Starting phenix.real_space_refine on Fri May 30 06:40:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqz_47119/05_2025/9dqz_47119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqz_47119/05_2025/9dqz_47119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dqz_47119/05_2025/9dqz_47119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqz_47119/05_2025/9dqz_47119.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqz_47119/05_2025/9dqz_47119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqz_47119/05_2025/9dqz_47119.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.009 sd= 0.059 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 244 5.16 5 C 21076 2.51 5 N 5745 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33465 Number of models: 1 Model: "" Number of chains: 28 Chain: "D" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "E" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "F" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "G" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "H" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "I" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "J" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "K" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "L" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "M" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "N" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "O" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain breaks: 1 Chain: "A" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "C" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "P" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.25, per 1000 atoms: 0.55 Number of scatterers: 33465 At special positions: 0 Unit cell: (188.68, 175.96, 204.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 244 16.00 O 6392 8.00 N 5745 7.00 C 21076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=80, symmetry=0 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=2.02 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.04 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 226 " distance=2.04 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.04 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.04 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.02 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.02 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.04 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 45 " distance=2.03 Simple disulfide: pdb=" SG CYS M 40 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 52 " - pdb=" SG CYS M 67 " distance=2.03 Simple disulfide: pdb=" SG CYS M 72 " - pdb=" SG CYS M 84 " distance=2.03 Simple disulfide: pdb=" SG CYS M 79 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 108 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 45 " distance=2.03 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 52 " - pdb=" SG CYS N 67 " distance=2.03 Simple disulfide: pdb=" SG CYS N 72 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS N 79 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 108 " distance=2.03 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 45 " distance=2.03 Simple disulfide: pdb=" SG CYS O 40 " - pdb=" SG CYS O 58 " distance=2.03 Simple disulfide: pdb=" SG CYS O 52 " - pdb=" SG CYS O 67 " distance=2.03 Simple disulfide: pdb=" SG CYS O 72 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS O 79 " - pdb=" SG CYS O 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 108 " 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=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 33 " - pdb=" SG CYS P 45 " distance=2.03 Simple disulfide: pdb=" SG CYS P 40 " - pdb=" SG CYS P 58 " distance=2.03 Simple disulfide: pdb=" SG CYS P 52 " - pdb=" SG CYS P 67 " distance=2.03 Simple disulfide: pdb=" SG CYS P 72 " - pdb=" SG CYS P 84 " distance=2.03 Simple disulfide: pdb=" SG CYS P 79 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 108 " 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 139 " " NAG A 502 " - " ASN A 245 " " NAG B 501 " - " ASN B 196 " " NAG B 502 " - " ASN B 318 " " NAG D 501 " - " ASN D 139 " " NAG D 502 " - " ASN D 245 " " NAG E 501 " - " ASN E 196 " " NAG E 502 " - " ASN E 318 " " NAG G 501 " - " ASN G 139 " " NAG G 502 " - " ASN G 245 " " NAG H 501 " - " ASN H 196 " " NAG H 502 " - " ASN H 318 " " NAG J 501 " - " ASN J 139 " " NAG J 502 " - " ASN J 245 " " NAG K 501 " - " ASN K 196 " " NAG K 502 " - " ASN K 318 " Time building additional restraints: 7.42 Conformation dependent library (CDL) restraints added in 4.1 seconds 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7982 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 97 sheets defined 13.3% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'D' and resid 111 through 116 removed outlier: 4.346A pdb=" N THR D 115 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 116 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.542A pdb=" N THR D 254 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.148A pdb=" N GLY D 258 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 259' Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.840A pdb=" N VAL D 402 " --> pdb=" O PHE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 438 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 363 through 402 Proline residue: E 399 - end of helix Processing helix chain 'F' and resid 7 through 11 Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.975A pdb=" N LYS F 73 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.646A pdb=" N GLY F 100 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.853A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 402 removed outlier: 3.949A pdb=" N VAL G 402 " --> pdb=" O PHE G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 438 Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 222 through 226 removed outlier: 3.564A pdb=" N GLN H 225 " --> pdb=" O LYS H 222 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS H 226 " --> pdb=" O ALA H 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 222 through 226' Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 363 through 402 removed outlier: 3.512A pdb=" N THR H 367 " --> pdb=" O HIS H 363 " (cutoff:3.500A) Proline residue: H 399 - end of helix removed outlier: 3.662A pdb=" N LEU H 402 " --> pdb=" O THR H 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 47 through 52 removed outlier: 3.535A pdb=" N ALA I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 removed outlier: 4.123A pdb=" N GLY I 100 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 255 Processing helix chain 'J' and resid 256 through 259 Processing helix chain 'J' and resid 403 through 438 Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 363 through 402 Proline residue: K 399 - end of helix removed outlier: 3.572A pdb=" N LEU K 402 " --> pdb=" O THR K 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 98 through 101 Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'M' and resid 100 through 104 removed outlier: 3.592A pdb=" N GLU M 103 " --> pdb=" O GLY M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 100 through 104 removed outlier: 3.519A pdb=" N SER N 104 " --> pdb=" O SER N 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'O' and resid 100 through 104 removed outlier: 3.597A pdb=" N GLU O 103 " --> pdb=" O GLY O 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.051A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.817A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 438 Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.715A pdb=" N CYS B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.506A pdb=" N ILE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 402 Proline residue: B 399 - end of helix Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 47 through 52 removed outlier: 4.265A pdb=" N ALA C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 61 through 66 removed outlier: 3.698A pdb=" N ASN P 66 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 7 removed outlier: 4.068A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 19 removed