Starting phenix.real_space_refine on Mon Jul 6 17:49:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dww_27763/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.cif" model { file = "/net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dww_27763/07_2026/8dww_27763.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.12, per 1000 atoms: 0.19 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: 2.68 Conformation dependent library (CDL) restraints added in 1.6 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: 1.47 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: 9.16 Time building geometry restraints manager: 3.61 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: 21355 17.99 - 35.98: 1359 35.98 - 53.97: 389 53.97 - 71.96: 91 71.96 - 89.94: 34 Dihedral angle restraints: 23228 sinusoidal: 9012 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 23225 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: 0.02 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: 3.850 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 33.430 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 13.542 89.944 13928 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/Z covalent geometry : bond 0.00273 / 0.14 (38844) covalent geometry : angle 0.64374 / 0.36 (52900) SS BOND : bond 0.00405 / 0.30 ( 68) SS BOND : angle 1.89993 / 1.43 ( 136) hydrogen bonds : bond 0.30697 / 20.70 ( 1445) hydrogen bonds : angle 8.18269 / 5.64 ( 3732) link_NAG-ASN : bond 0.00451 / 0.23 ( 12) link_NAG-ASN : angle 4.43035 / 3.02 ( 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 : 1.475 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: 0.2186 time to fit residues: 238.8481 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 : 1.047 ------------------------------------------------------------------------------- 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... 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 = 0.3860 r_free = 0.3860 target = 0.148614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116180 restraints weight = 61702.859| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.46 r_work: 0.3321 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1045 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= 0.150 Angle : 0.599 10.332 53072 Z= 0.331 Chirality : 0.046 0.316 5960 Planarity : 0.005 0.089 6804 Dihedral : 4.737 50.909 5332 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.63 % Allowed : 10.98 % Favored : 87.39 % 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: 0.94 (0.12), residues: 4876 helix: 2.70 (0.25), residues: 419 sheet: 1.21 (0.12), residues: 1811 loop : -0.10 (0.11), residues: 2646 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 0.015 0.001 PHE M 115 TRP 0.014 0.001 TRP N 330 HIS 0.006 0.001 HIS P 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (38844) covalent geometry : angle 0.59142 / 0.33 (52900) SS BOND : bond 0.00473 / 0.35 ( 68) SS BOND : angle 1.11866 / 0.80 ( 136) hydrogen bonds : bond 0.09426 / 6.36 ( 1445) hydrogen bonds : angle 6.30337 / 4.36 ( 3732) link_NAG-ASN : bond 0.00513 / 0.23 ( 12) link_NAG-ASN : angle 3.32201 / 2.27 ( 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 748 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 680 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 143 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8026 (t) REVERT: N 150 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7582 (mm-30) REVERT: R 221 LYS cc_start: 0.8076 (mppt) cc_final: 0.7825 (mppt) REVERT: A 1 TYR cc_start: 0.7941 (t80) cc_final: 0.7578 (t80) REVERT: A 209 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6866 (mp0) REVERT: A 223 ARG cc_start: 0.8521 (ttt-90) cc_final: 0.8258 (ttt-90) REVERT: A 434 VAL cc_start: 0.8318 (t) cc_final: 0.8005 (p) REVERT: M 19 CYS cc_start: 0.7603 (t) cc_final: 0.7298 (t) REVERT: M 56 ILE cc_start: 0.8600 (mt) cc_final: 0.8248 (tt) REVERT: M 193 ASN cc_start: 0.8124 (m110) cc_final: 0.7637 (m110) REVERT: M 225 CYS cc_start: 0.6745 (m) cc_final: 0.6333 (m) REVERT: M 356 ILE cc_start: 0.8139 (mm) cc_final: 0.7930 (tp) REVERT: C 410 VAL cc_start: 0.8755 (t) cc_final: 0.8520 (p) REVERT: O 117 ASP cc_start: 0.6930 (t0) cc_final: 0.6656 (t0) REVERT: O 384 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8471 (t) REVERT: S 133 LYS cc_start: 0.8180 (mttm) cc_final: 0.7966 (mmmt) REVERT: D 42 LEU cc_start: 0.8190 (mt) cc_final: 0.7927 (mp) REVERT: D 299 MET cc_start: 0.7900 (mtp) cc_final: 0.7592 (mtm) REVERT: D 434 VAL cc_start: 0.7878 (t) cc_final: 0.7585 (p) REVERT: T 229 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8369 (pt) outliers start: 68 outliers final: 40 residues processed: 711 average time/residue: 0.1922 time to fit residues: 224.2329 Evaluate side-chains 686 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 642 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain H residue 25 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 173 SER 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 214 ASP Chi-restraints excluded: chain M residue 230 THR 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 63 SER Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 365 THR 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: 3.9990 chunk 322 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 345 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 326 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** C 439 HIS O 313 HIS D 331 HIS T 170 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.146433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114173 restraints weight = 61252.383| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.40 r_work: 0.3275 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1764 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= 0.167 Angle : 0.609 9.420 53072 Z= 0.335 Chirality : 0.046 0.360 5960 Planarity : 0.006 0.058 6804 Dihedral : 4.615 37.385 5314 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.38 % Allowed : 11.55 % 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: 0.46 (0.11), residues: 4876 helix: 2.69 (0.25), residues: 419 sheet: 0.97 (0.11), residues: 1904 loop : -0.64 (0.11), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 156 TYR 0.021 0.002 TYR A 122 PHE 0.019 0.002 PHE C 436 TRP 0.018 0.001 TRP O 330 HIS 0.010 0.002 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (38844) covalent geometry : angle 0.60171 / 0.33 (52900) SS BOND : bond 0.00409 / 0.27 ( 68) SS BOND : angle 1.26371 / 0.92 ( 136) hydrogen bonds : bond 0.07708 / 5.21 ( 