Starting phenix.real_space_refine on Sat Mar 7 03:56:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dww_27763/03_2026/8dww_27763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dww_27763/03_2026/8dww_27763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dww_27763/03_2026/8dww_27763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dww_27763/03_2026/8dww_27763.map" model { file = "/net/cci-nas-00/data/ceres_data/8dww_27763/03_2026/8dww_27763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dww_27763/03_2026/8dww_27763.cif" } resolution = 3.13 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= 0.050 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 23856 2.51 5 N 6520 2.21 5 O 7264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37900 Number of models: 1 Model: "" Number of chains: 28 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: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "V" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "U" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "X" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "W" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "Z" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 911 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Y" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 807 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} 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: "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: "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: "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: "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: "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: "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: "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: "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: "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: 9.08, per 1000 atoms: 0.24 Number of scatterers: 37900 At special positions: 0 Unit cell: (185.6, 212.28, 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 7264 8.00 N 6520 7.00 C 23856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 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=2.04 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 H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 28 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 105 " distance=2.03 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 266 " distance=2.04 Simple disulfide: pdb=" SG CYS N 201 " - pdb=" SG CYS N 225 " distance=2.03 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 220 " distance=2.03 Simple disulfide: pdb=" SG CYS N 396 " - pdb=" SG CYS N 417 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 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 V 22 " - pdb=" SG CYS V 96 " distance=2.04 Simple disulfide: pdb=" SG CYS U 23 " - pdb=" SG CYS U 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 125 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 28 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 105 " distance=2.04 Simple disulfide: pdb=" SG CYS M 153 " - pdb=" SG CYS M 266 " distance=2.03 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 C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.02 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.04 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 X 22 " - pdb=" SG CYS X 96 " distance=2.04 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " 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=2.02 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 105 " distance=2.04 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 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=2.04 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 Z 22 " - pdb=" SG CYS Z 96 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 125 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 28 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 105 " distance=2.03 Simple disulfide: pdb=" SG CYS P 153 " - pdb=" SG CYS P 266 " distance=2.04 Simple disulfide: pdb=" SG CYS P 201 " - pdb=" SG CYS P 225 " distance=2.03 Simple disulfide: pdb=" SG CYS P 203 " - pdb=" SG CYS P 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 396 " - pdb=" SG CYS P 417 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 141 " " NAG B 501 " - " ASN B 141 " " NAG C 501 " - " ASN C 141 " " NAG D 501 " - " ASN D 141 " " NAG M 501 " - " ASN M 263 " " NAG M 502 " - " ASN M 345 " " NAG N 501 " - " ASN N 263 " " NAG N 502 " - " ASN N 345 " " NAG O 501 " - " ASN O 263 " " NAG O 502 " - " ASN O 345 " " NAG P 501 " - " ASN P 263 " " NAG P 502 " - " ASN P 345 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9096 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 105 sheets defined 12.8% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.971A pdb=" N TYR B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.743A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 403 through 439 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.766A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.128A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 10 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 361 Processing helix chain 'N' and resid 363 through 403 removed outlier: 3.551A pdb=" N ALA N 385 " --> pdb=" O MET N 381 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.530A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 3.523A 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 'R' and resid 148 through 152 Processing helix chain 'R' and resid 168 through 175 removed outlier: 5.036A pdb=" N SER R 173 " --> pdb=" O HIS R 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.548A pdb=" N LYS A 115 " --> pdb=" O GLU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 4.003A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.583A pdb=" N THR A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 439 removed outlier: 3.502A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 32 Processing helix chain 'V' and resid 62 through 65 removed outlier: 3.741A pdb=" N LYS V 65 " --> pdb=" O ASP V 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 62 through 65' Processing helix chain 'U' and resid 79 through 83 removed outlier: 3.982A pdb=" N PHE U 83 " --> pdb=" O PRO U 80 " (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 351 through 361 removed outlier: 3.599A pdb=" N LEU M 357 " --> pdb=" O HIS M 353 " (cutoff:3.500A) Processing helix chain 'M' and resid 363 through 398 removed outlier: 3.505A pdb=" N VAL M 368 " --> pdb=" O PRO M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 402 Processing helix chain 'M' and resid 409 through 415 Processing helix chain 'Q' and resid 148 through 152 Processing helix chain 'Q' and resid 168 through 175 removed outlier: 5.157A pdb=" N SER Q 173 " --> pdb=" O HIS Q 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.685A pdb=" N LYS C 115 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.185A pdb=" N TYR C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.633A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 259 Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 403 through 439 Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 62 through 65 removed outlier: 3.821A pdb=" N LYS X 65 " --> pdb=" O ASP X 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 62 through 65' Processing helix chain 'W' and resid 79 through 83 removed outlier: 3.833A pdb=" N PHE W 83 " --> pdb=" O PRO W 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 10 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: 3.552A pdb=" N LEU O 357 " --> pdb=" O HIS O 353 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 403 Proline residue: O 399 - end of helix removed outlier: 3.609A pdb=" N THR O 403 " --> pdb=" O PRO O 399 " (cutoff:3.500A) Processing helix chain 'O' and resid 409 through 415 Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.550A pdb=" N LYS S 151 " --> pdb=" O ASP S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 175 removed outlier: 5.184A pdb=" N SER S 173 " --> pdb=" O HIS S 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.559A pdb=" N LYS D 115 " --> pdb=" O GLU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.993A pdb=" N TYR D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 246 " --> pdb=" O TYR D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.770A pdb=" N THR D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 403 through 439 removed outlier: 3.502A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 32 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 3.953A pdb=" N PHE Y 83 " --> pdb=" O PRO Y 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 10 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: 3.540A pdb=" N LEU P 357 " --> pdb=" O HIS P 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 403 removed outlier: 3.594A pdb=" N VAL P 368 " --> pdb=" O PRO P 364 " (cutoff:3.500A) Proline residue: P 399 - end of helix removed outlier: 3.698A pdb=" N LEU P 402 " --> pdb=" O THR P 398 " (cutoff:3.500A) removed outlier: 3.611A 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 'T' and resid 148 through 152 Processing helix chain 'T' and resid 168 through 175 removed outlier: 4.993A pdb=" N SER T 173 " --> pdb=" O HIS T 170 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.729A pdb=" N LYS B 160 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 19 removed outlier: 4.073A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 126 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 42 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 124 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 44 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 122 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 46 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER B 120 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 120 " --> pdb=" O VAL B 179 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 140 through 147 removed outlier: 4.910A pdb=" N SER B 120 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 46 