outlier: 6.114A pdb=" N ILE D 13 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL D 33 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.814A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.842A pdb=" N GLN D 59 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN D 102 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 80 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER D 104 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS D 78 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA D 106 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 76 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 74 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'D' and resid 296 through 304 removed outlier: 4.664A pdb=" N GLU D 298 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 321 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 315 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.511A pdb=" N HIS E 256 " --> pdb=" O THR E 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 35 removed outlier: 8.495A pdb=" N ILE E 31 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N SER E 48 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN E 33 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR E 99 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN E 104 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG E 93 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 83 through 86 removed outlier: 4.300A pdb=" N ASP E 109 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AB8, first strand: chain 'E' and resid 180 through 183 Processing sheet with id=AB9, first strand: chain 'E' and resid 206 through 211 removed outlier: 3.813A pdb=" N GLU E 200 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE E 227 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 276 through 279 Processing sheet with id=AC2, first strand: chain 'F' and resid 44 through 45 removed outlier: 3.540A pdb=" N GLY F 26 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR F 27 " --> pdb=" O PRO F 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 88 through 89 Processing sheet with id=AC4, first strand: chain 'F' and resid 117 through 119 removed outlier: 8.163A pdb=" N ALA F 127 " --> pdb=" O TRP F 146 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N TRP F 146 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL F 129 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL F 144 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.936A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.503A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.811A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.792A pdb=" N GLN G 59 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN G 102 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL G 80 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER G 104 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS G 78 " --> pdb=" O SER G 104 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA G 106 " --> pdb=" O TYR G 76 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR G 76 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AD1, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD2, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD3, first strand: chain 'G' and resid 296 through 303 removed outlier: 3.838A pdb=" N GLU G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AD5, first strand: chain 'G' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD7, first strand: chain 'H' and resid 14 through 16 removed outlier: 3.748A pdb=" N CYS H 16 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS H 25 " --> pdb=" O CYS H 16 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 31 through 35 removed outlier: 8.443A pdb=" N ILE H 31 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 48 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN H 33 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N SER H 48 " --> pdb=" O MET H 67 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET H 67 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS H 63 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 31 through 35 removed outlier: 8.443A pdb=" N ILE H 31 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 48 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN H 33 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR H 99 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA H 49 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LYS H 97 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N PHE H 51 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY H 95 " --> pdb=" O PHE H 51 " (cutoff:3.500A) removed outlier: 15.517A pdb=" N TYR H 53 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 17.918A pdb=" N ARG H 93 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 83 through 86 removed outlier: 4.343A pdb=" N ASP H 109 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AE3, first strand: chain 'H' and resid 237 through 238 removed outlier: 5.511A pdb=" N ILE H 257 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR H 165 " --> pdb=" O LEU H 255 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU H 255 " --> pdb=" O TYR H 165 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR H 167 " --> pdb=" O GLY H 253 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY H 253 " --> pdb=" O THR H 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 180 through 183 removed outlier: 4.126A pdb=" N ILE H 189 " --> pdb=" O THR H 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR H 215 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 206 through 211 Processing sheet with id=AE6, first strand: chain 'H' and resid 276 through 279 removed outlier: 3.657A pdb=" N GLY H 282 " --> pdb=" O TRP H 279 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 44 through 45 removed outlier: 3.667A pdb=" N GLY I 26 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR I 27 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 94 through 95 removed outlier: 6.725A pdb=" N ILE I 118 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL I 126 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP I 146 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER I 142 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY I 132 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA I 140 " --> pdb=" O GLY I 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 94 through 95 removed outlier: 6.725A pdb=" N ILE I 118 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL I 126 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP I 146 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER I 142 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY I 132 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA I 140 " --> pdb=" O GLY I 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.885A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 12 through 20 removed outlier: 6.111A pdb=" N ILE J 13 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL J 33 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU J 29 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR J 137 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE J 31 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE J 135 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL J 33 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU J 133 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER J 35 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL J 131 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU J 37 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU J 129 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR J 39 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA J 127 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER J 41 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA J 119 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.623A pdb=" N ALA J 119 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER J 41 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA J 127 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR J 39 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU J 129 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU J 37 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL J 131 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER J 35 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU J 133 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL J 33 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE J 135 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE J 31 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR J 137 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU J 29 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 59 through 62 removed outlier: 3.672A pdb=" N GLN J 59 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 87 through 88 removed outlier: 3.514A pdb=" N GLY J 91 " --> pdb=" O MET J 88 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 203 through 205 Processing sheet with id=AF7, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF8, first strand: chain 'J' and resid 299 through 304 removed outlier: 4.295A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 343 through 346 Processing sheet with id=AG1, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.846A pdb=" N ARG K 291 " --> pdb=" O GLY K 313 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY K 313 " --> pdb=" O ARG K 291 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 14 through 16 Processing sheet with id=AG3, first strand: chain 'K' and resid 31 through 35 removed outlier: 8.514A pdb=" N ILE K 31 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER K 48 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N SER K 48 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET K 67 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS K 63 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 31 through 35 removed outlier: 8.514A pdb=" N ILE K 31 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER K 48 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR K 99 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA K 49 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LYS K 97 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE K 51 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.598A pdb=" N GLY K 95 " --> pdb=" O PHE K 51 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 83 through 86 removed outlier: 4.428A pdb=" N ASP K 109 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 150 through 155 Processing sheet with id=AG7, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AG8, first strand: chain 'K' and resid 180 through 182 Processing sheet with id=AG9, first strand: chain 'K' and resid 207 through 211 Processing sheet with id=AH1, first strand: chain 'K' and resid 276 through 279 Processing sheet with id=AH2, first strand: chain 'L' and resid 44 through 45 removed outlier: 6.672A pdb=" N PHE L 16 " --> pdb=" O TYR L 27 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR L 27 " --> pdb=" O PHE L 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE L 18 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR L 27 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 87 through 89 Processing sheet with id=AH4, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.695A pdb=" N ALA L 127 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AH6, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AH7, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AH8, first strand: chain 'N' and resid 76 through 78 Processing sheet with id=AH9, first strand: chain 'O' and resid 37 through 39 Processing sheet with id=AI1, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AI2, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.937A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'A' and resid 12 through 19 removed outlier: 5.972A pdb=" N ILE A 13 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL A 33 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 29 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR A 137 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 33 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 35 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 131 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 129 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA A 127 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER A 41 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.456A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER A 41 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA A 127 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 129 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 131 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 35 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 33 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR A 137 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 29 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.870A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 102 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL A 80 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 104 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS A 78 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 106 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 76 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 74 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.514A pdb=" N GLY A 91 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AI8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AI9, first strand: chain 'A' and resid 296 through 304 Processing sheet with id=AJ1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AJ2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AJ3, first strand: chain 'B' and resid 14 through 16 removed outlier: 3.529A pdb=" N GLY B 14 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 27 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B 25 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.796A pdb=" N GLN B 46 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 34 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 102 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'B' and resid 51 through 53 removed outlier: 4.783A pdb=" N GLY B 52 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AJ7, first strand: chain 'B' and resid 150 through 155 Processing sheet with id=AJ8, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AJ9, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AK1, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AK2, first strand: chain 'B' and resid 276 through 279 Processing sheet with id=AK3, first strand: chain 'C' and resid 44 through 45 removed outlier: 4.001A pdb=" N GLY C 26 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR C 27 " --> pdb=" O PRO C 38 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'C' and resid 88 through 90 removed outlier: 8.837A pdb=" N ALA C 94 " --> pdb=" O PRO C 105 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE C 102 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 140 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY C 132 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 142 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 127 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'C' and resid 88 through 90 removed outlier: 8.837A pdb=" N ALA C 94 " --> pdb=" O PRO C 105 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE C 102 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AK7, first strand: chain 'P' and resid 76 through 78 1114 hydrogen bonds defined for protein. 