1445) hydrogen bonds : angle 5.55907 / 3.85 ( 3732) link_NAG-ASN : bond 0.00348 / 0.16 ( 12) link_NAG-ASN : angle 2.96740 / 2.03 ( 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 779 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 680 time to evaluate : 1.409 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.8324 (p) cc_final: 0.8087 (t) REVERT: N 56 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8288 (tt) REVERT: N 150 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7858 (mm-30) REVERT: N 202 ASN cc_start: 0.8245 (t0) cc_final: 0.8017 (t0) REVERT: N 224 GLN cc_start: 0.7582 (mm110) cc_final: 0.7042 (mm-40) REVERT: A 9 ASN cc_start: 0.8338 (t0) cc_final: 0.7996 (t0) REVERT: A 61 LYS cc_start: 0.7494 (tttp) cc_final: 0.7275 (ttmt) REVERT: A 209 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: A 223 ARG cc_start: 0.8560 (ttt-90) cc_final: 0.8292 (ttt-90) REVERT: A 374 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7643 (m) REVERT: A 434 VAL cc_start: 0.8024 (t) cc_final: 0.7781 (p) REVERT: M 19 CYS cc_start: 0.7790 (t) cc_final: 0.7464 (t) REVERT: M 87 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7327 (t) REVERT: M 171 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8216 (ttp) REVERT: M 193 ASN cc_start: 0.8333 (m110) cc_final: 0.7814 (m110) REVERT: Q 171 MET cc_start: 0.7240 (mtt) cc_final: 0.7015 (mtt) REVERT: Q 218 PHE cc_start: 0.8580 (m-80) cc_final: 0.8282 (m-80) REVERT: C 112 GLU cc_start: 0.8010 (tp30) cc_final: 0.7768 (tp30) REVERT: C 434 VAL cc_start: 0.8084 (t) cc_final: 0.7873 (p) REVERT: X 49 SER cc_start: 0.7344 (m) cc_final: 0.7117 (p) REVERT: O 87 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7441 (t) REVERT: O 159 SER cc_start: 0.7732 (t) cc_final: 0.7519 (t) REVERT: O 165 GLU cc_start: 0.7732 (tt0) cc_final: 0.7432 (mt-10) REVERT: O 255 ILE cc_start: 0.7870 (pt) cc_final: 0.7380 (mt) REVERT: O 384 THR cc_start: 0.8838 (m) cc_final: 0.8525 (t) REVERT: S 133 LYS cc_start: 0.8175 (mttm) cc_final: 0.7946 (mmmt) REVERT: S 242 VAL cc_start: 0.8495 (p) cc_final: 0.8202 (t) REVERT: D 15 TYR cc_start: 0.7691 (m-80) cc_final: 0.7432 (m-80) REVERT: D 42 LEU cc_start: 0.8279 (mt) cc_final: 0.8011 (mp) REVERT: D 299 MET cc_start: 0.8047 (mtp) cc_final: 0.7811 (mtm) REVERT: D 319 LYS cc_start: 0.8023 (mttp) cc_final: 0.7817 (mttm) REVERT: D 434 VAL cc_start: 0.7714 (t) cc_final: 0.7443 (p) REVERT: Z 34 MET cc_start: 0.6348 (mmm) cc_final: 0.6138 (mmm) REVERT: P 24 GLU cc_start: 0.7922 (tp30) cc_final: 0.7611 (tp30) REVERT: P 171 MET cc_start: 0.8581 (ttt) cc_final: 0.8375 (ttt) REVERT: T 240 LEU cc_start: 0.8711 (mt) cc_final: 0.8401 (mt) outliers start: 99 outliers final: 62 residues processed: 736 average time/residue: 0.2039 time to fit residues: 244.7357 Evaluate side-chains 725 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 657 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 325 LYS 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 245 ASN Chi-restraints excluded: chain N residue 255 ILE Chi-restraints excluded: chain N residue 382 VAL Chi-restraints excluded: chain R residue 173 SER 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 171 THR 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 372 SER 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 229 LEU 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 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 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 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 222 ILE 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 233 ASN 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 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 247 LYS 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: 0.0470 chunk 52 optimal weight: 10.0000 chunk 440 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 475 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 chunk 455 optimal weight: 2.9990 chunk 144 optimal weight: 0.1980 chunk 358 optimal weight: 5.9990 chunk 433 optimal weight: 5.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 349 ASN A 34 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS O 146 GLN O 158 GLN O 313 HIS Y 38 GLN T 170 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111154 restraints weight = 60783.000| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.30 r_work: 0.3240 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38924 Z= 0.190 Angle : 0.635 10.300 53072 Z= 0.350 Chirality : 0.047 0.325 5960 Planarity : 0.006 0.058 6804 Dihedral : 4.764 32.319 5312 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.74 % Allowed : 12.22 % Favored : 85.04 % 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: 0.06 (0.11), residues: 4876 helix: 2.61 (0.25), residues: 419 sheet: 0.88 (0.12), residues: 1814 loop : -1.05 (0.11), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 289 TYR 0.023 0.002 TYR C 122 PHE 0.018 0.002 PHE C 436 TRP 0.018 0.002 TRP O 330 HIS 0.012 0.002 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 (38844) covalent geometry : angle 0.62655 / 0.35 (52900) SS BOND : bond 0.00518 / 0.39 ( 68) SS BOND : angle 1.53280 / 1.16 ( 136) hydrogen bonds : bond 0.07910 / 5.34 ( 1445) hydrogen bonds : angle 5.48292 / 3.79 ( 3732) link_NAG-ASN : bond 0.00375 / 0.18 ( 12) link_NAG-ASN : angle 3.06999 / 2.10 ( 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 800 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 686 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 143 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8131 (t) REVERT: B 288 THR cc_start: 0.8056 (m) cc_final: 0.7768 (p) REVERT: N 56 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8295 (tt) REVERT: N 177 ASP cc_start: 0.8499 (t0) cc_final: 0.8226 (t0) REVERT: N 202 ASN cc_start: 0.8387 (t0) cc_final: 0.8124 (t0) REVERT: N 224 GLN cc_start: 0.7672 (mm110) cc_final: 0.7170 (mm-40) REVERT: A 61 LYS cc_start: 0.7844 (tttp) cc_final: 0.7625 (ttmt) REVERT: A 138 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7424 (mt0) REVERT: A 209 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: A 434 VAL cc_start: 0.8065 (t) cc_final: 0.7807 (p) REVERT: M 87 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7188 (t) REVERT: M 171 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8128 (ttp) REVERT: M 193 ASN cc_start: 0.8415 (m110) cc_final: 0.8045 (m110) REVERT: Q 124 MET cc_start: 0.6982 (mmm) cc_final: 0.6613 (mmp) REVERT: Q 218 PHE cc_start: 0.8616 (m-80) cc_final: 0.8270 (m-80) REVERT: C 385 ASP cc_start: 0.7622 (m-30) cc_final: 0.7313 (m-30) REVERT: C 434 VAL cc_start: 0.8093 (t) cc_final: 0.7787 (p) REVERT: O 87 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7412 (p) REVERT: O 165 GLU cc_start: 0.7744 (tt0) cc_final: 0.7500 (mt-10) REVERT: O 255 ILE cc_start: 0.7916 (pt) cc_final: 0.7400 (mt) REVERT: O 366 MET cc_start: 0.7404 (mpp) cc_final: 0.7067 (mpp) REVERT: O 384 THR cc_start: 0.8845 (m) cc_final: 0.8586 (t) REVERT: S 133 LYS cc_start: 0.8229 (mttm) cc_final: 0.7972 (mmmt) REVERT: S 242 VAL cc_start: 0.8576 (p) cc_final: 0.8307 (t) REVERT: D 15 TYR cc_start: 0.7673 (m-80) cc_final: 0.7438 (m-80) REVERT: D 42 LEU cc_start: 0.8429 (mt) cc_final: 0.8161 (mp) REVERT: D 299 MET cc_start: 0.8209 (mtp) cc_final: 0.7932 (mtm) REVERT: D 434 VAL cc_start: 0.7738 (t) cc_final: 0.7481 (p) REVERT: Z 34 MET cc_start: 0.6214 (mmm) cc_final: 0.5965 (mmm) REVERT: Y 31 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7835 (p) REVERT: P 24 GLU cc_start: 0.8018 (tp30) cc_final: 0.7723 (tp30) REVERT: P 52 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7815 (pp) REVERT: T 249 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.7024 (pp) outliers start: 114 outliers final: 73 residues processed: 749 average time/residue: 0.2060 time to fit residues: 252.2219 Evaluate side-chains 747 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 665 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 423 VAL 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 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 156 ARG Chi-restraints excluded: chain R residue 173 SER 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 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 203 ILE 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 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 244 THR Chi-restraints excluded: chain C residue 2 GLU 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 397 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain X residue 31 SER 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 54 ILE 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 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 143 THR 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 31 SER Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 30 SER 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 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 247 LYS 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: 9.9990 chunk 254 optimal weight: 5.9990 chunk 434 optimal weight: 0.7980 chunk 225 optimal weight: 7.9990 chunk 427 optimal weight: 1.9990 chunk 478 optimal weight: 0.8980 chunk 351 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 281 optimal weight: 0.0030 chunk 79 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 26 HIS N 224 GLN A 34 GLN A 175 ASN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN O 313 HIS O 341 GLN P 299 ASN T 170 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.143424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111204 restraints weight = 60431.037| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.34 r_work: 0.3239 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 38924 Z= 0.168 Angle : 0.601 10.294 53072 Z= 0.329 Chirality : 0.046 0.327 5960 Planarity : 0.006 0.055 6804 Dihedral : 4.698 31.544 5312 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.64 % Allowed : 13.30 % Favored : 84.05 % 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: -0.08 (0.12), residues: 4876 helix: 2.51 (0.25), residues: 431 sheet: 0.72 (0.12), residues: 1880 loop : -1.15 (0.11), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 156 TYR 0.020 0.002 TYR C 122 PHE 0.019 0.002 PHE C 436 TRP 0.016 0.001 TRP O 330 HIS 0.010 0.001 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (38844) covalent geometry : angle 0.59305 / 0.33 (52900) SS BOND : bond 0.00470 / 0.34 ( 68) SS BOND : angle 1.43826 / 1.05 ( 136) hydrogen bonds : bond 0.07331 / 4.95 ( 1445) hydrogen bonds : angle 5.30802 / 3.67 ( 3732) link_NAG-ASN : bond 0.00381 / 0.19 ( 12) link_NAG-ASN : angle 2.93086 / 1.99 ( 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: 110 poor density : 686 time to evaluate : 1.440 Fit side-chains revert: symmetry clash REVERT: B 143 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8150 (t) REVERT: B 196 ARG cc_start: 0.8067 (mmt-90) cc_final: 0.7682 (mmt-90) REVERT: B 288 THR cc_start: 0.8191 (m) cc_final: 0.7818 (p) REVERT: N 56 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8300 (tt) REVERT: N 202 ASN cc_start: 0.8388 (t0) cc_final: 0.8109 (t0) REVERT: N 224 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7249 (mm-40) REVERT: N 372 SER cc_start: 0.7894 (p) cc_final: 0.7549 (m) REVERT: A 61 LYS cc_start: 0.7732 (tttp) cc_final: 0.7532 (ttmt) REVERT: A 209 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: A 374 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 434 VAL cc_start: 0.7903 (t) cc_final: 0.7637 (p) REVERT: M 87 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7091 (t) REVERT: M 171 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8108 (ttp) REVERT: M 193 ASN cc_start: 0.8420 (m110) cc_final: 0.8016 (m110) REVERT: Q 124 MET cc_start: 0.6941 (mmm) cc_final: 0.6666 (mmp) REVERT: Q 218 PHE cc_start: 0.8624 (m-80) cc_final: 0.8294 (m-80) REVERT: C 385 ASP cc_start: 0.7665 (m-30) cc_final: 0.7328 (m-30) REVERT: C 434 VAL cc_start: 0.7948 (t) cc_final: 0.7618 (p) REVERT: O 87 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7370 (p) REVERT: O 165 GLU cc_start: 0.7766 (tt0) cc_final: 0.7527 (mt-10) REVERT: O 255 ILE cc_start: 0.7892 (pt) cc_final: 0.7376 (mt) REVERT: O 366 MET cc_start: 0.7177 (mpp) cc_final: 0.6910 (mpp) REVERT: O 384 THR cc_start: 0.8802 (m) cc_final: 0.8576 (t) REVERT: S 241 SER cc_start: 0.8073 (t) cc_final: 0.7854 (p) REVERT: D 15 TYR cc_start: 0.7681 (m-80) cc_final: 0.7465 (m-80) REVERT: D 42 LEU cc_start: 0.8461 (mt) cc_final: 0.8191 (mp) REVERT: D 130 SER cc_start: 0.8696 (p) cc_final: 0.8369 (m) REVERT: D 319 LYS cc_start: 0.8002 (mttm) cc_final: 0.7785 (mttm) REVERT: D 434 VAL cc_start: 0.7680 (t) cc_final: 0.7383 (p) REVERT: Z 34 MET cc_start: 0.6271 (mmm) cc_final: 0.6054 (mmm) REVERT: Y 4 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.4066 (mtm) REVERT: P 24 GLU cc_start: 0.8050 (tp30) cc_final: 0.7813 (tp30) REVERT: P 52 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7809 (pp) outliers start: 110 outliers final: 82 residues processed: 754 average time/residue: 0.2205 time to fit residues: 270.7462 Evaluate side-chains 749 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 