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR B 122 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 44 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA B 124 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 42 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 126 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER B 130 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL B 36 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LYS B 132 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 30 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.506A pdb=" N ALA B 106 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 296 through 306 removed outlier: 4.518A pdb=" N ASP B 298 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL B 315 " --> pdb=" O PRO B 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 343 through 346 Processing sheet with id=AB2, first strand: chain 'B' and resid 387 through 388 removed outlier: 3.541A pdb=" N TYR N 297 " --> pdb=" O HIS N 307 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.064A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.064A pdb=" N GLY H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR H 109 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.152A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AB9, first strand: chain 'N' and resid 74 through 79 removed outlier: 6.004A pdb=" N LYS N 66 " --> pdb=" O GLY N 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN N 53 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET N 70 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 10.838A pdb=" N SER N 51 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N HIS N 99 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N LEU N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N MET N 97 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 10.045A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.345A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) removed outlier: 17.002A pdb=" N ILE N 56 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 19.906A pdb=" N ILE N 93 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 84 through 86 removed outlier: 4.336A pdb=" N GLU N 109 " --> pdb=" O PHE N 129 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 148 through 156 Processing sheet with id=AC3, first strand: chain 'N' and resid 236 through 237 removed outlier: 4.085A pdb=" N GLY N 253 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 175 through 176 removed outlier: 3.694A pdb=" N GLY N 209 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 181 through 184 Processing sheet with id=AC6, first strand: chain 'N' and resid 275 through 279 removed outlier: 3.883A pdb=" N LYS N 315 " --> pdb=" O LEU N 287 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 143 through 144 removed outlier: 3.541A pdb=" N GLY R 125 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N HIS R 119 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL R 123 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TYR R 126 " --> pdb=" O PRO R 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 249 through 253 removed outlier: 5.315A pdb=" N PHE R 201 " --> pdb=" O LEU R 240 " (cutoff:3.500A) removed outlier: 9.268A pdb=" N ALA R 193 " --> pdb=" O PRO R 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY R 185 " --> pdb=" O TYR R 196 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE R 217 " --> pdb=" O VAL R 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 249 through 253 removed outlier: 4.369A pdb=" N ALA R 239 " --> pdb=" O ALA R 232 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY R 230 " --> pdb=" O SER R 241 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL R 243 " --> pdb=" O VAL R 228 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL R 228 " --> pdb=" O VAL R 243 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TRP R 245 " --> pdb=" O ALA R 226 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA R 226 " --> pdb=" O TRP R 245 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AD2, first strand: chain 'A' and resid 15 through 19 removed outlier: 3.805A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 120 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 140 through 147 removed outlier: 4.999A pdb=" N SER A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR A 46 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 124 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU A 42 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 38 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER A 130 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL A 36 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS A 132 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 30 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.539A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.539A pdb=" N HIS A 107 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 106 " --> pdb=" O SER A 77 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AD7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AD8, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AD9, first strand: chain 'A' and resid 296 through 306 removed outlier: 4.491A pdb=" N ASP A 298 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 300 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL A 315 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AE2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AE3, first strand: chain 'V' and resid 3 through 7 removed outlier: 3.511A pdb=" N SER V 21 " --> pdb=" O SER V 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 10 through 12 removed outlier: 6.138A pdb=" N GLY V 10 " --> pdb=" O THR V 117 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 114 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N MET V 34 " --> pdb=" O TYR V 50 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR V 50 " --> pdb=" O HIS V 59 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 10 through 12 removed outlier: 6.138A pdb=" N GLY V 10 " --> pdb=" O THR V 117 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 114 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR V 109 " --> pdb=" O ARG V 98 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 4 through 7 removed outlier: 3.749A pdb=" N VAL U 19 " --> pdb=" O ILE U 75 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 10 through 12 removed outlier: 6.037A pdb=" N LEU U 11 " --> pdb=" O GLU U 105 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 17 through 19 Processing sheet with id=AE9, first strand: chain 'M' and resid 74 through 79 removed outlier: 5.981A pdb=" N LYS M 66 " --> pdb=" O GLY M 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET M 70 " --> pdb=" O SER M 51 " (cutoff:3.500A) removed outlier: 10.790A pdb=" N SER M 51 " --> pdb=" O MET M 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA M 103 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N HIS M 99 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N LEU M 52 " --> pdb=" O MET M 97 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N MET M 97 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ILE M 54 " --> pdb=" O GLY M 95 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N GLY M 95 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 17.053A pdb=" N ILE M 56 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 19.912A pdb=" N ILE M 93 " --> pdb=" O ILE M 56 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 84 through 86 removed outlier: 4.327A pdb=" N GLU M 109 " --> pdb=" O PHE M 129 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 149 through 156 removed outlier: 3.599A pdb=" N CYS M 153 " --> pdb=" O VAL M 264 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 236 through 237 removed outlier: 3.898A pdb=" N GLY M 253 " --> pdb=" O VAL M 169 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 175 through 176 removed outlier: 3.534A pdb=" N GLY M 209 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 181 through 184 Processing sheet with id=AF6, first strand: chain 'M' and resid 275 through 279 removed outlier: 4.052A pdb=" N LYS M 315 " --> pdb=" O LEU M 287 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 143 through 144 removed outlier: 6.855A pdb=" N PHE Q 115 " --> pdb=" O TYR Q 126 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR Q 126 " --> pdb=" O PHE Q 115 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL Q 117 " --> pdb=" O MET Q 124 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N TYR Q 126 " --> pdb=" O PRO Q 137 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 249 through 253 removed outlier: 6.914A pdb=" N ALA Q 239 " --> pdb=" O GLY Q 231 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY Q 231 " --> pdb=" O ALA Q 239 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER Q 241 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N TRP Q 245 " --> pdb=" O VAL Q 225 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL Q 225 " --> pdb=" O TRP Q 245 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA Q 226 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN Q 188 " --> pdb=" O PHE Q 218 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N ALA Q 193 " --> pdb=" O PRO Q 204 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N PHE Q 201 " --> pdb=" O LEU Q 240 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU Q 240 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.600A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.928A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 42 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 44 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C 122 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR C 46 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 120 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 140 through 147 removed outlier: 4.884A pdb=" N SER C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR C 46 " --> pdb=" O SER C 120 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C 122 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 44 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA C 124 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 42 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 38 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER C 130 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 36 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS C 132 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 30 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AG4, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AG5, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AG6, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AG7, first strand: chain 'C' and resid 219 through 221 Processing sheet with id=AG8, first strand: chain 'C' and resid 296 through 306 removed outlier: 4.588A pdb=" N ASP C 298 " --> pdb=" O THR C 321 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 321 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL C 315 " --> pdb=" O PRO C 304 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 343 through 346 Processing sheet with id=AH1, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.517A pdb=" N TYR O 297 " --> pdb=" O HIS O 307 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 3 through 7 removed outlier: 3.540A pdb=" N SER X 71 " --> pdb=" O TYR X 80 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.584A pdb=" N THR X 114 " --> pdb=" O TYR X 94 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET X 34 " --> pdb=" O TYR X 50 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N TYR X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'W' and resid 10 through 12 removed outlier: 6.371A pdb=" N LEU W 11 " --> pdb=" O GLU W 105 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 10 through 12 removed outlier: 6.371A pdb=" N LEU W 11 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR W 97 " --> pdb=" O GLN W 90 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 17 through 19 removed outlier: 3.511A pdb=" N CYS O 28 " --> pdb=" O CYS O 19 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 74 through 79 removed outlier: 5.975A pdb=" N LYS O 66 " --> pdb=" O GLY O 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN O 53 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET O 70 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N SER O 51 " --> pdb=" O MET O 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA O 103 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N HIS O 99 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N LEU O 52 " --> pdb=" O MET O 97 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N MET O 97 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE O 54 " --> pdb=" O GLY O 95 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N GLY O 95 " --> pdb=" O ILE O 54 " (cutoff:3.500A) removed outlier: 17.134A pdb=" N ILE O 56 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 19.961A pdb=" N ILE O 93 " --> pdb=" O ILE O 56 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 84 through 86 removed outlier: 4.246A pdb=" N GLU O 109 " --> pdb=" O PHE O 129 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'O' and resid 149 through 156 Processing sheet with id=AI2, first strand: chain 'O' and resid 236 through 237 removed outlier: 4.136A pdb=" N GLY O 253 " --> pdb=" O VAL O 169 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'O' and resid 175 through 176 removed outlier: 3.804A pdb=" N GLY O 209 " --> pdb=" O TYR O 199 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'O' and resid 181 through 184 removed outlier: 3.530A pdb=" N LYS O 215 " --> pdb=" O ILE O 190 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 275 through 279 removed outlier: 3.889A pdb=" N LYS O 315 " --> pdb=" O LEU O 287 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'S' and resid 143 through 144 removed outlier: 6.643A pdb=" N PHE S 115 " --> pdb=" O TYR S 126 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR S 126 " --> pdb=" O PHE S 115 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL S 117 " --> pdb=" O MET S 124 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N TYR S 126 " --> pdb=" O PRO S 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU S 162 " --> pdb=" O SER S 157 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER S 157 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS S 164 " --> pdb=" O LYS S 155 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS S 155 " --> pdb=" O CYS S 164 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'S' and resid 249 through 253 removed outlier: 4.515A pdb=" N GLY S 230 " --> pdb=" O SER S 241 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL S 243 " --> pdb=" O VAL S 228 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL S 228 " --> pdb=" O VAL S 243 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N TRP S 245 " --> pdb=" O ALA S 226 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA S 226 " --> pdb=" O TRP S 245 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE S 217 " --> pdb=" O VAL S 225 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN S 188 " --> pdb=" O PHE S 218 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY S 185 " --> pdb=" O TYR S 196 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N ALA S 193 " --> pdb=" O PRO S 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG S 200 " --> pdb=" O SER S 197 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE S 201 " --> pdb=" O LEU S 240 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.565A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 15 through 19 removed outlier: 9.726A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 120 " --> pdb=" O VAL D 179 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.758A pdb=" N ALA D 119 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA D 121 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR D 41 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA D 127 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU D 39 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 129 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR D 37 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA D 131 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER D 35 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 133 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU D 33 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL D 135 " --> pdb=" O MET D 31 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N MET D 31 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N TYR D 137 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N LEU D 29 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AJ3, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.526A pdb=" N SER D 104 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 79 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AJ5, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AJ6, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AJ7, first strand: chain 'D' and resid 296 through 306 removed outlier: 4.293A pdb=" N ASP D 298 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL D 315 " --> pdb=" O PRO D 304 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER D 350 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AJ9, first strand: chain 'D' and resid 387 through 388 removed outlier: 3.511A pdb=" N TYR P 297 " --> pdb=" O HIS P 307 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Z' and resid 3 through 7 Processing sheet with id=AK2, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY Z 10 " --> pdb=" O THR Z 117 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET Z 34 " --> pdb=" O TYR Z 50 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N TYR Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Z' and resid 10 through 12 removed outlier: 6.243A pdb=" N GLY Z 10 " --> pdb=" O THR Z 117 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR Z 109 " --> pdb=" O ARG Z 98 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.763A pdb=" N VAL Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Y' and resid 10 through 12 removed outlier: 6.105A pdb=" N LEU Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 17 through 19 removed outlier: 3.520A pdb=" N CYS P 28 " --> pdb=" O CYS P 19 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'P' and resid 74 through 79 removed outlier: 5.898A pdb=" N LYS P 66 " --> pdb=" O GLY P 55 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET P 70 " --> pdb=" O SER P 51 " (cutoff:3.500A) removed outlier: 10.764A pdb=" N SER P 51 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N HIS P 99 " --> pdb=" O VAL P 50 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU P 52 " --> pdb=" O MET P 97 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N MET P 97 " --> pdb=" O LEU P 52 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N ILE P 54 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 11.487A pdb=" N GLY P 95 " --> pdb=" O ILE P 54 " (cutoff:3.500A) removed outlier: 17.117A pdb=" N ILE P 56 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 20.000A pdb=" N ILE P 93 " --> pdb=" O ILE P 56 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'P' and resid 84 through 86 removed outlier: 4.369A pdb=" N GLU P 109 " --> pdb=" O PHE P 129 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'P' and resid 149 through 156 Processing sheet with id=AL1, first strand: chain 'P' and resid 236 through 237 removed outlier: 3.986A pdb=" N GLY P 253 " --> pdb=" O VAL P 169 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 175 through 176 removed outlier: 3.619A pdb=" N GLY P 209 " --> pdb=" O TYR P 199 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 181 through 184 removed outlier: 3.533A pdb=" N LYS P 215 " --> pdb=" O ILE P 190 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 275 through 279 removed outlier: 3.928A pdb=" N LYS P 315 " --> pdb=" O LEU P 287 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'T' and resid 143 through 144 removed outlier: 6.712A pdb=" N PHE T 115 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR T 126 " --> pdb=" O PHE T 115 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL T 117 " --> pdb=" O MET T 124 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N TYR T 126 " --> pdb=" O PRO T 137 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'T' and resid 249 through 253 removed outlier: 4.160A pdb=" N GLY T 230 " --> pdb=" O SER T 241 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL T 243 " --> pdb=" O VAL T 228 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL T 228 " --> pdb=" O VAL T 243 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N TRP T 245 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N ALA T 226 " --> pdb=" O TRP T 245 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE T 217 " --> pdb=" O VAL T 225 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN T 188 " --> pdb=" O PHE T 218 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ALA T 193 " --> pdb=" O PRO T 204 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG T 200 " --> pdb=" O SER T 197 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE T 201 " --> pdb=" O LEU T 240 " (cutoff:3.500A) 1497 hydrogen bonds defined for protein. 