2922 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: 12.44 Time building geometry restraints manager: 8.81 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: 10881 1.34 - 1.47: 8339 1.47 - 1.60: 14766 1.60 - 1.73: 1 1.73 - 1.85: 304 Bond restraints: 34291 Sorted by residual: bond pdb=" CG LEU J 428 " pdb=" CD2 LEU J 428 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" CB ASP H 36 " pdb=" CG ASP H 36 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.40e+00 bond pdb=" CA GLU E 342 " pdb=" CB GLU E 342 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.22e-02 6.72e+03 2.07e+00 bond pdb=" CA ASN C 47 " pdb=" CB ASN C 47 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 1.99e+00 bond pdb=" CB ASN L 47 " pdb=" CG ASN L 47 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 34286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 46045 2.96 - 5.91: 544 5.91 - 8.87: 51 8.87 - 11.82: 7 11.82 - 14.78: 4 Bond angle restraints: 46651 Sorted by residual: angle pdb=" C ASP C 46 " pdb=" N ASN C 47 " pdb=" CA ASN C 47 " ideal model delta sigma weight residual 121.54 132.61 -11.07 1.91e+00 2.74e-01 3.36e+01 angle pdb=" C VAL G 263 " pdb=" N GLU G 264 " pdb=" CA GLU G 264 " ideal model delta sigma weight residual 121.80 135.77 -13.97 2.44e+00 1.68e-01 3.28e+01 angle pdb=" CA CYS K 226 " pdb=" CB CYS K 226 " pdb=" SG CYS K 226 " ideal model delta sigma weight residual 114.40 126.96 -12.56 2.30e+00 1.89e-01 2.98e+01 angle pdb=" C LEU F 20 " pdb=" N ASN F 21 " pdb=" CA ASN F 21 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" CB MET C 19 " pdb=" CG MET C 19 " pdb=" SD MET C 19 " ideal model delta sigma weight residual 112.70 126.21 -13.51 3.00e+00 1.11e-01 2.03e+01 ... (remaining 46646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 19250 17.92 - 35.84: 1332 35.84 - 53.76: 231 53.76 - 71.68: 66 71.68 - 89.61: 24 Dihedral angle restraints: 20903 sinusoidal: 8448 harmonic: 12455 Sorted by residual: dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 -177.82 -89.18 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS K 152 " pdb=" SG CYS K 152 " pdb=" SG CYS K 266 " pdb=" CB CYS K 266 " ideal model delta sinusoidal sigma weight residual -86.00 -174.77 88.77 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual -86.00 -174.28 88.28 1 1.00e+01 1.00e-02 9.31e+01 ... (remaining 20900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4873 0.105 - 0.209: 360 0.209 - 0.314: 12 0.314 - 0.419: 0 0.419 - 0.523: 1 Chirality restraints: 5246 Sorted by residual: chirality pdb=" CB ILE G 307 " pdb=" CA ILE G 307 " pdb=" CG1 ILE G 307 " pdb=" CG2 ILE G 307 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CB THR B 314 " pdb=" CA THR B 314 " pdb=" OG1 THR B 314 " pdb=" CG2 THR B 314 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL J 136 " pdb=" CA VAL J 136 " pdb=" CG1 VAL J 136 " pdb=" CG2 VAL J 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 5243 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 163 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP F 163 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP F 163 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP F 163 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 163 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 163 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 163 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 163 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 163 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 163 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 264 " -0.057 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO D 265 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 245 " -0.006 2.00e-02 2.50e+03 2.96e-02 1.10e+01 pdb=" CG ASN A 245 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 245 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 245 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.028 2.00e-02 2.50e+03 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1355 2.72 - 3.27: 31987 3.27 - 3.81: 53874 3.81 - 4.36: 65505 4.36 - 4.90: 113325 Nonbonded interactions: 266046 Sorted by model distance: nonbonded pdb=" OE2 GLU G 30 " pdb=" OG1 THR G 32 " model vdw 2.175 3.040 nonbonded pdb=" OG SER B 27 " pdb=" O ILE B 29 " model vdw 2.211 3.040 nonbonded pdb=" O ASP F 113 " pdb=" NH1 ARG F 116 " model vdw 2.220 3.120 nonbonded pdb=" OG SER C 81 " pdb=" O ASN C 147 " model vdw 2.261 3.040 nonbonded pdb=" O ASP I 113 " pdb=" NH1 ARG I 116 " model vdw 2.262 3.120 ... (remaining 266041 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 33 through 68 or resid 72 or resid 75 through 110 or resid \ 201 through 202)) selection = (chain 'N' and (resid 33 through 68 or resid 72 or resid 75 through 110 or resid \ 201 through 202)) selection = (chain 'O' and (resid 33 through 68 or resid 72 through 110 or resid 201 through \ 202)) selection = (chain 'P' and (resid 33 through 72 or resid 75 through 110 or resid 201 through \ 202)) } 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.250 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 69.290 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 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 : 0.004 0.066 34387 Z= 0.174 Angle : 0.820 18.456 46859 Z= 0.423 Chirality : 0.054 0.523 5246 Planarity : 0.007 0.103 6004 Dihedral : 12.293 89.605 12681 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 4291 helix: 0.15 (0.22), residues: 446 sheet: -0.07 (0.15), residues: 1256 loop : -1.01 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP F 163 HIS 0.008 0.001 HIS D 125 PHE 0.021 0.002 PHE D 257 TYR 0.024 0.002 TYR D 273 ARG 0.015 0.001 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 16) link_NAG-ASN : angle 4.78541 ( 48) hydrogen bonds : bond 0.12227 ( 1070) hydrogen bonds : angle 6.34231 ( 2922) SS BOND : bond 0.00425 ( 80) SS BOND : angle 1.98175 ( 160) covalent geometry : bond 0.00392 (34291) covalent geometry : angle 0.79926 (46651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1083 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7519 (pp20) cc_final: 0.7258 (pp20) REVERT: D 99 GLU cc_start: 0.7760 (tp30) cc_final: 0.7554 (tp30) REVERT: D 202 ASP cc_start: 0.7714 (m-30) cc_final: 0.7270 (m-30) REVERT: D 234 THR cc_start: 0.8606 (m) cc_final: 0.8327 (t) REVERT: D 270 ASN cc_start: 0.8849 (m-40) cc_final: 0.8616 (m-40) REVERT: D 280 ILE cc_start: 0.8151 (mt) cc_final: 0.7674 (mp) REVERT: D 281 ASP cc_start: 0.7764 (t0) cc_final: 0.7525 (t0) REVERT: D 292 GLU cc_start: 0.8683 (mp0) cc_final: 0.8473 (mp0) REVERT: D 298 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6505 (tm-30) REVERT: D 320 TYR cc_start: 0.7748 (p90) cc_final: 0.7403 (p90) REVERT: D 321 LYS cc_start: 0.7931 (mttm) cc_final: 0.7593 (mmmm) REVERT: D 404 LYS cc_start: 0.8265 (ttpt) cc_final: 0.8009 (ttpt) REVERT: E 63 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8081 (ttmm) REVERT: E 82 LYS cc_start: 0.7956 (mttm) cc_final: 0.7677 (mtmm) REVERT: E 129 LYS cc_start: 0.8721 (tptt) cc_final: 0.8456 (tptt) REVERT: E 138 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 162 SER cc_start: 0.8359 (t) cc_final: 0.8122 (m) REVERT: E 176 TYR cc_start: 0.8782 (m-80) cc_final: 0.8348 (m-80) REVERT: E 178 SER cc_start: 0.8774 (t) cc_final: 0.8548 (t) REVERT: E 182 GLU cc_start: 0.7553 (tt0) cc_final: 0.7226 (tt0) REVERT: E 217 MET cc_start: 0.6365 (mmt) cc_final: 0.6093 (mmt) REVERT: E 222 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7994 (mtmm) REVERT: E 235 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7709 (mmmm) REVERT: E 248 ASP cc_start: 0.8336 (t0) cc_final: 0.7872 (t0) REVERT: E 250 SER cc_start: 0.8646 (m) cc_final: 0.8288 (m) REVERT: E 254 LYS cc_start: 0.8542 (mttm) cc_final: 0.8289 (mttm) REVERT: E 324 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7920 (mt-10) REVERT: E 391 LYS cc_start: 0.8601 (tppp) cc_final: 0.8333 (tppp) REVERT: E 400 TYR cc_start: 0.8923 (m-80) cc_final: 0.8709 (m-80) REVERT: F 6 MET cc_start: 0.4202 (tpt) cc_final: 0.3958 (tpt) REVERT: F 44 LYS cc_start: 0.8179 (tppt) cc_final: 0.7806 (tppt) REVERT: G 101 THR cc_start: 0.7997 (t) cc_final: 0.7606 (p) REVERT: G 114 CYS cc_start: 0.7517 (m) cc_final: 0.7254 (m) REVERT: G 145 ASP cc_start: 0.7651 (m-30) cc_final: 0.7434 (m-30) REVERT: G 289 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7729 (mmm160) REVERT: G 292 GLU cc_start: 0.8041 (mp0) cc_final: 0.7553 (mp0) REVERT: G 298 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6885 (tm-30) REVERT: G 341 GLU cc_start: 0.7992 (mp0) cc_final: 0.7739 (mp0) REVERT: H 61 VAL cc_start: 0.8140 (t) cc_final: 0.7935 (t) REVERT: H 129 LYS cc_start: 0.8459 (tptt) cc_final: 0.8163 (tmtt) REVERT: H 131 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7661 (mtm180) REVERT: H 134 PHE cc_start: 0.8615 (p90) cc_final: 0.8401 (p90) REVERT: H 178 SER cc_start: 0.8780 (m) cc_final: 0.8508 (m) REVERT: H 195 LYS cc_start: 0.8251 (mppt) cc_final: 0.7716 (mppt) REVERT: H 384 SER cc_start: 0.7982 (t) cc_final: 0.7507 (p) REVERT: H 391 LYS cc_start: 0.8426 (tppp) cc_final: 0.8095 (tppp) REVERT: H 393 ARG cc_start: 0.6283 (tpt170) cc_final: 0.5278 (tpt170) REVERT: I 62 ASP cc_start: 0.7941 (m-30) cc_final: 0.7660 (m-30) REVERT: I 72 MET cc_start: 0.7330 (mmp) cc_final: 0.6976 (mmp) REVERT: I 126 VAL cc_start: 0.8719 (p) cc_final: 0.8349 (t) REVERT: J 2 GLU cc_start: 0.7726 (pp20) cc_final: 0.7506 (pp20) REVERT: J 30 GLU cc_start: 0.7973 (pp20) cc_final: 0.7161 (pp20) REVERT: J 45 GLU cc_start: 0.7962 (tp30) cc_final: 0.7568 (tp30) REVERT: J 66 LEU cc_start: 0.8098 (tp) cc_final: 0.7742 (tp) REVERT: J 75 ASP cc_start: 0.8333 (t70) cc_final: 0.7991 (t0) REVERT: J 125 HIS cc_start: 0.7752 (m90) cc_final: 0.7446 (m170) REVERT: J 130 LYS cc_start: 0.8489 (tttt) cc_final: 0.8237 (ttmm) REVERT: J 202 ASP cc_start: 0.7571 (m-30) cc_final: 0.7147 (m-30) REVERT: J 218 ASP cc_start: 0.7121 (t0) cc_final: 0.6773 (t0) REVERT: J 241 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7801 (mm-30) REVERT: J 244 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8459 (mtmt) REVERT: J 292 GLU cc_start: 0.7890 (mp0) cc_final: 0.7517 (mp0) REVERT: J 433 MET cc_start: 0.6788 (mmm) cc_final: 0.6416 (mmm) REVERT: K 37 GLU cc_start: 0.7462 (mp0) cc_final: 0.6934 (mp0) REVERT: K 128 LYS cc_start: 0.8781 (tptt) cc_final: 0.8576 (tptt) REVERT: K 139 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6964 (tm-30) REVERT: K 181 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7786 (ttpp) REVERT: K 245 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8262 (ttp-170) REVERT: K 347 ASP cc_start: 0.7603 (t70) cc_final: 0.7308 (t0) REVERT: K 391 LYS cc_start: 0.8475 (tptm) cc_final: 0.8204 (tptm) REVERT: K 393 ARG cc_start: 0.8633 (ttt-90) cc_final: 0.7865 (tpt170) REVERT: L 64 GLU cc_start: 0.7635 (mp0) cc_final: 0.7340 (mp0) REVERT: M 57 ASP cc_start: 0.7743 (m-30) cc_final: 0.7198 (m-30) REVERT: A 105 GLU cc_start: 0.8371 (tp30) cc_final: 0.7497 (mm-30) REVERT: A 114 CYS cc_start: 0.7391 (m) cc_final: 0.7119 (m) REVERT: A 130 LYS cc_start: 0.8394 (tttt) cc_final: 0.8102 (ttmm) REVERT: A 187 TYR cc_start: 0.8703 (t80) cc_final: 0.8490 (t80) REVERT: A 202 ASP cc_start: 0.7480 (m-30) cc_final: 0.7056 (m-30) REVERT: A 218 ASP cc_start: 0.7578 (t0) cc_final: 0.7354 (t70) REVERT: A 267 ARG cc_start: 0.8181 (pmt170) cc_final: 0.7980 (ptt-90) REVERT: A 289 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7586 (mtp85) REVERT: A 292 GLU cc_start: 0.7759 (mp0) cc_final: 0.7413 (mp0) REVERT: A 335 THR cc_start: 0.8797 (p) cc_final: 0.8393 (t) REVERT: A 340 LYS cc_start: 0.8964 (tttp) cc_final: 0.8712 (tttp) REVERT: A 341 GLU cc_start: 0.7769 (mp0) cc_final: 0.7493 (mp0) REVERT: B 70 ASP cc_start: 0.6868 (p0) cc_final: 0.6625 (p0) REVERT: B 82 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8057 (mtpt) REVERT: B 138 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7324 (tm-30) REVERT: B 139 GLU cc_start: 0.7811 (tp30) cc_final: 0.7204 (tp30) REVERT: B 159 LYS cc_start: 0.8814 (pttt) cc_final: 0.8526 (ptmm) REVERT: B 217 MET cc_start: 0.7399 (mmp) cc_final: 0.6741 (mmt) REVERT: B 237 VAL cc_start: 0.7509 (t) cc_final: 0.7296 (p) REVERT: B 303 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7798 (mtm-85) REVERT: C 64 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 80 THR cc_start: 0.8568 (m) cc_final: 0.8366 (m) outliers start: 0 outliers final: 0 residues processed: 1083 average time/residue: 1.4694 time to fit residues: 1881.8965 Evaluate side-chains 902 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 902 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 381 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 HIS D 143 HIS D 186 ASN D 408 ASN F 23 GLN F 91 HIS G 143 HIS G 319 GLN G 364 ASN ** H 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN J 345 HIS K 104 GLN K 225 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN A 125 HIS B 146 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118811 restraints weight = 49969.546| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.18 r_work: 0.3359 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34387 Z= 0.224 Angle : 0.665 13.908 46859 Z= 0.338 Chirality : 0.048 0.272 5246 Planarity : 0.005 0.071 6004 Dihedral : 5.969 76.021 4985 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 2.18 % Allowed : 10.96 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4291 helix: 0.97 (0.23), residues: 450 sheet: 0.08 (0.15), residues: 1236 loop : -0.88 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 163 HIS 0.006 0.001 HIS D 125 PHE 0.019 0.002 PHE B 134 TYR 0.029 0.002 TYR F 97 ARG 0.009 0.001 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 16) link_NAG-ASN : angle 3.56337 ( 48) hydrogen bonds : bond 0.03586 ( 1070) hydrogen bonds : angle 5.18806 ( 2922) SS BOND : bond 0.00373 ( 80) SS BOND : angle 1.60021 ( 160) covalent geometry : bond 0.00514 (34291) covalent geometry : angle 0.64966 (46651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 957 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8321 (t80) cc_final: 0.7884 (t80) REVERT: D 30 GLU cc_start: 0.7595 (pp20) cc_final: 0.7257 (pp20) REVERT: D 31 ILE cc_start: 0.8796 (mm) cc_final: 0.8447 (mp) REVERT: D 99 GLU cc_start: 0.7902 (tp30) cc_final: 0.7665 (tp30) REVERT: D 101 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8180 (t) REVERT: D 202 ASP cc_start: 0.7797 (m-30) cc_final: 0.7467 (m-30) REVERT: D 298 GLU cc_start: 0.7071 (tm-30) cc_final: 0.6546 (tm-30) REVERT: D 320 TYR cc_start: 0.8065 (p90) cc_final: 0.7710 (p90) REVERT: D 404 LYS cc_start: 0.8317 (ttpt) cc_final: 0.8067 (ttpt) REVERT: E 20 ARG cc_start: 0.7762 (ttt180) cc_final: 0.7503 (ttt180) REVERT: E 76 LYS cc_start: 0.8645 (mttt) cc_final: 0.8359 (mtmm) REVERT: E 129 LYS cc_start: 0.8693 (tptt) cc_final: 0.8443 (tptt) REVERT: E 138 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 162 SER cc_start: 0.8440 (t) cc_final: 0.8143 (m) REVERT: E 177 LYS cc_start: 0.8513 (pttp) cc_final: 0.8257 (ttpp) REVERT: E 178 SER cc_start: 0.8851 (t) cc_final: 0.8642 (t) REVERT: E 182 GLU cc_start: 0.7719 (tt0) cc_final: 0.7359 (tt0) REVERT: E 195 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7510 (mmpt) REVERT: E 217 MET cc_start: 0.6778 (mmt) cc_final: 0.6384 (mmt) REVERT: E 248 ASP cc_start: 0.8382 (t0) cc_final: 0.7902 (t0) REVERT: E 250 SER cc_start: 0.8683 (m) cc_final: 0.8300 (m) REVERT: E 324 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 391 LYS cc_start: 0.8659 (tppp) cc_final: 0.8386 (tppp) REVERT: F 6 MET cc_start: 0.4391 (tpt) cc_final: 0.4097 (tpt) REVERT: F 44 LYS cc_start: 0.8296 (tppt) cc_final: 0.7896 (tppt) REVERT: F 78 GLN cc_start: 0.8337 (mp10) cc_final: 0.8071 (mp10) REVERT: F 99 ASN cc_start: 0.7992 (m-40) cc_final: 0.7549 (m-40) REVERT: F 148 GLN cc_start: 0.7826 (mt0) cc_final: 0.7552 (mt0) REVERT: F 149 LYS cc_start: 0.8555 (mppt) cc_final: 0.8343 (mppt) REVERT: G 63 CYS cc_start: 0.6628 (m) cc_final: 0.6398 (m) REVERT: G 114 CYS cc_start: 0.7576 (m) cc_final: 0.7292 (m) REVERT: G 145 ASP cc_start: 0.7820 (m-30) cc_final: 0.7610 (m-30) REVERT: G 292 GLU cc_start: 0.8186 (mp0) cc_final: 0.7584 (mp0) REVERT: G 298 GLU cc_start: 0.7480 (tm-30) cc_final: 0.6909 (tm-30) REVERT: G 327 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7738 (m-70) REVERT: G 341 GLU cc_start: 0.7982 (mp0) cc_final: 0.7717 (mp0) REVERT: G 372 LYS cc_start: 0.8778 (tppp) cc_final: 0.8555 (tptm) REVERT: H 25 CYS cc_start: 0.7060 (p) cc_final: 0.6735 (p) REVERT: H 129 LYS cc_start: 0.8443 (tptt) cc_final: 0.8142 (tmtt) REVERT: H 131 ARG cc_start: 0.7958 (mtm180) cc_final: 0.7655 (mtm180) REVERT: H 189 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7404 (pt) REVERT: H 224 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8156 (ttm-80) REVERT: H 239 ASN cc_start: 0.8083 (p0) cc_final: 0.7807 (p0) REVERT: H 391 LYS cc_start: 0.8377 (tppp) cc_final: 0.8156 (tppp) REVERT: H 393 ARG cc_start: 0.6442 (tpt170) cc_final: 0.5960 (tpt170) REVERT: I 62 ASP cc_start: 0.8038 (m-30) cc_final: 0.7735 (m-30) REVERT: J 2 GLU cc_start: 0.7823 (pp20) cc_final: 0.7584 (pp20) REVERT: J 30 GLU cc_start: 0.7787 (pp20) cc_final: 0.7211 (pp20) REVERT: J 45 GLU cc_start: 0.7913 (tp30) cc_final: 0.7582 (tp30) REVERT: J 116 ILE cc_start: 0.8754 (mp) cc_final: 0.8482 (mm) REVERT: J 125 HIS cc_start: 0.7879 (m90) cc_final: 0.7562 (m170) REVERT: J 149 ASN cc_start: 0.8730 (p0) cc_final: 0.8513 (p0) REVERT: J 195 MET cc_start: 0.7712 (ptt) cc_final: 0.7406 (ptt) REVERT: J 202 ASP cc_start: 0.7655 (m-30) cc_final: 0.7358 (m-30) REVERT: J 218 ASP cc_start: 0.7413 (t0) cc_final: 0.6919 (t0) REVERT: J 241 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7817 (mm-30) REVERT: J 260 LYS cc_start: 0.8308 (tmtt) cc_final: 0.7632 (tptp) REVERT: J 262 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7132 (mm-30) REVERT: J 289 ARG cc_start: 0.8441 (mmm-85) cc_final: 0.7882 (mmm160) REVERT: J 292 GLU cc_start: 0.8077 (mp0) cc_final: 0.7562 (mp0) REVERT: J 306 CYS cc_start: 0.7399 (t) cc_final: 0.7061 (t) REVERT: J 397 GLU cc_start: 0.7697 (mp0) cc_final: 0.7385 (mp0) REVERT: J 402 VAL cc_start: 0.8781 (t) cc_final: 0.8523 (t) REVERT: J 433 MET cc_start: 0.6826 (mmm) cc_final: 0.6432 (mmm) REVERT: K 37 GLU cc_start: 0.7603 (mp0) cc_final: 0.7119 (mp0) REVERT: K 139 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7273 (tm-30) REVERT: K 146 GLN cc_start: 0.8637 (tt0) cc_final: 0.8300 (tt0) REVERT: K 181 LYS cc_start: 0.8423 (ttpp) cc_final: 0.7896 (ttmm) REVERT: K 217 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.6866 (mtt) REVERT: K 260 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8240 (ttt90) REVERT: K 347 ASP cc_start: 0.7671 (t70) cc_final: 0.7282 (t70) REVERT: K 393 ARG cc_start: 0.8693 (ttt-90) cc_final: 0.8463 (ttp-170) REVERT: L 34 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7172 (mtp85) REVERT: L 64 GLU cc_start: 0.7790 (mp0) cc_final: 0.7439 (mp0) REVERT: L 83 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8533 (mttm) REVERT: M 57 ASP cc_start: 0.7754 (m-30) cc_final: 0.7173 (m-30) REVERT: A 105 GLU cc_start: 0.8186 (tp30) cc_final: 0.7492 (mm-30) REVERT: A 114 CYS cc_start: 0.7449 (m) cc_final: 0.7231 (m) REVERT: A 130 LYS cc_start: 0.8393 (tttt) cc_final: 0.8108 (ttmm) REVERT: A 146 THR cc_start: 0.8400 (t) cc_final: 0.8184 (p) REVERT: A 202 ASP cc_start: 0.7533 (m-30) cc_final: 0.7209 (m-30) REVERT: A 218 ASP cc_start: 0.7658 (t0) cc_final: 0.7382 (t0) REVERT: A 241 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7624 (mm-30) REVERT: A 267 ARG cc_start: 0.8261 (pmt170) cc_final: 0.7994 (ptt-90) REVERT: A 292 GLU cc_start: 0.8041 (mp0) cc_final: 0.7504 (mp0) REVERT: A 335 THR cc_start: 0.8829 (p) cc_final: 0.8422 (t) REVERT: A 340 LYS cc_start: 0.9023 (tttp) cc_final: 0.8748 (tttp) REVERT: A 341 GLU cc_start: 0.7801 (mp0) cc_final: 0.7509 (mp0) REVERT: B 60 ASP cc_start: 0.7796 (t0) cc_final: 0.7480 (t0) REVERT: B 70 ASP cc_start: 0.6921 (p0) cc_final: 0.6705 (p0) REVERT: B 80 MET cc_start: 0.8455 (ttp) cc_final: 0.8222 (ttp) REVERT: B 81 GLU cc_start: 0.7934 (mp0) cc_final: 0.7668 (mp0) REVERT: B 82 LYS cc_start: 0.8592 (mtpp) cc_final: 0.7978 (mtpt) REVERT: B 102 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8276 (tp) REVERT: B 157 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8283 (tpp-160) REVERT: B 199 TYR cc_start: 0.6358 (p90) cc_final: 0.6148 (p90) REVERT: B 217 MET cc_start: 0.7579 (mmp) cc_final: 0.6849 (mmp) REVERT: B 303 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: B 357 ILE cc_start: 0.8412 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 11 GLU cc_start: 0.7129 (tt0) cc_final: 0.6918 (tt0) REVERT: C 64 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7751 (mt-10) outliers start: 80 outliers final: 39 residues processed: 988 average time/residue: 1.3927 time to fit residues: 1638.7193 Evaluate side-chains 966 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 919 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 113 ASP Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 346 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 364 optimal weight: 2.9990 chunk 237 optimal weight: 8.9990 chunk 212 optimal weight: 0.0370 chunk 142 optimal weight: 0.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS D 186 ASN D 204 GLN E 286 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 HIS J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN J 246 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS B 146 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118513 restraints weight = 50265.489| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.18 r_work: 0.3357 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34387 Z= 0.181 Angle : 0.622 13.348 46859 Z= 0.317 Chirality : 0.047 0.308 5246 Planarity : 0.005 0.057 6004 Dihedral : 5.628 74.445 4985 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.43 % Favored : 94.45 % Rotamer: Outliers : 3.18 % Allowed : 13.33 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4291 helix: 1.31 (0.24), residues: 440 sheet: 0.17 (0.15), residues: 1216 loop : -0.80 (0.12), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 163 HIS 0.005 0.001 HIS H 256 PHE 0.015 0.001 PHE H 134 TYR 0.022 0.002 TYR D 308 ARG 0.009 0.001 ARG F 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 16) link_NAG-ASN : angle 3.41545 ( 48) hydrogen bonds : bond 0.03406 ( 1070) hydrogen bonds : angle 5.03119 ( 2922) SS BOND : bond 0.00320 ( 80) SS BOND : angle 1.48025 ( 160) covalent geometry : bond 0.00415 (34291) covalent geometry : angle 0.60796 (46651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 949 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8354 (t80) cc_final: 0.7884 (t80) REVERT: D 30 GLU cc_start: 0.7497 (pp20) cc_final: 0.7157 (pp20) REVERT: D 99 GLU cc_start: 0.7962 (tp30) cc_final: 0.7669 (tp30) REVERT: D 101 THR cc_start: 0.8489 (m) cc_final: 0.8112 (t) REVERT: D 149 ASN cc_start: 0.8324 (p0) cc_final: 0.8093 (p0) REVERT: D 202 ASP cc_start: 0.7728 (m-30) cc_final: 0.7414 (m-30) REVERT: D 280 ILE cc_start: 0.8122 (mp) cc_final: 0.7897 (mt) REVERT: D 281 ASP cc_start: 0.7801 (t0) cc_final: 0.7536 (t0) REVERT: D 298 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6618 (tm-30) REVERT: D 306 CYS cc_start: 0.7579 (t) cc_final: 0.7153 (t) REVERT: D 320 TYR cc_start: 0.8046 (p90) cc_final: 0.7716 (p90) REVERT: D 393 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8825 (mmtt) REVERT: D 404 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8062 (ttpt) REVERT: E 20 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7348 (ttt180) REVERT: E 70 ASP cc_start: 0.7349 (p0) cc_final: 0.7098 (p0) REVERT: E 76 LYS cc_start: 0.8732 (mttt) cc_final: 0.8383 (mtmm) REVERT: E 81 GLU cc_start: 0.7750 (pm20) cc_final: 0.7393 (pm20) REVERT: E 127 GLU cc_start: 0.8082 (tt0) cc_final: 0.7797 (tt0) REVERT: E 129 LYS cc_start: 0.8708 (tptt) cc_final: 0.8471 (tptt) REVERT: E 131 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7887 (mtp85) REVERT: E 138 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7400 (tm-30) REVERT: E 162 SER cc_start: 0.8437 (t) cc_final: 0.8170 (m) REVERT: E 177 LYS cc_start: 0.8517 (pttp) cc_final: 0.8241 (ttpp) REVERT: E 178 SER cc_start: 0.8841 (t) cc_final: 0.8631 (t) REVERT: E 182 GLU cc_start: 0.7701 (tt0) cc_final: 0.7363 (tt0) REVERT: E 202 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7834 (tptt) REVERT: E 217 MET cc_start: 0.7101 (mmt) cc_final: 0.6823 (mmp) REVERT: E 248 ASP cc_start: 0.8351 (t0) cc_final: 0.7885 (t0) REVERT: E 250 SER cc_start: 0.8695 (m) cc_final: 0.8302 (m) REVERT: E 291 ARG cc_start: 0.8302 (mmt90) cc_final: 0.8032 (mmt180) REVERT: E 324 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8041 (mt-10) REVERT: E 391 LYS cc_start: 0.8654 (tppp) cc_final: 0.8374 (tppp) REVERT: F 6 MET cc_start: 0.4456 (tpt) cc_final: 0.4155 (tpt) REVERT: F 44 LYS cc_start: 0.8295 (tppt) cc_final: 0.7865 (tppt) REVERT: F 78 GLN cc_start: 