658 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 210 SER 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 86 ARG Chi-restraints excluded: chain N residue 127 HIS Chi-restraints excluded: chain N residue 153 CYS 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 382 VAL Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 173 SER 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 R residue 260 GLU Chi-restraints excluded: chain A residue 19 VAL 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 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 230 THR 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 228 VAL 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 5 THR Chi-restraints excluded: chain C residue 63 CYS 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 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 8 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 54 ILE 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 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 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 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 52 LEU 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 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 247 LYS 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: 0.7980 chunk 8 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 chunk 228 optimal weight: 8.9990 chunk 139 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 336 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN A 175 ASN M 53 GLN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN S 166 GLN D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.145460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.113375 restraints weight = 60413.674| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.36 r_work: 0.3270 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2551 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= 0.128 Angle : 0.555 9.659 53072 Z= 0.300 Chirality : 0.045 0.312 5960 Planarity : 0.005 0.051 6804 Dihedral : 4.490 30.552 5312 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.67 % Allowed : 13.78 % Favored : 83.55 % 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: -0.04 (0.12), residues: 4876 helix: 2.74 (0.26), residues: 431 sheet: 0.78 (0.12), residues: 1835 loop : -1.15 (0.11), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 156 TYR 0.013 0.001 TYR C 122 PHE 0.019 0.001 PHE C 436 TRP 0.014 0.001 TRP O 330 HIS 0.006 0.001 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (38844) covalent geometry : angle 0.54826 / 0.30 (52900) SS BOND : bond 0.00416 / 0.31 ( 68) SS BOND : angle 1.17168 / 0.90 ( 136) hydrogen bonds : bond 0.06369 / 4.29 ( 1445) hydrogen bonds : angle 5.10189 / 3.53 ( 3732) link_NAG-ASN : bond 0.00424 / 0.21 ( 12) link_NAG-ASN : angle 2.73438 / 1.87 ( 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 773 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 662 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8069 (mt) REVERT: B 288 THR cc_start: 0.8129 (m) cc_final: 0.7863 (p) REVERT: N 171 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8092 (ttp) REVERT: N 202 ASN cc_start: 0.8391 (t0) cc_final: 0.8131 (t0) REVERT: N 224 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7206 (mm-40) REVERT: A 61 LYS cc_start: 0.7592 (tttp) cc_final: 0.7386 (ttmt) REVERT: A 209 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 434 VAL cc_start: 0.7705 (t) cc_final: 0.7421 (p) REVERT: M 87 THR cc_start: 0.7161 (OUTLIER) cc_final: 0.6787 (t) REVERT: M 171 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8023 (ttp) REVERT: M 193 ASN cc_start: 0.8362 (m110) cc_final: 0.7938 (m110) REVERT: M 224 GLN cc_start: 0.7580 (mm-40) cc_final: 0.6986 (mm-40) REVERT: Q 124 MET cc_start: 0.6874 (mmm) cc_final: 0.6617 (mmp) REVERT: Q 218 PHE cc_start: 0.8609 (m-80) cc_final: 0.8303 (m-80) REVERT: C 385 ASP cc_start: 0.7575 (m-30) cc_final: 0.7230 (m-30) REVERT: C 430 VAL cc_start: 0.8280 (t) cc_final: 0.7882 (t) REVERT: C 434 VAL cc_start: 0.7779 (t) cc_final: 0.7443 (p) REVERT: O 87 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7178 (p) REVERT: O 255 ILE cc_start: 0.7783 (pt) cc_final: 0.7290 (mt) REVERT: O 384 THR cc_start: 0.8708 (m) cc_final: 0.8497 (t) REVERT: O 402 LEU cc_start: 0.7802 (mt) cc_final: 0.7588 (mt) REVERT: D 15 TYR cc_start: 0.7642 (m-80) cc_final: 0.7425 (m-80) REVERT: D 42 LEU cc_start: 0.8390 (mt) cc_final: 0.8117 (mp) REVERT: D 112 GLU cc_start: 0.8018 (tp30) cc_final: 0.7770 (tp30) REVERT: D 130 SER cc_start: 0.8688 (p) cc_final: 0.8338 (m) REVERT: D 319 LYS cc_start: 0.7878 (mttm) cc_final: 0.7663 (mttm) REVERT: D 434 VAL cc_start: 0.7502 (t) cc_final: 0.7198 (p) REVERT: Y 4 MET cc_start: 0.4699 (OUTLIER) cc_final: 0.4113 (mtm) REVERT: P 24 GLU cc_start: 0.8028 (tp30) cc_final: 0.7804 (tp30) REVERT: P 52 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7723 (pp) REVERT: T 229 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8551 (pt) outliers start: 111 outliers final: 85 residues processed: 727 average time/residue: 0.2405 time to fit residues: 283.2164 Evaluate side-chains 752 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 658 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 157 LYS Chi-restraints excluded: chain B residue 210 SER 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 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 208 GLU Chi-restraints excluded: chain N residue 245 ASN 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 N residue 398 THR Chi-restraints excluded: chain R residue 173 SER 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 203 ILE 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 87 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 171 MET Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 372 SER Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 143 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 2 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 CYS 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 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 87 THR Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 159 SER Chi-restraints excluded: chain O residue 166 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 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 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 Y residue 60 SER 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 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 Chi-restraints excluded: chain T