3732 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: 11.10 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12309 1.34 - 1.47: 9317 1.47 - 1.59: 16862 1.59 - 1.71: 0 1.71 - 1.84: 356 Bond restraints: 38844 Sorted by residual: bond pdb=" N MET Q 124 " pdb=" CA MET Q 124 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.27e-02 6.20e+03 6.00e+00 bond pdb=" N MET Z 34 " pdb=" CA MET Z 34 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.27e-02 6.20e+03 5.91e+00 bond pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.46e+00 bond pdb=" CB CYS D 94 " pdb=" SG CYS D 94 " ideal model delta sigma weight residual 1.808 1.732 0.076 3.30e-02 9.18e+02 5.26e+00 ... (remaining 38839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 52327 2.49 - 4.98: 530 4.98 - 7.46: 32 7.46 - 9.95: 9 9.95 - 12.44: 2 Bond angle restraints: 52900 Sorted by residual: angle pdb=" C TYR A 93 " pdb=" N CYS A 94 " pdb=" CA CYS A 94 " ideal model delta sigma weight residual 122.81 115.48 7.33 1.57e+00 4.06e-01 2.18e+01 angle pdb=" CA CYS C 94 " pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " ideal model delta sigma weight residual 114.40 123.53 -9.13 2.30e+00 1.89e-01 1.58e+01 angle pdb=" CA ASN N 202 " pdb=" CB ASN N 202 " pdb=" CG ASN N 202 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" CA CYS D 94 " pdb=" CB CYS D 94 " pdb=" SG CYS D 94 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" CB LYS R 221 " pdb=" CG LYS R 221 " pdb=" CD LYS R 221 " ideal model delta sigma weight residual 111.30 120.00 -8.70 2.30e+00 1.89e-01 1.43e+01 ... (remaining 52895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 21585 17.99 - 35.98: 1367 35.98 - 53.97: 403 53.97 - 71.96: 91 71.96 - 89.94: 34 Dihedral angle restraints: 23480 sinusoidal: 9264 harmonic: 14216 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 28 " pdb=" CB CYS M 28 " ideal model delta sinusoidal sigma weight residual -86.00 -174.17 88.17 1 1.00e+01 1.00e-02 9.29e+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 -86.00 -167.91 81.91 1 1.00e+01 1.00e-02 8.25e+01 dihedral pdb=" CB CYS D 62 " pdb=" SG CYS D 62 " pdb=" SG CYS D 94 " pdb=" CB CYS D 94 " ideal model delta sinusoidal sigma weight residual -86.00 -161.52 75.52 1 1.00e+01 1.00e-02 7.20e+01 ... (remaining 23477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5236 0.075 - 0.150: 699 0.150 - 0.225: 16 0.225 - 0.300: 6 0.300 - 0.376: 3 Chirality restraints: 5960 Sorted by residual: chirality pdb=" C1 NAG P 501 " pdb=" ND2 ASN P 263 " pdb=" C2 NAG P 501 " pdb=" O5 NAG P 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+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 -2.04 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C1 NAG M 501 " pdb=" ND2 ASN M 263 " pdb=" C2 NAG M 501 " pdb=" O5 NAG M 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 5957 not shown) Planarity restraints: 6816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 254 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.62e+01 pdb=" N PRO S 255 " 0.260 5.00e-02 4.00e+02 pdb=" CA PRO S 255 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO S 255 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 254 " 0.056 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO R 255 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO R 255 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 255 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 136 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO Q 137 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO Q 137 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 137 " 0.046 5.00e-02 4.00e+02 ... (remaining 6813 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 175 2.63 - 3.20: 29483 3.20 - 3.76: 50716 3.76 - 4.33: 66645 4.33 - 4.90: 116057 Nonbonded interactions: 263076 Sorted by model distance: nonbonded pdb=" OD1 ASP O 117 " pdb=" N SER O 118 " model vdw 2.062 3.120 nonbonded pdb=" OD1 ASP M 117 " pdb=" N SER M 118 " model vdw 2.109 3.120 nonbonded pdb=" OG SER M 30 " pdb=" O ILE M 32 " model vdw 2.124 3.040 nonbonded pdb=" OG SER P 30 " pdb=" O ILE P 32 " model vdw 2.167 3.040 nonbonded pdb=" OG1 THR A 10 " pdb=" OH TYR A 15 " model vdw 2.202 3.040 ... (remaining 263071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'L' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.650 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.270 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:2.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 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 0.077 38924 Z= 0.143 Angle : 0.660 13.591 53072 Z= 0.367 Chirality : 0.047 0.376 5960 Planarity : 0.005 0.150 6804 Dihedral : 13.533 89.944 14180 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.35 % Favored : 98.52 % Rotamer: Outliers : 0.26 % Allowed : 11.74 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.11), residues: 4876 helix: 1.97 (0.23), residues: 427 sheet: 1.06 (0.11), residues: 1868 loop : 0.11 (0.11), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 395 TYR 0.020 0.001 TYR H 50 PHE 0.021 0.001 PHE D 436 TRP 0.015 0.001 TRP D 89 HIS 0.010 0.001 HIS O 313 Details of bonding type rmsd covalent geometry : bond 0.00273 (38844) covalent geometry : angle 0.64374 (52900) SS BOND : bond 0.00405 ( 68) SS BOND : angle 1.89993 ( 136) hydrogen bonds : bond 0.30697 ( 1445) hydrogen bonds : angle 8.18269 ( 3732) link_NAG-ASN : bond 0.00451 ( 12) link_NAG-ASN : angle 4.43035 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 669 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 70 MET cc_start: 0.8151 (tpp) cc_final: 0.7810 (tpp) REVERT: A 209 GLU cc_start: 0.6865 (mp0) cc_final: 0.6563 (mp0) REVERT: A 223 ARG cc_start: 0.8485 (ttt-90) cc_final: 0.8175 (ttt-90) REVERT: V 34 MET cc_start: 0.7022 (mmm) cc_final: 0.6495 (mmm) REVERT: C 410 VAL cc_start: 0.8951 (t) cc_final: 0.8716 (p) REVERT: P 171 MET cc_start: 0.8400 (ttt) cc_final: 0.8122 (ttt) outliers start: 11 outliers final: 9 residues processed: 675 average time/residue: 0.2408 time to fit residues: 262.4982 Evaluate side-chains 650 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 641 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 40 GLU Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 275 ASN Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain T residue 229 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN L 38 GLN N 26 HIS N 53 GLN N 202 ASN N 273 ASN A 34 GLN A 186 ASN A 216 ASN A 222 GLN A 389 ASN U 38 GLN M 127 HIS M 158 GLN M 226 HIS M 234 ASN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN C 252 GLN C 353 GLN W 38 GLN O 313 HIS O 341 GLN P 62 HIS P 131 HIS P 273 ASN P 299 ASN P 302 GLN T 170 HIS T 190 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.148941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116570 restraints weight = 61786.166| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.46 r_work: 0.3324 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38924 Z= 0.149 Angle : 0.600 10.402 53072 Z= 0.331 Chirality : 0.046 0.341 5960 Planarity : 0.005 0.089 6804 Dihedral : 5.274 52.557 5584 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.27 % Favored : 98.71 % Rotamer: Outliers : 1.68 % Allowed : 10.95 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.12), residues: 4876 helix: 2.71 (0.25), residues: 419 sheet: 1.19 (0.12), residues: 1812 loop : -0.11 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 289 TYR 0.012 0.001 TYR H 80 PHE 0.016 0.001 PHE M 115 TRP 0.014 0.001 TRP N 330 HIS 0.005 0.001 HIS O 313 Details of bonding type rmsd covalent geometry : bond 0.00274 (38844) covalent geometry : angle 0.59172 (52900) SS BOND : bond 0.00371 ( 68) SS BOND : angle 1.11138 ( 136) hydrogen bonds : bond 0.09177 ( 1445) hydrogen bonds : angle 6.22257 ( 3732) link_NAG-ASN : bond 0.00521 ( 12) link_NAG-ASN : angle 3.33600 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 683 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8024 (t) REVERT: B 319 LYS cc_start: 0.7606 (mttm) cc_final: 0.7375 (mttp) REVERT: B 407 MET cc_start: 0.7568 (tpt) cc_final: 0.7182 (tpt) REVERT: N 150 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7595 (mm-30) REVERT: R 221 LYS cc_start: 0.8083 (mppt) cc_final: 0.7830 (mppt) REVERT: A 1 TYR cc_start: 0.7942 (t80) cc_final: 0.7576 (t80) REVERT: A 209 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: A 223 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8257 (ttt-90) REVERT: A 434 VAL cc_start: 0.8297 (t) cc_final: 0.8002 (p) REVERT: M 19 CYS cc_start: 0.7616 (t) cc_final: 0.7304 (t) REVERT: M 56 ILE cc_start: 0.8603 (mt) cc_final: 0.8255 (tt) REVERT: M 193 ASN cc_start: 0.8124 (m110) cc_final: 0.7637 (m110) REVERT: M 225 CYS cc_start: 0.6683 (m) cc_final: 0.6266 (m) REVERT: M 356 ILE cc_start: 0.8128 (mm) cc_final: 0.7923 (tp) REVERT: C 410 VAL cc_start: 0.8735 (t) cc_final: 0.8504 (p) REVERT: O 117 ASP cc_start: 0.6922 (t0) cc_final: 0.6641 (t0) REVERT: O 384 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8465 (t) REVERT: S 133 LYS cc_start: 0.8177 (mttm) cc_final: 0.7956 (mmmt) REVERT: S 242 VAL cc_start: 0.8489 (p) cc_final: 0.8104 (t) REVERT: D 42 LEU cc_start: 0.8177 (mt) cc_final: 0.7909 (mp) REVERT: D 299 MET cc_start: 0.7893 (mtp) cc_final: 0.7674 (mtm) REVERT: D 434 VAL cc_start: 0.7862 (t) cc_final: 0.7567 (p) REVERT: P 171 MET cc_start: 0.8524 (ttt) cc_final: 0.8296 (ttt) REVERT: T 229 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8400 (pt) outliers start: 70 outliers final: 38 residues processed: 715 average time/residue: 0.2227 time to fit residues: 259.8256 Evaluate side-chains 682 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 640 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 134 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 260 GLU Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain Q residue 134 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 229 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 274 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 306 optimal weight: 0.7980 chunk 345 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 326 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 53 GLN N 202 ASN R 170 HIS A 34 GLN A 331 HIS M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS C 439 HIS O 146 GLN O 313 HIS D 331 HIS T 170 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.144611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112282 restraints weight = 61338.448| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.36 r_work: 0.3248 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38924 Z= 0.196 Angle : 0.651 12.122 53072 Z= 0.360 Chirality : 0.048 0.299 5960 Planarity : 0.006 0.061 6804 Dihedral : 5.338 52.277 5566 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.43 % Allowed : 11.50 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.11), residues: 4876 helix: 2.57 (0.25), residues: 419 sheet: 0.96 (0.11), residues: 1855 loop : -0.82 (0.11), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 156 TYR 0.024 0.002 TYR A 122 PHE 0.019 0.002 PHE C 436 TRP 0.020 0.002 TRP O 330 HIS 0.013 0.002 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00429 (38844) covalent geometry : angle 0.64205 (52900) SS BOND : bond 0.00456 ( 68) SS BOND : angle 1.47353 ( 136) hydrogen bonds : bond 0.08404 ( 1445) hydrogen bonds : angle 5.65466 ( 3732) link_NAG-ASN : bond 0.00382 ( 12) link_NAG-ASN : angle 3.26942 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 697 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: B 288 THR cc_start: 0.8058 (m) cc_final: 0.7670 (p) REVERT: B 319 LYS cc_start: 0.8058 (mttm) cc_final: 0.7757 (mttp) REVERT: B 407 MET cc_start: 0.7409 (tpt) cc_final: 0.6916 (tpt) REVERT: N 56 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8287 (tt) REVERT: N 70 MET cc_start: 0.8201 (tpp) cc_final: 0.7989 (tpp) REVERT: N 202 ASN cc_start: 0.8295 (t0) cc_final: 0.8080 (t0) REVERT: N 224 GLN cc_start: 0.7590 (mm110) cc_final: 0.6970 (mm-40) REVERT: A 9 ASN cc_start: 0.8394 (t0) cc_final: 0.8081 (t0) REVERT: A 61 LYS cc_start: 0.7636 (tttp) cc_final: 0.7415 (ttmt) REVERT: A 138 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7474 (mt0) REVERT: A 209 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: A 223 ARG cc_start: 0.8574 (ttt-90) cc_final: 0.8313 (ttt-90) REVERT: A 374 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7757 (m) REVERT: A 434 VAL cc_start: 0.8109 (t) cc_final: 0.7870 (p) REVERT: M 87 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7397 (t) REVERT: M 171 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8243 (ttp) REVERT: M 193 ASN cc_start: 0.8427 (m110) cc_final: 0.7887 (m110) REVERT: M 225 CYS cc_start: 0.6927 (m) cc_final: 0.6577 (m) REVERT: Q 124 MET cc_start: 0.7078 (mmm) cc_final: 0.6804 (mmp) REVERT: Q 171 MET cc_start: 0.7311 (mtt) cc_final: 0.7089 (mtt) REVERT: Q 218 PHE cc_start: 0.8590 (m-80) cc_final: 0.8267 (m-80) REVERT: C 434 VAL cc_start: 0.8142 (t) cc_final: 0.7936 (p) REVERT: X 49 SER cc_start: 0.7359 (m) cc_final: 0.7145 (p) REVERT: O 87 THR cc_start: 0.7890 (OUTLIER) cc_final: 0.7446 (p) REVERT: O 165 GLU cc_start: 0.7738 (tt0) cc_final: 0.7455 (mt-10) REVERT: O 255 ILE cc_start: 0.7923 (pt) cc_final: 0.7409 (mt) REVERT: O 384 THR cc_start: 0.8849 (m) cc_final: 0.8536 (t) REVERT: S 133 LYS cc_start: 0.8221 (mttm) cc_final: 0.7961 (mmmt) REVERT: S 242 VAL cc_start: 0.8548 (p) cc_final: 0.8309 (t) REVERT: D 15 TYR cc_start: 0.7711 (m-80) cc_final: 0.7467 (m-80) REVERT: D 42 LEU cc_start: 0.8351 (mt) cc_final: 0.8083 (mp) REVERT: D 299 MET cc_start: 0.8132 (mtp) cc_final: 0.7927 (mtm) REVERT: D 434 VAL cc_start: 0.7726 (t) cc_final: 0.7469 (p) REVERT: Z 34 MET cc_start: 0.6400 (mmm) cc_final: 0.6174 (mmm) REVERT: Z 102 SER cc_start: 0.7307 (t) cc_final: 0.7107 (t) REVERT: P 24 GLU cc_start: 0.7987 (tp30) cc_final: 0.7661 (tp30) REVERT: T 240 LEU cc_start: 0.8732 (mt) cc_final: 0.8508 (mt) outliers start: 101 outliers final: 64 residues processed: 753 average time/residue: 0.2211 time to fit residues: 271.5621 Evaluate side-chains 721 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 651 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 410 PHE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain X residue 31 SER Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 225 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 10 THR Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 264 VAL Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 373 optimal weight: 4.9990 chunk 466 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 440 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 475 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 455 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 433 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN P 299 ASN T 170 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.143431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111290 restraints weight = 60778.774| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.29 r_work: 0.3243 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38924 Z= 0.182 Angle : 0.624 12.282 53072 Z= 0.343 Chirality : 0.047 0.346 5960 Planarity : 0.006 0.058 6804 Dihedral : 5.316 52.606 5564 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.35 % Allowed : 12.75 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 are not related in a simple way. whole: -0.03 (0.11), residues: 4876 helix: 2.54 (0.25), residues: 419 sheet: 0.84 (0.12), residues: 1814 loop : -1.12 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 289 TYR 0.021 0.002 TYR C 122 PHE 0.018 0.002 PHE C 436 TRP 0.018 0.002 TRP O 330 HIS 0.011 0.002 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00412 (38844) covalent geometry : angle 0.61516 (52900) SS BOND : bond 0.00460 ( 68) SS BOND : angle 1.47681 ( 136) hydrogen bonds : bond 0.07762 ( 1445) hydrogen bonds : angle 5.47214 ( 3732) link_NAG-ASN : bond 0.00434 ( 12) link_NAG-ASN : angle 3.14141 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 675 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7909 (ttp-170) REVERT: B 143 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 288 THR cc_start: 0.8043 (m) cc_final: 0.7754 (p) REVERT: B 407 MET cc_start: 0.7337 (tpt) cc_final: 0.6813 (tpt) REVERT: N 56 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8290 (tt) REVERT: N 202 ASN cc_start: 0.8384 (t0) cc_final: 0.8122 (t0) REVERT: A 61 LYS cc_start: 0.7821 (tttp) cc_final: 0.7614 (ttmt) REVERT: A 209 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: A 434 VAL cc_start: 0.8101 (t) cc_final: 0.7825 (p) REVERT: M 87 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7170 (t) REVERT: M 171 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8117 (ttp) REVERT: M 193 ASN cc_start: 0.8431 (m110) cc_final: 0.8057 (m110) REVERT: Q 124 MET cc_start: 0.7011 (mmm) cc_final: 0.6654 (mmp) REVERT: Q 218 PHE cc_start: 0.8612 (m-80) cc_final: 0.8267 (m-80) REVERT: C 385 ASP cc_start: 0.7633 (m-30) cc_final: 0.7303 (m-30) REVERT: C 434 VAL cc_start: 0.8106 (t) cc_final: 0.7788 (p) REVERT: X 49 SER cc_start: 0.7347 (m) cc_final: 0.7143 (p) REVERT: O 87 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7458 (t) REVERT: O 165 GLU cc_start: 0.7764 (tt0) cc_final: 0.7524 (mt-10) REVERT: O 255 ILE cc_start: 0.7917 (pt) cc_final: 0.7405 (mt) REVERT: O 366 MET cc_start: 0.7394 (mpp) cc_final: 0.7086 (mpp) REVERT: O 384 THR cc_start: 0.8840 (m) cc_final: 0.8570 (t) REVERT: S 133 LYS cc_start: 0.8245 (mttm) cc_final: 0.7961 (mmmt) REVERT: S 242 VAL cc_start: 0.8536 (p) cc_final: 0.8314 (t) REVERT: D 15 TYR cc_start: 0.7664 (m-80) cc_final: 0.7429 (m-80) REVERT: D 42 LEU cc_start: 0.8438 (mt) cc_final: 0.8169 (mp) REVERT: D 130 SER cc_start: 0.8707 (p) cc_final: 0.8350 (m) REVERT: D 299 MET cc_start: 0.8201 (mtp) cc_final: 0.7930 (mtm) REVERT: D 434 VAL cc_start: 0.7660 (t) cc_final: 0.7399 (p) REVERT: Z 34 MET cc_start: 0.6307 (mmm) cc_final: 0.6068 (mmm) REVERT: Z 102 SER cc_start: 0.7409 (t) cc_final: 0.7205 (t) REVERT: Y 31 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7840 (p) REVERT: P 24 GLU cc_start: 0.8022 (tp30) cc_final: 0.7786 (tp30) REVERT: P 52 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7858 (pp) REVERT: T 229 LEU cc_start: 0.8863 (pt) cc_final: 0.8609 (pp) REVERT: T 249 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7020 (pp) outliers start: 98 outliers final: 65 residues processed: 733 average time/residue: 0.2239 time to fit residues: 267.7750 Evaluate side-chains 735 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 661 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 260 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 266 CYS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 58 optimal weight: 10.0000 chunk 254 optimal weight: 0.9980 chunk 434 optimal weight: 0.6980 chunk 225 optimal weight: 10.0000 chunk 427 optimal weight: 0.9990 chunk 478 optimal weight: 0.6980 chunk 351 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 ASN N 26 HIS A 34 GLN A 175 ASN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 341 GLN P 299 ASN T 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112388 restraints weight = 60454.664| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.35 r_work: 0.3248 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38924 