0.8323 (mp10) cc_final: 0.8071 (mp10) REVERT: F 99 ASN cc_start: 0.8034 (m-40) cc_final: 0.7572 (m-40) REVERT: F 149 LYS cc_start: 0.8508 (mppt) cc_final: 0.8217 (mppt) REVERT: G 114 CYS cc_start: 0.7619 (m) cc_final: 0.7337 (m) REVERT: G 246 ASN cc_start: 0.7944 (m-40) cc_final: 0.7642 (m-40) REVERT: G 292 GLU cc_start: 0.8195 (mp0) cc_final: 0.7601 (mp0) REVERT: G 298 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6929 (tm-30) REVERT: G 327 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7692 (m-70) REVERT: G 341 GLU cc_start: 0.7997 (mp0) cc_final: 0.7721 (mp0) REVERT: H 25 CYS cc_start: 0.7052 (p) cc_final: 0.6745 (p) REVERT: H 60 ASP cc_start: 0.8077 (t0) cc_final: 0.7832 (t0) REVERT: H 127 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7892 (tm-30) REVERT: H 129 LYS cc_start: 0.8403 (tptt) cc_final: 0.8183 (tmtt) REVERT: H 131 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7708 (mtm180) REVERT: H 189 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7527 (pt) REVERT: H 224 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8168 (ttm-80) REVERT: H 239 ASN cc_start: 0.8109 (p0) cc_final: 0.7823 (p0) REVERT: H 281 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.8014 (mttm) REVERT: H 393 ARG cc_start: 0.6474 (tpt170) cc_final: 0.5263 (tpt170) REVERT: J 2 GLU cc_start: 0.7834 (pp20) cc_final: 0.7519 (pp20) REVERT: J 30 GLU cc_start: 0.7783 (pp20) cc_final: 0.7240 (pp20) REVERT: J 114 CYS cc_start: 0.7334 (m) cc_final: 0.7081 (m) REVERT: J 116 ILE cc_start: 0.8891 (mp) cc_final: 0.8623 (mm) REVERT: J 125 HIS cc_start: 0.7858 (m90) cc_final: 0.7544 (m170) REVERT: J 149 ASN cc_start: 0.8679 (p0) cc_final: 0.8441 (p0) REVERT: J 191 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7843 (mm-30) REVERT: J 241 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7928 (mm-30) REVERT: J 260 LYS cc_start: 0.8343 (tmtt) cc_final: 0.7636 (tptp) REVERT: J 289 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.7985 (mmm160) REVERT: J 292 GLU cc_start: 0.8104 (mp0) cc_final: 0.7546 (mp0) REVERT: J 295 THR cc_start: 0.8518 (p) cc_final: 0.8222 (p) REVERT: J 306 CYS cc_start: 0.7332 (t) cc_final: 0.7013 (t) REVERT: J 397 GLU cc_start: 0.7657 (mp0) cc_final: 0.7373 (mp0) REVERT: J 402 VAL cc_start: 0.8759 (t) cc_final: 0.8506 (t) REVERT: J 433 MET cc_start: 0.6760 (mmm) cc_final: 0.6384 (mmm) REVERT: K 20 ARG cc_start: 0.7522 (mtt-85) cc_final: 0.7158 (mtt180) REVERT: K 37 GLU cc_start: 0.7633 (mp0) cc_final: 0.7218 (mp0) REVERT: K 60 ASP cc_start: 0.7927 (t0) cc_final: 0.7670 (t0) REVERT: K 139 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7309 (tm-30) REVERT: K 146 GLN cc_start: 0.8635 (tt0) cc_final: 0.8362 (tt0) REVERT: K 181 LYS cc_start: 0.8397 (ttpp) cc_final: 0.7831 (ttmm) REVERT: K 217 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6895 (mtt) REVERT: K 347 ASP cc_start: 0.7663 (t70) cc_final: 0.7222 (t70) REVERT: K 393 ARG cc_start: 0.8681 (ttt-90) cc_final: 0.8440 (ttp-170) REVERT: L 34 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7303 (mtp180) REVERT: L 64 GLU cc_start: 0.7715 (mp0) cc_final: 0.7363 (mp0) REVERT: L 83 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8560 (mttm) REVERT: M 57 ASP cc_start: 0.7738 (m-30) cc_final: 0.7133 (m-30) REVERT: A 105 GLU cc_start: 0.8249 (tp30) cc_final: 0.7847 (tp30) REVERT: A 114 CYS cc_start: 0.7519 (m) cc_final: 0.7301 (m) REVERT: A 130 LYS cc_start: 0.8409 (tttt) cc_final: 0.8124 (ttmm) REVERT: A 202 ASP cc_start: 0.7586 (m-30) cc_final: 0.7200 (m-30) REVERT: A 218 ASP cc_start: 0.7707 (t0) cc_final: 0.7413 (t0) REVERT: A 289 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7626 (mtp85) REVERT: A 292 GLU cc_start: 0.8079 (mp0) cc_final: 0.7508 (mp0) REVERT: A 341 GLU cc_start: 0.7793 (mp0) cc_final: 0.7479 (mp0) REVERT: B 60 ASP cc_start: 0.7749 (t0) cc_final: 0.7381 (t0) REVERT: B 70 ASP cc_start: 0.6871 (p0) cc_final: 0.6632 (p0) REVERT: B 81 GLU cc_start: 0.7944 (mp0) cc_final: 0.7685 (mp0) REVERT: B 82 LYS cc_start: 0.8567 (mtpp) cc_final: 0.7940 (mtpt) REVERT: B 157 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8283 (tpp-160) REVERT: B 159 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8536 (ptpt) REVERT: B 177 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8140 (ttmm) REVERT: B 199 TYR cc_start: 0.6359 (p90) cc_final: 0.6024 (p90) REVERT: B 217 MET cc_start: 0.7575 (mmp) cc_final: 0.6836 (mmt) REVERT: B 266 CYS cc_start: 0.7964 (p) cc_final: 0.7558 (p) REVERT: B 303 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: B 357 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8244 (mt) REVERT: C 11 GLU cc_start: 0.7182 (tt0) cc_final: 0.6964 (tt0) REVERT: C 19 MET cc_start: 0.8370 (mmm) cc_final: 0.8139 (mmm) REVERT: C 64 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7733 (mt-10) REVERT: C 155 ASP cc_start: 0.7559 (m-30) cc_final: 0.7328 (m-30) outliers start: 117 outliers final: 66 residues processed: 1000 average time/residue: 1.3468 time to fit residues: 1607.4699 Evaluate side-chains 996 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 920 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 396 CYS Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 202 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 401 optimal weight: 0.0040 chunk 300 optimal weight: 0.9980 chunk 296 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 259 optimal weight: 10.0000 chunk 411 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 415 optimal weight: 2.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS D 204 GLN E 286 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118447 restraints weight = 50269.190| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.17 r_work: 0.3356 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34387 Z= 0.157 Angle : 0.608 12.771 46859 Z= 0.308 Chirality : 0.047 0.334 5246 Planarity : 0.005 0.065 6004 Dihedral : 5.447 73.035 4985 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 3.35 % Allowed : 15.29 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 4291 helix: 1.45 (0.24), residues: 440 sheet: 0.11 (0.15), residues: 1260 loop : -0.72 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 163 HIS 0.005 0.001 HIS L 92 PHE 0.016 0.001 PHE H 134 TYR 0.020 0.001 TYR A 308 ARG 0.008 0.000 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00566 ( 16) link_NAG-ASN : angle 3.25643 ( 48) hydrogen bonds : bond 0.03254 ( 1070) hydrogen bonds : angle 4.92883 ( 2922) SS BOND : bond 0.00302 ( 80) SS BOND : angle 1.51423 ( 160) covalent geometry : bond 0.00361 (34291) covalent geometry : angle 0.59417 (46651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 930 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8365 (t80) cc_final: 0.7881 (t80) REVERT: D 30 GLU cc_start: 0.7482 (pp20) cc_final: 0.7187 (pp20) REVERT: D 99 GLU cc_start: 0.7926 (tp30) cc_final: 0.7639 (tp30) REVERT: D 101 THR cc_start: 0.8463 (m) cc_final: 0.8108 (m) REVERT: D 149 ASN cc_start: 0.8324 (p0) cc_final: 0.8071 (p0) REVERT: D 202 ASP cc_start: 0.7748 (m-30) cc_final: 0.7413 (m-30) REVERT: D 298 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6633 (tm-30) REVERT: D 306 CYS cc_start: 0.7549 (t) cc_final: 0.7120 (t) REVERT: D 320 TYR cc_start: 0.8024 (p90) cc_final: 0.7535 (p90) REVERT: D 393 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8832 (mmtt) REVERT: D 404 LYS cc_start: 0.8293 (ttpt) cc_final: 0.8021 (ttpt) REVERT: E 20 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7329 (ttt180) REVERT: E 70 ASP cc_start: 0.7283 (p0) cc_final: 0.7009 (p0) REVERT: E 76 LYS cc_start: 0.8739 (mttt) cc_final: 0.8370 (mtmm) REVERT: E 127 GLU cc_start: 0.8089 (tt0) cc_final: 0.7812 (tt0) REVERT: E 138 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7372 (tm-30) REVERT: E 162 SER cc_start: 0.8450 (t) cc_final: 0.8181 (m) REVERT: E 177 LYS cc_start: 0.8505 (pttp) cc_final: 0.8197 (ttpp) REVERT: E 178 SER cc_start: 0.8834 (t) cc_final: 0.8618 (t) REVERT: E 182 GLU cc_start: 0.7701 (tt0) cc_final: 0.7376 (tt0) REVERT: E 195 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7541 (mmpt) REVERT: E 217 MET cc_start: 0.7182 (mmt) cc_final: 0.6741 (mmp) REVERT: E 248 