residue 229 LEU 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: 0.9980 chunk 142 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 359 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 181 optimal weight: 40.0000 chunk 240 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN A 175 ASN M 53 GLN M 158 GLN M 299 ASN C 394 HIS O 131 HIS O 313 HIS D 375 HIS P 299 ASN T 170 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.139796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107413 restraints weight = 60294.333| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.34 r_work: 0.3176 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 38924 Z= 0.277 Angle : 0.732 11.339 53072 Z= 0.402 Chirality : 0.051 0.344 5960 Planarity : 0.007 0.066 6804 Dihedral : 5.141 33.208 5312 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.00 % Allowed : 14.39 % Favored : 82.61 % 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: -0.56 (0.11), residues: 4876 helix: 2.19 (0.25), residues: 431 sheet: 0.72 (0.12), residues: 1712 loop : -1.62 (0.10), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 156 TYR 0.035 0.003 TYR C 122 PHE 0.025 0.003 PHE S 201 TRP 0.023 0.002 TRP T 189 HIS 0.014 0.002 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.28 (38844) covalent geometry : angle 0.72285 / 0.40 (52900) SS BOND : bond 0.00649 / 0.48 ( 68) SS BOND : angle 1.75509 / 1.29 ( 136) hydrogen bonds : bond 0.08840 / 5.99 ( 1445) hydrogen bonds : angle 5.51075 / 3.79 ( 3732) link_NAG-ASN : bond 0.00346 / 0.15 ( 12) link_NAG-ASN : angle 3.14753 / 2.11 ( 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 828 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 703 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8162 (mt) REVERT: B 196 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7796 (mmt-90) REVERT: B 288 THR cc_start: 0.8268 (m) cc_final: 0.7926 (p) REVERT: B 290 VAL cc_start: 0.7928 (p) cc_final: 0.7649 (t) REVERT: B 311 ASP cc_start: 0.7601 (t0) cc_final: 0.7354 (t0) REVERT: B 385 ASP cc_start: 0.7829 (m-30) cc_final: 0.7541 (m-30) REVERT: N 56 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8362 (tt) REVERT: N 171 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8176 (ttp) REVERT: N 202 ASN cc_start: 0.8398 (t0) cc_final: 0.8155 (t0) REVERT: N 291 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7160 (p-80) REVERT: N 372 SER cc_start: 0.7888 (p) cc_final: 0.7600 (m) REVERT: R 161 ASP cc_start: 0.8028 (m-30) cc_final: 0.7776 (m-30) REVERT: A 61 LYS cc_start: 0.7913 (tttp) cc_final: 0.7707 (ttmt) REVERT: A 187 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.8062 (ttm) REVERT: A 209 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: A 434 VAL cc_start: 0.8079 (t) cc_final: 0.7791 (p) REVERT: M 19 CYS cc_start: 0.7845 (t) cc_final: 0.7579 (t) REVERT: M 43 ASP cc_start: 0.8311 (m-30) cc_final: 0.8094 (m-30) REVERT: M 53 GLN cc_start: 0.8144 (mt0) cc_final: 0.7838 (mt0) REVERT: M 171 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8157 (ttp) REVERT: M 193 ASN cc_start: 0.8524 (m110) cc_final: 0.8134 (m110) REVERT: Q 124 MET cc_start: 0.6815 (mmm) cc_final: 0.6359 (mmp) REVERT: Q 218 PHE cc_start: 0.8676 (m-80) cc_final: 0.8338 (m-80) REVERT: C 13 VAL cc_start: 0.8175 (t) cc_final: 0.7768 (m) REVERT: C 385 ASP cc_start: 0.7890 (m-30) cc_final: 0.7568 (m-30) REVERT: C 434 VAL cc_start: 0.8094 (t) cc_final: 0.7816 (p) REVERT: W 52 SER cc_start: 0.8517 (m) cc_final: 0.8307 (p) REVERT: O 87 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7539 (p) REVERT: O 127 HIS cc_start: 0.8363 (OUTLIER) cc_final: 0.7814 (m170) REVERT: O 165 GLU cc_start: 0.7866 (tt0) cc_final: 0.7640 (mt-10) REVERT: O 255 ILE cc_start: 0.7934 (pt) cc_final: 0.7414 (mt) REVERT: O 384 THR cc_start: 0.8820 (m) cc_final: 0.8565 (t) REVERT: O 407 THR cc_start: 0.8583 (m) cc_final: 0.8316 (p) REVERT: S 124 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7667 (mmp) REVERT: S 177 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7851 (mmmm) REVERT: D 15 TYR cc_start: 0.7662 (m-80) cc_final: 0.7456 (m-80) REVERT: D 42 LEU cc_start: 0.8507 (mt) cc_final: 0.8244 (mp) REVERT: D 112 GLU cc_start: 0.8103 (tp30) cc_final: 0.7767 (tp30) REVERT: D 130 SER cc_start: 0.8705 (p) cc_final: 0.8364 (m) REVERT: D 132 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8237 (ttmm) REVERT: D 434 VAL cc_start: 0.7792 (t) cc_final: 0.7539 (p) REVERT: Y 4 MET cc_start: 0.4709 (OUTLIER) cc_final: 0.4129 (mtm) REVERT: P 52 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7737 (pp) REVERT: P 61 SER cc_start: 0.8296 (t) cc_final: 0.7874 (p) REVERT: T 114 ILE cc_start: 0.8570 (mt) cc_final: 0.8359 (mt) REVERT: T 229 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8617 (pt) outliers start: 125 outliers final: 98 residues processed: 770 average time/residue: 0.2344 time to fit residues: 292.5841 Evaluate side-chains 792 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 681 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 157 LYS 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 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 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 291 HIS Chi-restraints excluded: chain N residue 318 THR 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 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 10 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 72 SER 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 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 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 5 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 154 VAL 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 C residue 431 VAL 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 43 ASP 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 179 THR Chi-restraints excluded: chain O residue 211 THR Chi-restraints excluded: chain O residue 285 MET 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 225 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 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 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 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 229 LEU Chi-restraints excluded: chain T residue 247 LYS 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: 1.9990 chunk 424 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 412 optimal weight: 6.9990 chunk 335 optimal weight: 4.9990 chunk 305 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 456 optimal weight: 2.9990 chunk 239 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 