Z= 0.153 Angle : 0.584 12.262 53072 Z= 0.318 Chirality : 0.046 0.340 5960 Planarity : 0.006 0.054 6804 Dihedral : 5.190 52.593 5564 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.86 % Allowed : 13.02 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.11), residues: 4876 helix: 2.58 (0.25), residues: 431 sheet: 0.73 (0.12), residues: 1850 loop : -1.18 (0.11), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 156 TYR 0.018 0.001 TYR C 122 PHE 0.019 0.002 PHE C 436 TRP 0.014 0.001 TRP O 330 HIS 0.008 0.001 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00331 (38844) covalent geometry : angle 0.57647 (52900) SS BOND : bond 0.00409 ( 68) SS BOND : angle 1.23675 ( 136) hydrogen bonds : bond 0.07107 ( 1445) hydrogen bonds : angle 5.26670 ( 3732) link_NAG-ASN : bond 0.00409 ( 12) link_NAG-ASN : angle 2.91199 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 677 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 134 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7819 (ttp-170) REVERT: B 196 ARG cc_start: 0.8073 (mmt-90) cc_final: 0.7703 (mmt-90) REVERT: B 288 THR cc_start: 0.8170 (m) cc_final: 0.7803 (p) REVERT: B 407 MET cc_start: 0.7190 (tpt) cc_final: 0.6636 (tpt) REVERT: N 56 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8300 (tt) REVERT: N 202 ASN cc_start: 0.8396 (t0) cc_final: 0.8102 (t0) REVERT: N 224 GLN cc_start: 0.7719 (mm110) cc_final: 0.7277 (mm-40) REVERT: N 372 SER cc_start: 0.7868 (p) cc_final: 0.7520 (m) REVERT: A 112 GLU cc_start: 0.7945 (tp30) cc_final: 0.7729 (tp30) REVERT: A 209 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: A 374 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7729 (m) REVERT: A 434 VAL cc_start: 0.7872 (t) cc_final: 0.7608 (p) REVERT: M 87 THR cc_start: 0.7426 (OUTLIER) cc_final: 0.7060 (t) REVERT: M 171 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8103 (ttp) REVERT: M 193 ASN cc_start: 0.8408 (m110) cc_final: 0.8004 (m110) REVERT: Q 124 MET cc_start: 0.6989 (mmm) cc_final: 0.6757 (mmp) REVERT: Q 218 PHE cc_start: 0.8631 (m-80) cc_final: 0.8306 (m-80) REVERT: C 112 GLU cc_start: 0.8183 (tp30) cc_final: 0.7887 (tp30) REVERT: C 385 ASP cc_start: 0.7648 (m-30) cc_final: 0.7306 (m-30) REVERT: C 434 VAL cc_start: 0.7921 (t) cc_final: 0.7602 (p) REVERT: X 49 SER cc_start: 0.7284 (m) cc_final: 0.7071 (p) REVERT: O 87 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7393 (t) REVERT: O 165 GLU cc_start: 0.7766 (tt0) cc_final: 0.7519 (mt-10) REVERT: O 255 ILE cc_start: 0.7877 (pt) cc_final: 0.7366 (mt) REVERT: O 366 MET cc_start: 0.7199 (mpp) cc_final: 0.6943 (mpp) REVERT: O 384 THR cc_start: 0.8801 (m) cc_final: 0.8577 (t) REVERT: S 133 LYS cc_start: 0.8259 (mttm) cc_final: 0.8038 (mmmt) REVERT: D 15 TYR cc_start: 0.7673 (m-80) cc_final: 0.7460 (m-80) REVERT: D 42 LEU cc_start: 0.8466 (mt) cc_final: 0.8202 (mp) REVERT: D 130 SER cc_start: 0.8696 (p) cc_final: 0.8364 (m) REVERT: D 246 GLU cc_start: 0.8473 (pt0) cc_final: 0.8221 (pt0) REVERT: D 299 MET cc_start: 0.8251 (mtp) cc_final: 0.8049 (mtm) REVERT: D 319 LYS cc_start: 0.7956 (mttp) cc_final: 0.7745 (mttm) REVERT: D 434 VAL cc_start: 0.7649 (t) cc_final: 0.7373 (p) REVERT: Z 34 MET cc_start: 0.6290 (mmm) cc_final: 0.6075 (mmm) REVERT: Y 4 MET cc_start: 0.4676 (OUTLIER) cc_final: 0.4069 (mtm) REVERT: P 24 GLU cc_start: 0.8047 (tp30) cc_final: 0.7819 (tp30) REVERT: P 52 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7815 (pp) REVERT: T 229 LEU cc_start: 0.8846 (pt) cc_final: 0.8606 (pp) outliers start: 119 outliers final: 79 residues processed: 744 average time/residue: 0.2215 time to fit residues: 267.8422 Evaluate side-chains 750 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 662 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 245 LYS Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 410 PHE Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 186 TYR Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 168 GLU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 61 optimal weight: 40.0000 chunk 447 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 139 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN A 175 ASN M 53 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.113900 restraints weight = 60545.464| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.36 r_work: 0.3283 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 38924 Z= 0.121 Angle : 0.549 12.197 53072 Z= 0.294 Chirality : 0.045 0.310 5960 Planarity : 0.005 0.051 6804 Dihedral : 5.001 52.745 5564 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.52 % Allowed : 13.90 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 are not related in a simple way. whole: -0.00 (0.12), residues: 4876 helix: 2.80 (0.26), residues: 431 sheet: 0.81 (0.12), residues: 1825 loop : -1.13 (0.11), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 156 TYR 0.012 0.001 TYR Q 187 PHE 0.020 0.001 PHE C 436 TRP 0.013 0.001 TRP O 330 HIS 0.006 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00243 (38844) covalent geometry : angle 0.54151 (52900) SS BOND : bond 0.00423 ( 68) SS BOND : angle 1.26957 ( 136) hydrogen bonds : bond 0.06084 ( 1445) hydrogen bonds : angle 5.04406 ( 3732) link_NAG-ASN : bond 0.00415 ( 12) link_NAG-ASN : angle 2.68034 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 676 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 288 THR cc_start: 0.8109 (m) cc_final: 0.7834 (p) REVERT: B 407 MET cc_start: 0.6857 (tpt) cc_final: 0.6416 (tpt) REVERT: L 31 SER cc_start: 0.8411 (m) cc_final: 0.8206 (p) REVERT: N 171 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8103 (ttp) REVERT: N 202 ASN cc_start: 0.8400 (t0) cc_final: 0.8090 (t0) REVERT: N 224 GLN cc_start: 0.7755 (mm110) cc_final: 0.7291 (mm-40) REVERT: A 9 ASN cc_start: 0.8515 (t0) cc_final: 0.7968 (t0) REVERT: A 112 GLU cc_start: 0.7878 (tp30) cc_final: 0.7623 (tp30) REVERT: A 138 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7377 (mt0) REVERT: A 209 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: A 374 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7638 (p) REVERT: A 434 VAL cc_start: 0.7664 (t) cc_final: 0.7377 (p) REVERT: M 53 GLN cc_start: 0.7944 (mt0) cc_final: 0.7724 (mt0) REVERT: M 87 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6915 (t) REVERT: M 171 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8007 (ttp) REVERT: M 193 ASN cc_start: 0.8373 (m110) cc_final: 0.7950 (m110) REVERT: M 224 GLN cc_start: 0.7498 (mm-40) cc_final: 0.6926 (mm-40) REVERT: Q 124 MET cc_start: 0.6987 (mmm) cc_final: 0.6759 (mmp) REVERT: Q 218 PHE cc_start: 0.8608 (m-80) cc_final: 0.8305 (m-80) REVERT: C 385 ASP cc_start: 0.7544 (m-30) cc_final: 0.7218 (m-30) REVERT: C 430 VAL cc_start: 0.8237 (t) cc_final: 0.7856 (t) REVERT: C 434 VAL cc_start: 0.7740 (t) cc_final: 0.7413 (p) REVERT: X 49 SER cc_start: 0.7250 (m) cc_final: 0.7003 (p) REVERT: O 87 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7239 (t) REVERT: O 255 ILE cc_start: 0.7826 (pt) cc_final: 0.7305 (mt) REVERT: S 133 LYS cc_start: 0.8237 (mttm) cc_final: 0.8010 (mmmt) REVERT: D 15 TYR cc_start: 0.7663 (m-80) cc_final: 0.7459 (m-80) REVERT: D 42 LEU cc_start: 0.8418 (mt) cc_final: 0.8149 (mp) REVERT: D 112 GLU cc_start: 0.7999 (tp30) cc_final: 0.7753 (tp30) REVERT: D 130 SER cc_start: 0.8707 (p) cc_final: 0.8363 (m) REVERT: D 434 VAL cc_start: 0.7532 (t) cc_final: 0.7226 (p) REVERT: Z 34 MET cc_start: 0.6255 (mmm) cc_final: 0.6040 (mmm) REVERT: Y 4 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.4097 (mtm) REVERT: P 24 GLU cc_start: 0.8004 (tp30) cc_final: 0.7793 (tp30) REVERT: P 52 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7767 (pp) REVERT: P 200 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7915 (tttm) REVERT: T 229 LEU cc_start: 0.8852 (pt) cc_final: 0.8602 (pp) outliers start: 105 outliers final: 80 residues processed: 733 average time/residue: 0.2218 time to fit residues: 264.8904 Evaluate side-chains 756 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 668 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 260 GLU Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 186 TYR Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain O residue 36 ARG Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 79 LYS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 210 LEU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 75 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 266 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 chunk 240 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN N 224 GLN ** R 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN M 158 GLN M 299 ASN C 394 HIS O 131 HIS O 158 GLN O 313 HIS S 166 GLN D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106903 restraints weight = 60391.037| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.31 r_work: 0.3167 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 38924 Z= 0.302 Angle : 0.765 13.369 53072 Z= 0.421 Chirality : 0.052 0.357 5960 Planarity : 0.007 0.068 6804 Dihedral : 5.795 52.534 5564 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.31 % Allowed : 13.95 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.11), residues: 4876 helix: 2.13 (0.25), residues: 423 sheet: 0.68 (0.12), residues: 1712 loop : -1.68 (0.10), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 156 TYR 0.038 0.003 TYR C 122 PHE 0.028 0.003 PHE S 201 TRP 0.022 0.002 TRP T 189 HIS 0.015 0.003 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00748 (38844) covalent geometry : angle 0.75591 (52900) SS BOND : bond 0.00770 ( 68) SS BOND : angle 1.91317 ( 136) hydrogen bonds : bond 0.09224 ( 1445) hydrogen bonds : angle 5.58694 ( 3732) link_NAG-ASN : bond 0.00335 ( 12) link_NAG-ASN : angle 3.22174 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 698 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 196 ARG cc_start: 0.8167 (mmt-90) cc_final: 0.7782 (mmt-90) REVERT: B 288 THR cc_start: 0.8275 (m) cc_final: 0.7944 (p) REVERT: B 290 VAL cc_start: 0.7998 (p) cc_final: 0.7711 (t) REVERT: B 292 ASP cc_start: 0.7490 (t70) cc_final: 0.7275 (t0) REVERT: B 311 ASP cc_start: 0.7615 (t0) cc_final: 0.7380 (t0) REVERT: B 407 MET