 0.8692 (t) cc_final: 0.8319 (p) REVERT: N 357 LEU cc_start: 0.7839 (tp) cc_final: 0.7624 (tp) REVERT: O 24 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7523 (mm-30) REVERT: O 64 TRP cc_start: 0.7205 (p-90) cc_final: 0.6533 (p-90) REVERT: O 87 THR cc_start: 0.7392 (p) cc_final: 0.7119 (t) REVERT: O 179 THR cc_start: 0.8592 (m) cc_final: 0.8264 (p) REVERT: O 181 MET cc_start: 0.8431 (mtm) cc_final: 0.8200 (mtt) REVERT: O 195 GLN cc_start: 0.8037 (mt0) cc_final: 0.7715 (mt0) REVERT: O 223 ASP cc_start: 0.8172 (t0) cc_final: 0.7965 (t0) REVERT: O 366 MET cc_start: 0.6631 (mpp) cc_final: 0.6370 (mpp) REVERT: O 382 VAL cc_start: 0.8422 (t) cc_final: 0.8181 (p) REVERT: P 177 ASP cc_start: 0.7956 (t0) cc_final: 0.7723 (t0) REVERT: P 181 MET cc_start: 0.7599 (mtt) cc_final: 0.7365 (mtt) REVERT: P 223 ASP cc_start: 0.7414 (t0) cc_final: 0.7129 (t0) REVERT: P 265 THR cc_start: 0.8658 (p) cc_final: 0.8304 (m) REVERT: P 305 ASN cc_start: 0.8014 (m-40) cc_final: 0.7696 (t0) REVERT: R 172 LYS cc_start: 0.8221 (mtmm) cc_final: 0.7820 (mttp) outliers start: 92 outliers final: 77 residues processed: 723 average time/residue: 0.2154 time to fit residues: 252.7538 Evaluate side-chains 728 residues out of total 4208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 644 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 213 VAL Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 289 ARG Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 94 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 45 THR Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 236 GLN Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 57 LYS Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 149 LYS Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 313 HIS Chi-restraints excluded: chain O residue 54 ILE Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 191 THR Chi-restraints excluded: chain O residue 236 GLN Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 286 LEU Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 87 THR Chi-restraints excluded: chain P residue 91 CYS Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 182 THR Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 347 THR Chi-restraints excluded: chain P residue 349 HIS Chi-restraints excluded: chain P residue 418 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 203 ILE Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 181 GLU Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain S residue 130 VAL Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 203 ILE Chi-restraints excluded: chain Z residue 2 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 348 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 468 optimal weight: 9.9990 chunk 180 optimal weight: 0.3980 chunk 171 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 375 HIS ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.153308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118067 restraints weight = 63292.502| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.43 r_work: 0.3238 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39280 Z= 0.143 Angle : 0.583 10.955 53584 Z= 0.305 Chirality : 0.046 0.412 6036 Planarity : 0.006 0.054 6848 Dihedral : 5.112 53.233 5605 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.26 % Allowed : 16.56 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.12), residues: 4916 helix: 1.59 (0.26), residues: 460 sheet: 0.31 (0.13), residues: 1687 loop : -1.55 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 156 TYR 0.021 0.001 TYR S 160 PHE 0.024 0.001 PHE R 178 TRP 0.013 0.001 TRP O 330 HIS 0.007 0.001 HIS C 375 Details of bonding type rmsd covalent geometry : bond 0.00325 (39196) covalent geometry : angle 0.57522 (53404) SS BOND : bond 0.00400 ( 72) SS BOND : angle 1.39563 ( 144) hydrogen bonds : bond 0.05831 ( 1322) hydrogen bonds : angle 4.85036 ( 3606) link_NAG-ASN : bond 0.00536 ( 12) link_NAG-ASN : angle 2.74607 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12411.81 seconds wall clock time: 212 minutes 5.23 seconds (12725.23 seconds total)