ASN M 158 GLN C 349 ASN O 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 = 0.3800 r_free = 0.3800 target = 0.144080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.112023 restraints weight = 60008.149| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.34 r_work: 0.3249 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 38924 Z= 0.134 Angle : 0.586 12.617 53072 Z= 0.315 Chirality : 0.045 0.314 5960 Planarity : 0.006 0.054 6804 Dihedral : 4.685 32.172 5312 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.76 % Allowed : 14.96 % Favored : 82.28 % 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: 2.54 (0.26), residues: 431 sheet: 0.68 (0.12), residues: 1793 loop : -1.49 (0.11), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 298 TYR 0.022 0.001 TYR M 297 PHE 0.021 0.001 PHE C 436 TRP 0.013 0.001 TRP D 89 HIS 0.006 0.001 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (38844) covalent geometry : angle 0.57607 / 0.31 (52900) SS BOND : bond 0.00410 / 0.29 ( 68) SS BOND : angle 1.64699 / 1.31 ( 136) hydrogen bonds : bond 0.06680 / 4.50 ( 1445) hydrogen bonds : angle 5.18173 / 3.58 ( 3732) link_NAG-ASN : bond 0.00477 / 0.24 ( 12) link_NAG-ASN : angle 2.89354 / 1.96 ( 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: 115 poor density : 677 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 SER cc_start: 0.8575 (p) cc_final: 0.8286 (m) REVERT: B 133 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 196 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7768 (mmt-90) REVERT: B 288 THR cc_start: 0.8187 (m) cc_final: 0.7940 (p) REVERT: B 290 VAL cc_start: 0.7926 (p) cc_final: 0.7630 (t) REVERT: B 311 ASP cc_start: 0.7547 (t0) cc_final: 0.7317 (t0) REVERT: B 385 ASP cc_start: 0.7675 (m-30) cc_final: 0.7365 (m-30) REVERT: L 31 SER cc_start: 0.8461 (m) cc_final: 0.8253 (p) REVERT: N 56 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8316 (tt) REVERT: N 171 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8106 (ttp) REVERT: N 202 ASN cc_start: 0.8405 (t0) cc_final: 0.8126 (t0) REVERT: N 224 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7413 (mm-40) REVERT: N 291 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6955 (p-80) REVERT: N 372 SER cc_start: 0.7818 (p) cc_final: 0.7522 (m) REVERT: A 61 LYS cc_start: 0.7772 (tttp) cc_final: 0.7554 (ttmt) REVERT: A 209 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: A 434 VAL cc_start: 0.7847 (t) cc_final: 0.7563 (p) REVERT: M 53 GLN cc_start: 0.7993 (mt0) cc_final: 0.7711 (mt0) REVERT: M 87 THR cc_start: 0.7158 (OUTLIER) cc_final: 0.6794 (t) REVERT: M 171 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8025 (ttp) REVERT: M 193 ASN cc_start: 0.8432 (m110) cc_final: 0.8042 (m110) REVERT: M 224 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7138 (mm-40) REVERT: M 302 GLN cc_start: 0.8204 (tt0) cc_final: 0.8001 (tt0) REVERT: Q 124 MET cc_start: 0.6725 (mmm) cc_final: 0.6303 (mmp) REVERT: Q 218 PHE cc_start: 0.8611 (m-80) cc_final: 0.8304 (m-80) REVERT: C 13 VAL cc_start: 0.8091 (t) cc_final: 0.7651 (m) REVERT: C 44 LEU cc_start: 0.8248 (tt) cc_final: 0.7998 (tp) REVERT: C 385 ASP cc_start: 0.7717 (m-30) cc_final: 0.7391 (m-30) REVERT: C 430 VAL cc_start: 0.8389 (t) cc_final: 0.7954 (t) REVERT: X 70 ILE cc_start: 0.7581 (tt) cc_final: 0.7232 (pt) REVERT: W 52 SER cc_start: 0.8476 (m) cc_final: 0.8247 (p) REVERT: O 87 THR cc_start: 0.7736 (OUTLIER) cc_final: 0.7491 (t) REVERT: O 127 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7583 (m170) REVERT: O 255 ILE cc_start: 0.7875 (pt) cc_final: 0.7344 (mt) REVERT: O 384 THR cc_start: 0.8755 (m) cc_final: 0.8551 (t) REVERT: S 124 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7584 (mmp) REVERT: S 241 SER cc_start: 0.8170 (t) cc_final: 0.7913 (p) REVERT: D 15 TYR cc_start: 0.7707 (m-80) cc_final: 0.7506 (m-80) REVERT: D 42 LEU cc_start: 0.8502 (mt) cc_final: 0.8250 (mp) REVERT: D 112 GLU cc_start: 0.8049 (tp30) cc_final: 0.7711 (tp30) REVERT: D 130 SER cc_start: 0.8704 (p) cc_final: 0.8367 (m) REVERT: D 156 VAL cc_start: 0.7697 (t) cc_final: 0.7415 (p) REVERT: D 319 LYS cc_start: 0.8006 (mttp) cc_final: 0.7802 (mttm) REVERT: D 434 VAL cc_start: 0.7608 (t) cc_final: 0.7303 (p) REVERT: Y 4 MET cc_start: 0.4712 (OUTLIER) cc_final: 0.4141 (mtm) REVERT: P 52 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7724 (pp) outliers start: 115 outliers final: 87 residues processed: 743 average time/residue: 0.2342 time to fit residues: 282.8236 Evaluate side-chains 762 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 663 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 275 ASN 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 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 56 ILE 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 245 ASN 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 382 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain R residue 173 SER 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 A residue 19 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE 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 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 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 5 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 364 GLU 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 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 127 HIS Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 285 MET 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 124 MET 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 245 LYS 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 24 GLU 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 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: 3.9990 chunk 120 optimal weight: 4.9990 chunk 378 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 80 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN M 158 GLN O 158 GLN O 313 HIS 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 = 0.3775 r_free = 0.3775 target = 0.142389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110308 restraints weight = 60193.148| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.35 r_work: 0.3209 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 38924 Z= 0.195 Angle : 0.646 13.371 53072 Z= 0.349 Chirality : 0.048 0.325 5960 Planarity : 0.006 0.059 6804 Dihedral : 4.847 32.355 5312 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.67 % Allowed : 15.03 % Favored : 82.30 % 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: -0.49 (0.11), residues: 