cc_start: 0.7638 (tpt) cc_final: 0.7135 (tpt) REVERT: N 56 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8351 (tt) REVERT: N 171 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8191 (ttp) REVERT: N 202 ASN cc_start: 0.8418 (t0) cc_final: 0.8201 (t0) REVERT: N 372 SER cc_start: 0.7924 (p) cc_final: 0.7658 (m) REVERT: A 209 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 273 VAL cc_start: 0.8263 (t) cc_final: 0.7970 (m) REVERT: A 434 VAL cc_start: 0.8118 (t) cc_final: 0.7820 (p) REVERT: M 24 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8117 (mp0) REVERT: M 43 ASP cc_start: 0.8329 (m-30) cc_final: 0.8095 (m-30) REVERT: M 171 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8187 (ttp) REVERT: M 193 ASN cc_start: 0.8554 (m110) cc_final: 0.8099 (m110) REVERT: Q 124 MET cc_start: 0.7064 (mmm) cc_final: 0.6863 (mmp) REVERT: Q 218 PHE cc_start: 0.8667 (m-80) cc_final: 0.8320 (m-80) REVERT: C 13 VAL cc_start: 0.8240 (t) cc_final: 0.7844 (m) REVERT: C 385 ASP cc_start: 0.7938 (m-30) cc_final: 0.7638 (m-30) REVERT: C 434 VAL cc_start: 0.8196 (t) cc_final: 0.7917 (p) REVERT: W 52 SER cc_start: 0.8515 (m) cc_final: 0.8302 (p) REVERT: O 87 THR cc_start: 0.7990 (OUTLIER) cc_final: 0.7585 (p) REVERT: O 127 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.7866 (m170) REVERT: O 165 GLU cc_start: 0.7880 (tt0) cc_final: 0.7656 (mt-10) REVERT: O 255 ILE cc_start: 0.8002 (pt) cc_final: 0.7477 (mt) REVERT: O 407 THR cc_start: 0.8573 (m) cc_final: 0.8317 (p) REVERT: S 124 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7694 (mmp) REVERT: D 130 SER cc_start: 0.8705 (p) cc_final: 0.8382 (m) REVERT: D 434 VAL cc_start: 0.7879 (t) cc_final: 0.7645 (p) REVERT: Z 34 MET cc_start: 0.6396 (mmm) cc_final: 0.6140 (mmm) REVERT: Y 4 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4154 (mtm) REVERT: P 52 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7798 (pp) REVERT: P 119 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8186 (mtt-85) REVERT: P 224 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7235 (mm-40) REVERT: T 114 ILE cc_start: 0.8590 (mt) cc_final: 0.8316 (mt) REVERT: T 229 LEU cc_start: 0.8861 (pt) cc_final: 0.8629 (pp) outliers start: 138 outliers final: 105 residues processed: 771 average time/residue: 0.2244 time to fit residues: 278.6363 Evaluate side-chains 807 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 692 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 86 ARG Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 153 CYS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 107 LYS Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 382 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain M residue 410 PHE Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 105 GLU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 357 LEU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 228 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 63 CYS Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 224 GLN Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 144 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 364 optimal weight: 0.9980 chunk 424 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 412 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 305 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 456 optimal weight: 0.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 170 HIS A 175 ASN M 53 GLN M 158 GLN P 299 ASN T 170 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.143228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111302 restraints weight = 60040.890| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.31 r_work: 0.3237 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38924 Z= 0.144 Angle : 0.604 13.515 53072 Z= 0.325 Chirality : 0.046 0.321 5960 Planarity : 0.006 0.056 6804 Dihedral : 5.383 53.389 5564 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.40 % Allowed : 15.27 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 are not related in a simple way. whole: -0.48 (0.12), residues: 4876 helix: 2.40 (0.26), residues: 431 sheet: 0.67 (0.12), residues: 1783 loop : -1.57 (0.11), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 156 TYR 0.014 0.001 TYR C 122 PHE 0.015 0.001 PHE A 436 TRP 0.014 0.001 TRP O 330 HIS 0.007 0.001 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00300 (38844) covalent geometry : angle 0.59235 (52900) SS BOND : bond 0.00477 ( 68) SS BOND : angle 1.81073 ( 136) hydrogen bonds : bond 0.06976 ( 1445) hydrogen bonds : angle 5.23421 ( 3732) link_NAG-ASN : bond 0.00473 ( 12) link_NAG-ASN : angle 2.99786 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 692 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8144 (mt) REVERT: B 196 ARG cc_start: 0.8132 (mmt-90) cc_final: 0.7757 (mmt-90) REVERT: B 288 THR cc_start: 0.8209 (m) cc_final: 0.7872 (p) REVERT: B 290 VAL cc_start: 0.7943 (p) cc_final: 0.7660 (t) REVERT: B 292 ASP cc_start: 0.7474 (t70) cc_final: 0.7266 (t0) REVERT: B 311 ASP cc_start: 0.7555 (t0) cc_final: 0.7328 (t0) REVERT: B 407 MET cc_start: 0.7265 (tpt) cc_final: 0.6680 (tpt) REVERT: L 31 SER cc_start: 0.8490 (m) cc_final: 0.8284 (p) REVERT: N 43 ASP cc_start: 0.7750 (m-30) cc_final: 0.7445 (p0) REVERT: N 171 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8121 (ttp) REVERT: N 202 ASN cc_start: 0.8410 (t0) cc_final: 0.8151 (t0) REVERT: N 291 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.6922 (p-80) REVERT: N 372 SER cc_start: 0.7864 (p) cc_final: 0.7587 (m) REVERT: R 213 SER cc_start: 0.8085 (p) cc_final: 0.7323 (m) REVERT: A 209 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: A 434 VAL cc_start: 0.7990 (t) cc_final: 0.7705 (p) REVERT: M 87 THR cc_start: 0.7191 (OUTLIER) cc_final: 0.6826 (t) REVERT: M 171 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8045 (ttp) REVERT: M 193 ASN cc_start: 0.8420 (m110) cc_final: 0.8044 (m110) REVERT: M 224 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7171 (mm-40) REVERT: M 384 THR cc_start: 0.8539 (t) cc_final: 0.8236 (p) REVERT: Q 124 MET cc_start: 0.6904 (mmm) cc_final: 0.6617 (mmp) REVERT: Q 218 PHE cc_start: 0.8614 (m-80) cc_final: 0.8294 (m-80) REVERT: C 13 VAL cc_start: 0.8113 (t) cc_final: 0.7693 (m) REVERT: C 44 LEU cc_start: 0.8264 (tt) cc_final: 0.8027 (tp) REVERT: C 385 ASP cc_start: 0.7768 (m-30) cc_final: 0.7469 (m-30) REVERT: C 430 VAL cc_start: 0.8455 (t) cc_final: 0.8037 (t) REVERT: C 434 VAL cc_start: 0.7946 (t) cc_final: 0.7654 (p) REVERT: W 52 SER cc_start: 0.8485 (m) cc_final: 0.8263 (p) REVERT: O 87 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7430 (p) REVERT: O 127 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7522 (m170) REVERT: O 165 GLU cc_start: 0.7776 (tt0) cc_final: 0.7551 (mt-10) REVERT: O 255 ILE cc_start: 0.7900 (pt) cc_final: 0.7372 (mt) REVERT: S 155 LYS cc_start: 0.8158 (mttt) cc_final: 0.7843 (mtmt) REVERT: D 42 LEU cc_start: 0.8518 (mt) cc_final: 0.8278 (mp) REVERT: D 130 SER cc_start: 0.8704 (p) cc_final: 0.8378 (m) REVERT: D 132 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8151 (ttmm) REVERT: D 156 VAL cc_start: 0.7700 (t) cc_final: 0.7412 (p) REVERT: D 319 LYS cc_start: 0.8140 (mttp) cc_final: 0.7905 (mttm) REVERT: D 434 VAL cc_start: 0.7563 (t) cc_final: 0.7280 (p) REVERT: Z 34 MET cc_start: 0.6305 (mmm) cc_final: 0.6080 (mmm) REVERT: Y 4 MET cc_start: 0.4748 (OUTLIER) cc_final: 0.4110 (mtm) REVERT: Y 60 SER cc_start: 0.7151 (p) cc_final: 0.6853 (m) REVERT: P 52 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7767 (pp) REVERT: T 114 ILE cc_start: 0.8652 (mt) cc_final: 0.8448 (mt) REVERT: T 229 LEU cc_start: 0.8869 (pt) cc_final: 0.8610 (pp) outliers start: 100 outliers final: 77 residues processed: 745 average time/residue: 0.2204 time to fit residues: 267.4704 Evaluate side-chains 763 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 676 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 186 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 2 GLU Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain O residue 401 GLU Chi-restraints excluded: chain S residue 171 MET Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 241 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 378 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 229 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 341 GLN A 175 ASN M 53 GLN M 158 GLN C 349 ASN O 158 GLN P 299 ASN T 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112544 restraints weight = 60395.375| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.38 r_work: 0.3256 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38924 Z= 0.133 Angle : 0.581 14.351 53072 Z= 0.308 Chirality : 0.045 0.310 5960 Planarity : 0.006 0.055 6804 Dihedral : 5.172 52.071 5564 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.31 % Allowed : 15.44 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4876 helix: 2.64 (0.26), residues: 431 sheet: 0.68 (0.12), residues: 1790 loop : -1.52 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 156 TYR 0.015 0.001 TYR C 122 PHE 0.022 0.001 PHE C 436 TRP 0.013 0.001 TRP O 330 HIS 0.006 0.001 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00278 (38844) covalent geometry : angle 0.57294 (52900) SS BOND : bond 0.00488 ( 68) SS BOND : angle 1.43327 ( 136) hydrogen bonds : bond 0.06291 ( 1445) hydrogen bonds : angle 5.02820 ( 3732) link_NAG-ASN : bond 0.00388 ( 12) link_NAG-ASN : angle 2.63607 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 672 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 SER cc_start: 0.8570 (p) cc_final: 0.8276 (m) REVERT: B 133 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 196 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7788 (mmt-90) REVERT: B 288 THR cc_start: 0.8191 (m) cc_final: 0.7845 (p) REVERT: B 290 VAL cc_start: 0.7880 (p) cc_final: 0.7578 (t) REVERT: B 292 ASP cc_start: 0.7472 (t70) cc_final: 0.7253 (t0) REVERT: B 311 ASP cc_start: 0.7576 (t0) cc_final: 0.7326 (t0) REVERT: B 407 MET cc_start: 0.6994 (tpt) cc_final: 0.6332 (tpt) REVERT: L 31 SER cc_start: 0.8520 (m) cc_final: 0.8238 (p) REVERT: N 171 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8131 (ttp) REVERT: N 202 ASN cc_start: 0.8384 (t0) cc_final: 0.8122 (t0) REVERT: N 224 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7443 (mm-40) REVERT: N 291 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.6864 (p-80) REVERT: N 372 SER cc_start: 0.7734 (p) cc_final: 0.7400 (m) REVERT: R 213 SER cc_start: 0.8132 (p) cc_final: 0.7383 (m) REVERT: A 209 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 434 VAL cc_start: 0.7652 (t) cc_final: 0.7375 (p) REVERT: M 53 GLN cc_start: 0.7970 (mt0) cc_final: 0.7688 (mt0) REVERT: M 171 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8025 (ttp) REVERT: M 193 ASN cc_start: 0.8374 (m110) cc_final: 0.8023 (m110) REVERT: M 224 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7133 (mm-40) REVERT: Q 124 MET cc_start: 0.6963 (mmm) cc_final: 0.6718 (mmp) REVERT: Q 218 PHE cc_start: 0.8636 (m-80) cc_final: 0.8318 (m-80) REVERT: C 44 LEU cc_start: 0.8236 (tt) cc_final: 0.8001 (tp) REVERT: C 385 ASP cc_start: 0.7679 (m-30) cc_final: 0.7384 (m-30) REVERT: C 430 VAL cc_start: 0.8244 (t) cc_final: 0.8040 (t) REVERT: X 70 ILE cc_start: 0.7440 (tt) cc_final: 0.7139 (pt) REVERT: W 52 SER cc_start: 0.8477 (m) cc_final: 0.8270 (p) REVERT: O 87 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7346 (t) REVERT: O 127 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7599 (m170) REVERT: O 165 GLU cc_start: 0.7793 (tt0) cc_final: 0.7567 (mt-10) REVERT: O 254 LYS cc_start: 0.8351 (pttt) cc_final: 0.7966 (ptpp) REVERT: S 124 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7559 (mmp) REVERT: D 42 LEU cc_start: 0.8474 (mt) cc_final: 0.8217 (mp) REVERT: D 130 SER cc_start: 0.8664 (p) cc_final: 0.8341 (m) REVERT: D 156 VAL cc_start: 0.7616 (t) cc_final: 0.7336 (p) REVERT: D 434 VAL cc_start: 0.7571 (t) cc_final: 0.7236 (p) REVERT: Z 34 MET cc_start: 0.6320 (mmm) cc_final: 0.6088 (mmm) REVERT: Y 4 MET cc_start: 0.4756 (OUTLIER) cc_final: 0.4132 (mtm) REVERT: Y 60 SER cc_start: 0.7128 (p) cc_final: 0.6832 (m) REVERT: P 52 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7675 (pp) REVERT: T 229 LEU cc_start: 0.8840 (pt) cc_final: 0.8599 (pp) outliers start: 96 outliers final: 72 residues processed: 723 average time/residue: 0.2255 time to fit residues: 265.3180 Evaluate side-chains 752 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 670 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 208 GLU Chi-restraints excluded: chain N residue 210 LEU Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 186 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 288 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 445 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 181 optimal weight: 40.0000 chunk 139 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN M 158 GLN C 349 ASN C 375 HIS O 202 ASN O 313 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.109782 restraints weight = 59796.872| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.36 r_work: 0.3213 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38924 Z= 0.191 Angle : 0.650 15.074 53072 Z= 0.350 Chirality : 0.048 0.326 5960 Planarity : 0.006 0.059 6804 Dihedral : 5.406 52.226 5564 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.31 % Allowed : 15.63 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.12), residues: 4876 helix: 2.52 (0.26), residues: 423 sheet: 0.67 (0.12), residues: 1728 loop : -1.62 (0.11), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 156 TYR 0.027 0.002 TYR C 122 PHE 0.021 0.002 PHE C 436 TRP 0.016 0.002 TRP O 330 HIS 0.011 0.002 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00446 (38844) covalent geometry : angle 0.64135 (52900) SS BOND : bond 0.00546 ( 68) SS BOND : angle 1.68621 ( 136) hydrogen bonds : bond 0.07405 ( 1445) hydrogen bonds : angle 5.19951 ( 3732) link_NAG-ASN : bond 0.00369 ( 12) link_NAG-ASN : angle 2.84259 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9752 Ramachandran restraints generated. 4876 Oldfield, 0 Emsley, 4876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 688 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 SER cc_start: 0.8607 (p) cc_final: 0.8297 (m) REVERT: B 133 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 196 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7779 (mmt-90) REVERT: B 288 THR cc_start: 0.8241 (m) cc_final: 0.7910 (p) REVERT: B 290 VAL cc_start: 0.7874 (p) cc_final: 0.7594 (t) REVERT: B 292 ASP cc_start: 0.7485 (t70) cc_final: 0.7259 (t0) REVERT: B 311 ASP cc_start: 0.7634 (t0) cc_final: 0.7381 (t0) REVERT: B 385 ASP cc_start: 0.7707 (m-30) cc_final: 0.7400 (m-30) REVERT: B 407 MET cc_start: 0.7242 (tpt) cc_final: 0.6643 (tpt) REVERT: L 31 SER cc_start: 0.8454 (m) cc_final: 0.8163 (p) REVERT: N 56 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8324 (tt) REVERT: N 171 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8138 (ttp) REVERT: N 202 ASN cc_start: 0.8381 (t0) cc_final: 0.8153 (t0) REVERT: N 291 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.7005 (p-80) REVERT: N 372 SER cc_start: 0.7800 (p) cc_final: 0.7495 (m) REVERT: R 213 SER cc_start: 0.8262 (p) cc_final: 0.7522 (m) REVERT: A 209 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 273 VAL cc_start: 0.8199 (t) cc_final: 0.7909 (m) REVERT: A 434 VAL cc_start: 0.7743 (t) cc_final: 0.7446 (p) REVERT: M 53 GLN cc_start: 0.8036 (mt0) cc_final: 0.7661 (mt0) REVERT: M 171 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8093 (ttp) REVERT: M 193 ASN cc_start: 0.8411 (m110) cc_final: 0.8064 (m110) REVERT: M 224 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7178 (mm-40) REVERT: Q 124 MET cc_start: 0.6889 (mmm) cc_final: 0.6595 (mmp) REVERT: Q 218 PHE cc_start: 0.8671 (m-80) cc_final: 0.8354 (m-80) REVERT: C 13 VAL cc_start: 0.8123 (t) cc_final: 0.7726 (m) REVERT: C 385 ASP cc_start: 0.7812 (m-30) cc_final: 0.7513 (m-30) REVERT: C 430 VAL cc_start: 0.8257 (t) cc_final: 0.7826 (t) REVERT: X 70 ILE cc_start: 0.7531 (tt) cc_final: 0.7218 (pt) REVERT: W 52 SER cc_start: 0.8500 (m) cc_final: 0.8278 (p) REVERT: O 87 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7463 (p) REVERT: O 127 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7846 (m170) REVERT: O 165 GLU cc_start: 0.7839 (tt0) cc_final: 0.7606 (mt-10) REVERT: S 124 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7485 (mmp) REVERT: D 42 LEU cc_start: 0.8513 (mt) cc_final: 0.8270 (mp) REVERT: D 130 SER cc_start: 0.8694 (p) cc_final: 0.8353 (m) REVERT: D 132 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8186 (ttmm) REVERT: D 156 VAL cc_start: 0.7689 (t) cc_final: 0.7429 (p) REVERT: D 434 VAL cc_start: 0.7775 (t) cc_final: 0.7470 (p) REVERT: Z 34 MET cc_start: 0.6360 (mmm) cc_final: 0.6127 (mmm) REVERT: Y 4 MET cc_start: 0.4741 (OUTLIER) cc_final: 0.4124 (mtm) REVERT: Y 60 SER cc_start: 0.7190 (OUTLIER) cc_final: 0.6918 (m) REVERT: P 52 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7690 (pp) REVERT: T 114 ILE cc_start: 0.8644 (mt) cc_final: 0.8412 (mt) REVERT: T 229 LEU cc_start: 0.8855 (pt) cc_final: 0.8615 (pp) outliers start: 96 outliers final: 75 residues processed: 742 average time/residue: 0.2335 time to fit residues: 282.1738 Evaluate side-chains 774 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 687 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain N residue 56 ILE Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 171 MET Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 263 ASN Chi-restraints excluded: chain N residue 291 HIS Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 356 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain R residue 228 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 56 ILE Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 191 THR Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 179 THR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 240 LEU Chi-restraints excluded: chain Q residue 244 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain X residue 53 SER Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 163 THR Chi-restraints excluded: chain O residue 291 HIS Chi-restraints excluded: chain O residue 384 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 124 MET Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 245 LYS Chi-restraints excluded: chain D residue 325 LYS Chi-restraints excluded: chain D residue 338 THR Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 208 GLU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain P residue 265 THR Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain P residue 324 GLU Chi-restraints excluded: chain P residue 388 MET Chi-restraints excluded: chain P residue 397 ILE Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 224 VAL Chi-restraints excluded: chain T residue 228 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 229 optimal weight: 8.9990 chunk 455 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 449 optimal weight: 0.6980 chunk 344 optimal weight: 0.2980 chunk 248 optimal weight: 0.5980 chunk 391 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.144290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.112235 restraints weight = 60217.682| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.40 r_work: 0.3254 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 38924 Z= 0.132 Angle : 0.579 15.082 53072 Z= 0.307 Chirality : 0.045 0.299 5960 Planarity : 0.006 0.053 6804 Dihedral : 5.167 52.734 5564 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.26 % Allowed : 15.66 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 4876 helix: 2.66 (0.26), residues: 435 sheet: 0.62 (0.12), residues: 1843 loop : -1.59 (0.11), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 156 TYR 0.013 0.001 TYR C 122 PHE 0.022 0.001 PHE C 436 TRP 0.014 0.001 TRP O 330 HIS 0.007 0.001 HIS P 99 Details of bonding type rmsd covalent geometry : bond 0.00278 (38844) covalent geometry : angle 0.57206 (52900) SS BOND : bond 0.00472 ( 68) SS BOND : angle 1.31471 ( 136) hydrogen bonds : bond 0.06234 ( 1445) hydrogen bonds : angle 5.00248 ( 3732) link_NAG-ASN : bond 0.00437 ( 12) link_NAG-ASN : angle 2.68698 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13148.82 seconds wall clock time: 224 minutes 8.88 seconds (13448.88 seconds total)