4876 helix: 2.46 (0.26), residues: 431 sheet: 0.70 (0.12), residues: 1730 loop : -1.58 (0.11), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 156 TYR 0.026 0.002 TYR C 122 PHE 0.021 0.002 PHE C 436 TRP 0.015 0.002 TRP O 330 HIS 0.011 0.002 HIS P 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (38844) covalent geometry : angle 0.63639 / 0.35 (52900) SS BOND : bond 0.00553 / 0.41 ( 68) SS BOND : angle 1.71590 / 1.33 ( 136) hydrogen bonds : bond 0.07561 / 5.11 ( 1445) hydrogen bonds : angle 5.25555 / 3.62 ( 3732) link_NAG-ASN : bond 0.00374 / 0.17 ( 12) link_NAG-ASN : angle 2.91186 / 1.95 ( 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 788 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 677 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 133 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8182 (mt) REVERT: B 196 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7790 (mmt-90) REVERT: B 288 THR cc_start: 0.8261 (m) cc_final: 0.7926 (p) REVERT: B 290 VAL cc_start: 0.7945 (p) cc_final: 0.7648 (t) REVERT: B 311 ASP cc_start: 0.7603 (t0) cc_final: 0.7367 (t0) REVERT: B 385 ASP cc_start: 0.7767 (m-30) cc_final: 0.7446 (m-30) REVERT: L 31 SER cc_start: 0.8443 (m) cc_final: 0.8165 (p) REVERT: N 56 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8357 (tt) REVERT: N 171 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: N 202 ASN cc_start: 0.8407 (t0) cc_final: 0.8167 (t0) REVERT: N 291 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.7115 (p-80) REVERT: N 372 SER cc_start: 0.7841 (p) cc_final: 0.7561 (m) REVERT: A 209 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 434 VAL cc_start: 0.7898 (t) cc_final: 0.7591 (p) REVERT: M 19 CYS cc_start: 0.7741 (t) cc_final: 0.7450 (t) REVERT: M 53 GLN cc_start: 0.8055 (mt0) cc_final: 0.7792 (mt0) REVERT: M 87 THR cc_start: 0.7252 (OUTLIER) cc_final: 0.6892 (t) REVERT: M 171 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8081 (ttp) REVERT: M 193 ASN cc_start: 0.8459 (m110) cc_final: 0.8090 (m110) REVERT: Q 124 MET cc_start: 0.6770 (mmm) cc_final: 0.6320 (mmp) REVERT: Q 218 PHE cc_start: 0.8657 (m-80) cc_final: 0.8352 (m-80) REVERT: C 13 VAL cc_start: 0.8146 (t) cc_final: 0.7721 (m) REVERT: C 385 ASP cc_start: 0.7808 (m-30) cc_final: 0.7512 (m-30) REVERT: C 430 VAL cc_start: 0.8535 (t) cc_final: 0.8138 (t) REVERT: C 434 VAL cc_start: 0.7972 (t) cc_final: 0.7656 (p) REVERT: X 70 ILE cc_start: 0.7600 (tt) cc_final: 0.7238 (pt) REVERT: W 52 SER cc_start: 0.8504 (m) cc_final: 0.8303 (p) REVERT: O 87 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7436 (p) REVERT: O 127 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7811 (m170) REVERT: O 165 GLU cc_start: 0.7828 (tt0) cc_final: 0.7596 (mt-10) REVERT: O 255 ILE cc_start: 0.7906 (pt) cc_final: 0.7372 (mt) REVERT: O 384 THR cc_start: 0.8804 (m) cc_final: 0.8592 (t) REVERT: S 124 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7538 (mmp) REVERT: S 241 SER cc_start: 0.8239 (t) cc_final: 0.7863 (p) REVERT: D 42 LEU cc_start: 0.8514 (mt) cc_final: 0.8262 (mp) REVERT: D 112 GLU cc_start: 0.8122 (tp30) cc_final: 0.7774 (tp30) REVERT: D 130 SER cc_start: 0.8700 (p) cc_final: 0.8368 (m) REVERT: D 156 VAL cc_start: 0.7731 (t) cc_final: 0.7467 (p) REVERT: D 319 LYS cc_start: 0.8078 (mttp) cc_final: 0.7868 (mttm) REVERT: D 434 VAL cc_start: 0.7668 (t) cc_final: 0.7387 (p) REVERT: Y 4 MET cc_start: 0.4743 (OUTLIER) cc_final: 0.4110 (mtm) REVERT: Y 60 SER cc_start: 0.7157 (OUTLIER) cc_final: 0.6868 (m) REVERT: P 52 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7740 (pp) REVERT: P 61 SER cc_start: 0.8277 (t) cc_final: 0.7879 (p) REVERT: T 114 ILE cc_start: 0.8643 (mt) cc_final: 0.8431 (mt) REVERT: T 229 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8590 (pt) outliers start: 111 outliers final: 87 residues processed: 737 average time/residue: 0.2194 time to fit residues: 263.4866 Evaluate side-chains 768 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 667 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 157 LYS Chi-restraints excluded: chain B residue 275 ASN 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 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 86 ARG Chi-restraints excluded: chain N residue 127 HIS 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 291 HIS Chi-restraints excluded: chain N residue 318 THR 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 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 144 VAL 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 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 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 5 THR Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 364 GLU 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 W residue 9 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 54 ILE 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 159 SER Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 179 THR Chi-restraints excluded: chain O residue 285 MET 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 124 MET Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 133 LEU 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 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 24 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 87 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 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 229 LEU Chi-restraints excluded: chain T residue 247 LYS 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: 0.0270 chunk 121 optimal weight: 0.0010 chunk 445 optimal weight: 4.9990 chunk 209 optimal weight: 3.9990 chunk 276 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 181 optimal weight: 40.0000 chunk 139 optimal weight: 0.0970 chunk 240 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 HIS N 341 GLN A 175 ASN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 HIS C 349 ASN 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 = 0.3843 r_free = 0.3843 target = 0.147443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115676 restraints weight = 60717.397| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.39 r_work: 0.3303 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 38924 Z= 0.109 Angle : 0.552 15.677 53072 Z= 0.290 Chirality : 0.044 0.311 5960 Planarity : 0.005 0.049 6804 Dihedral : 4.398 39.313 5312 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.78 % Allowed : 16.19 % Favored : 82.04 % 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: -0.26 (0.12), residues: 4876 helix: 2.82 (0.26), residues: 435 sheet: 0.72 (0.12), residues: 1802 loop : -1.41 (0.11), residues: 2639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 156 TYR 0.011 0.001 TYR Q 187 PHE 0.022 0.001 PHE C 436 TRP 0.017 0.001 TRP D 89 HIS 0.008 0.001 HIS C 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (38844) covalent geometry : angle 0.54379 / 0.29 (52900) SS BOND : bond 0.00364 / 0.27 ( 68) SS BOND : angle 1.30623 / 1.04 ( 136) hydrogen bonds : bond 0.05337 / 3.59 ( 1445) hydrogen bonds : angle 4.93404 / 3.41 ( 3732) link_NAG-ASN : bond 0.00585 / 0.31 ( 12) link_NAG-ASN : angle 2.73573 / 1.88 ( 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 746 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 672 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 SER cc_start: 0.8532 (p) cc_final: 0.8293 (m) REVERT: B 133 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8111 (mt) REVERT: B 288 THR cc_start: 0.8163 (m) cc_final: 0.7915 (p) REVERT: B 290 VAL cc_start: 0.7870 (p) cc_final: 0.7544 (t) REVERT: B 311 ASP cc_start: 0.7562 (t0) cc_final: 0.7324 (t0) REVERT: N 202 ASN cc_start: 0.8403 (t0) cc_final: 0.8135 (t0) REVERT: N 224 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7471 (mm-40) REVERT: N 291 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6632 (p-80) REVERT: A 9 ASN cc_start: 0.8464 (t0) cc_final: 0.7974 (t0) REVERT: A 209 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 434 VAL cc_start: 0.7543 (t) cc_final: 0.7231 (p) REVERT: M 53 GLN cc_start: 0.7815 (mt0) cc_final: 0.7550 (mt0) REVERT: M 56 ILE cc_start: 0.8569 (mt) cc_final: 0.8361 (tt) REVERT: M 193 ASN cc_start: 0.8364 (m110) cc_final: 0.7997 (m110) REVERT: M 224 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7071 (mm-40) REVERT: M 264 VAL cc_start: 0.8040 (OUTLIER) cc_final: 0.7775 (m) REVERT: Q 124 MET cc_start: 0.6834 (mmm) cc_final: 0.6469 (mmp) REVERT: Q 218 PHE cc_start: 0.8614 (m-80) cc_final: 0.8312 (m-80) REVERT: C 112 GLU cc_start: 0.8208 (tp30) cc_final: 0.7944 (tp30) REVERT: C 385 ASP cc_start: 0.7548 (m-30) cc_final: 0.7236 (m-30) REVERT: X 70 ILE cc_start: 0.7524 (tt) cc_final: 0.7242 (pt) REVERT: W 52 SER cc_start: 0.8484 (m) cc_final: 0.8255 (p) REVERT: O 127 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7445 (m170) REVERT: O 165 GLU cc_start: 0.7777 (tt0) cc_final: 0.7550 (mt-10) REVERT: O 178 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7856 (mtp85) REVERT: S 241 SER cc_start: 0.8271 (t) cc_final: 0.8040 (p) REVERT: D 42 LEU cc_start: 0.8411 (mt) cc_final: 0.8138 (mp) REVERT: D 112 GLU cc_start: 0.8054 (tp30) cc_final: 0.7761 (tp30) REVERT: D 130 SER cc_start: 0.8711 (p) cc_final: 0.8351 (m) REVERT: D 156 VAL cc_start: 0.7625 (t) cc_final: 0.7352 (p) REVERT: Y 4 MET cc_start: 0.4702 (OUTLIER) cc_final: 0.4088 (mtm) REVERT: Y 60 SER cc_start: 0.7125 (p) cc_final: 0.6825 (m) REVERT: P 61 SER cc_start: 0.8251 (t) cc_final: 0.7839 (p) REVERT: T 229 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (pp) outliers start: 74 outliers final: 53 residues processed: 716 average time/residue: 0.2363 time to fit residues: 275.3064 Evaluate side-chains 714 residues out of total 4164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 654 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 87 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 275 ASN 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 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 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 398 THR Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 223 ARG Chi-restraints excluded: chain A residue 72 SER 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 U residue 31 SER Chi-restraints excluded: chain M residue 22 CYS Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 264 VAL Chi-restraints excluded: chain M residue 386 VAL Chi-restraints excluded: chain Q residue 130 VAL Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 CYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 364 GLU 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 63 SER Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 105 CYS Chi-restraints excluded: chain O residue 127 HIS Chi-restraints excluded: chain O residue 166 GLU Chi-restraints excluded: chain O residue 285 MET Chi-restraints excluded: chain O residue 397 ILE Chi-restraints excluded: chain S residue 176 SER Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain D residue 79 LYS 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 Y residue 4 MET Chi-restraints excluded: chain P residue 22 CYS Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 291 HIS Chi-restraints excluded: chain T residue 184 GLU Chi-restraints excluded: chain T residue 228 VAL Chi-restraints excluded: chain T residue 229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 229 optimal weight: 10.0000 chunk 455 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 chunk 137 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 449 optimal weight: 0.9980 chunk 344 optimal weight: 0.4980 chunk 248 optimal weight: 0.9990 chunk 391 optimal weight: 5.9990 chunk 360 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 HIS A 175 ASN M 158 GLN ** M 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 302 GLN C 349 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 = 0.3833 r_free = 0.3833 target = 0.146792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115024 restraints weight = 60852.250| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.38 r_work: 0.3293 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 38924 Z= 0.114 Angle : 0.563 15.580 53072 Z= 0.292 Chirality : 0.045 0.304 5960 Planarity : 0.005 0.056 6804 Dihedral : 4.274 33.621 5312 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.49 % Allowed : 16.81 % Favored : 81.70 % 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: -0.16 (0.12), residues: 4876 helix: 2.86 (0.26), residues: 435 sheet: 0.74 (0.12), residues: 1854 loop : -1.34 (0.11), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 156 TYR 0.012 0.001 TYR C 122 PHE 0.022 0.001 PHE C 436 TRP 0.012 0.001 TRP O 330 HIS 0.010 0.001 HIS C 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (38844) covalent geometry : angle 0.55524 / 0.29 (52900) SS BOND : bond 0.00362 / 0.26 ( 68) SS BOND : angle 1.39728 / 1.11 ( 136) hydrogen bonds : bond 0.05343 / 3.60 ( 1445) hydrogen bonds : angle 4.81621 / 3.33 ( 3732) link_NAG-ASN : bond 0.00402 / 0.20 ( 12) link_NAG-ASN : angle 2.47287 / 1.68 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12817.66 seconds wall clock time: 218 minutes 42.52 seconds (13122.52 seconds total)