ASP cc_start: 0.8324 (t0) cc_final: 0.7881 (t0) REVERT: E 250 SER cc_start: 0.8690 (m) cc_final: 0.8287 (m) REVERT: E 324 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8000 (mt-10) REVERT: E 391 LYS cc_start: 0.8653 (tppp) cc_final: 0.8375 (tppp) REVERT: F 6 MET cc_start: 0.4421 (tpt) cc_final: 0.4122 (tpt) REVERT: F 44 LYS cc_start: 0.8286 (tppt) cc_final: 0.7861 (tppt) REVERT: F 78 GLN cc_start: 0.8325 (mp10) cc_final: 0.8063 (mp10) REVERT: F 99 ASN cc_start: 0.8010 (m-40) cc_final: 0.7559 (m-40) REVERT: F 149 LYS cc_start: 0.8541 (mppt) cc_final: 0.8316 (mppt) REVERT: G 32 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8475 (t) REVERT: G 99 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6693 (tm-30) REVERT: G 114 CYS cc_start: 0.7598 (m) cc_final: 0.7329 (m) REVERT: G 134 ARG cc_start: 0.8396 (ttp80) cc_final: 0.7930 (ttp80) REVERT: G 246 ASN cc_start: 0.7948 (m-40) cc_final: 0.7647 (m-40) REVERT: G 292 GLU cc_start: 0.8243 (mp0) cc_final: 0.7686 (mp0) REVERT: G 298 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6906 (tm-30) REVERT: G 327 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7634 (m-70) REVERT: G 341 GLU cc_start: 0.8006 (mp0) cc_final: 0.7690 (mp0) REVERT: G 393 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8739 (mttm) REVERT: G 404 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7961 (ttpt) REVERT: H 25 CYS cc_start: 0.7085 (p) cc_final: 0.6780 (p) REVERT: H 60 ASP cc_start: 0.8097 (t0) cc_final: 0.7834 (t0) REVERT: H 78 ASP cc_start: 0.8237 (t0) cc_final: 0.7991 (t0) REVERT: H 129 LYS cc_start: 0.8393 (tptt) cc_final: 0.8173 (tmtt) REVERT: H 131 ARG cc_start: 0.8007 (mtm180) cc_final: 0.7744 (mtm180) REVERT: H 189 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7610 (pt) REVERT: H 224 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8162 (ttm-80) REVERT: H 239 ASN cc_start: 0.8085 (p0) cc_final: 0.7768 (p0) REVERT: H 393 ARG cc_start: 0.6479 (tpt170) cc_final: 0.5047 (ttm170) REVERT: J 2 GLU cc_start: 0.7843 (pp20) cc_final: 0.7524 (pp20) REVERT: J 30 GLU cc_start: 0.7750 (pp20) cc_final: 0.7206 (pp20) REVERT: J 61 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: J 102 GLN cc_start: 0.8831 (tt0) cc_final: 0.8591 (tt0) REVERT: J 114 CYS cc_start: 0.7342 (m) cc_final: 0.7100 (m) REVERT: J 116 ILE cc_start: 0.8946 (mp) cc_final: 0.8675 (mm) REVERT: J 125 HIS cc_start: 0.7842 (m90) cc_final: 0.7530 (m170) REVERT: J 174 ASP cc_start: 0.8247 (m-30) cc_final: 0.8030 (m-30) REVERT: J 191 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7822 (mm-30) REVERT: J 241 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7820 (mm-30) REVERT: J 260 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7728 (tptp) REVERT: J 262 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7188 (mm-30) REVERT: J 289 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8062 (mmm160) REVERT: J 292 GLU cc_start: 0.8128 (mp0) cc_final: 0.7590 (mp0) REVERT: J 295 THR cc_start: 0.8510 (p) cc_final: 0.8232 (p) REVERT: J 306 CYS cc_start: 0.7323 (t) cc_final: 0.6993 (t) REVERT: J 397 GLU cc_start: 0.7646 (mp0) cc_final: 0.7346 (mp0) REVERT: J 402 VAL cc_start: 0.8739 (t) cc_final: 0.8471 (t) REVERT: J 408 ASN cc_start: 0.8411 (m-40) cc_final: 0.8193 (m-40) REVERT: J 433 MET cc_start: 0.6786 (mmm) cc_final: 0.6435 (mmm) REVERT: K 20 ARG cc_start: 0.7518 (mtt-85) cc_final: 0.7140 (mtt180) REVERT: K 37 GLU cc_start: 0.7662 (mp0) cc_final: 0.7243 (mp0) REVERT: K 60 ASP cc_start: 0.7902 (t0) cc_final: 0.7633 (t0) REVERT: K 139 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7323 (tm-30) REVERT: K 146 GLN cc_start: 0.8655 (tt0) cc_final: 0.8377 (tt0) REVERT: K 181 LYS cc_start: 0.8384 (ttpp) cc_final: 0.7836 (ttmm) REVERT: K 217 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6856 (mtt) REVERT: K 347 ASP cc_start: 0.7652 (t70) cc_final: 0.7287 (t70) REVERT: K 393 ARG cc_start: 0.8639 (ttt-90) cc_final: 0.8366 (ttp-170) REVERT: L 64 GLU cc_start: 0.7766 (mp0) cc_final: 0.7335 (mp0) REVERT: L 83 LYS cc_start: 0.8872 (mtmm) cc_final: 0.8524 (mttm) REVERT: M 57 ASP cc_start: 0.7712 (m-30) cc_final: 0.7110 (m-30) REVERT: A 78 CYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6592 (m) REVERT: A 105 GLU cc_start: 0.8193 (tp30) cc_final: 0.7808 (mm-30) REVERT: A 114 CYS cc_start: 0.7539 (m) cc_final: 0.7335 (m) REVERT: A 202 ASP cc_start: 0.7563 (m-30) cc_final: 0.7216 (m-30) REVERT: A 218 ASP cc_start: 0.7694 (t0) cc_final: 0.7406 (t0) REVERT: A 240 TYR cc_start: 0.8380 (t80) cc_final: 0.8056 (t80) REVERT: A 289 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7618 (mtp85) REVERT: A 292 GLU cc_start: 0.8079 (mp0) cc_final: 0.7506 (mp0) REVERT: A 341 GLU cc_start: 0.7782 (mp0) cc_final: 0.7455 (mp0) REVERT: B 60 ASP cc_start: 0.7753 (t0) cc_final: 0.7364 (t0) REVERT: B 70 ASP cc_start: 0.6822 (p0) cc_final: 0.6546 (p0) REVERT: B 80 MET cc_start: 0.8558 (ttp) cc_final: 0.8343 (ttp) REVERT: B 81 GLU cc_start: 0.7910 (mp0) cc_final: 0.7641 (mp0) REVERT: B 82 LYS cc_start: 0.8553 (mtpp) cc_final: 0.7908 (mtpt) REVERT: B 102 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8342 (tp) REVERT: B 159 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8525 (ptpt) REVERT: B 177 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8178 (ttmm) REVERT: B 199 TYR cc_start: 0.6361 (p90) cc_final: 0.6051 (p90) REVERT: B 217 MET cc_start: 0.7548 (mmp) cc_final: 0.6837 (mmt) REVERT: B 303 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: B 357 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8211 (mt) REVERT: C 11 GLU cc_start: 0.7218 (tt0) cc_final: 0.7002 (tt0) REVERT: C 37 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8840 (pptt) REVERT: C 64 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 155 ASP cc_start: 0.7554 (m-30) cc_final: 0.7305 (m-30) outliers start: 123 outliers final: 78 residues processed: 985 average time/residue: 1.3555 time to fit residues: 1594.6249 Evaluate side-chains 1008 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 917 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 10 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 159 optimal weight: 0.3980 chunk 365 optimal weight: 10.0000 chunk 233 optimal weight: 0.3980 chunk 19 optimal weight: 0.0030 chunk 381 optimal weight: 4.9990 chunk 296 optimal weight: 0.4980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS D 204 GLN E 21 HIS E 286 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN H 349 HIS J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS A 362 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119682 restraints weight = 50107.886| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.20 r_work: 0.3381 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34387 Z= 0.107 Angle : 0.582 12.511 46859 Z= 0.294 Chirality : 0.045 0.347 5246 Planarity : 0.004 0.059 6004 Dihedral : 5.174 72.023 4985 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 2.88 % Allowed : 16.62 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4291 helix: 1.58 (0.24), residues: 440 sheet: 0.14 (0.15), residues: 1260 loop : -0.65 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 279 HIS 0.005 0.001 HIS L 40 PHE 0.016 0.001 PHE H 134 TYR 0.023 0.001 TYR F 97 ARG 0.011 0.000 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 16) link_NAG-ASN : angle 3.12225 ( 48) hydrogen bonds : bond 0.03001 ( 1070) hydrogen bonds : angle 4.82261 ( 2922) SS BOND : bond 0.00231 ( 80) SS BOND : angle 1.19336 ( 160) covalent geometry : bond 0.00243 (34291) covalent geometry : angle 0.56989 (46651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 955 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7414 (pp20) cc_final: 0.7154 (pp20) REVERT: D 99 GLU cc_start: 0.7997 (tp30) cc_final: 0.7663 (tp30) REVERT: D 101 THR cc_start: 0.8411 (m) cc_final: 0.8059 (m) REVERT: D 102 GLN cc_start: 0.8853 (tt0) cc_final: 0.8625 (tt0) REVERT: D 149 ASN cc_start: 0.8282 (p0) cc_final: 0.8046 (p0) REVERT: D 202 ASP cc_start: 0.7715 (m-30) cc_final: 0.7390 (m-30) REVERT: D 247 SER cc_start: 0.8593 (p) cc_final: 0.8333 (t) REVERT: D 298 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6687 (tm-30) REVERT: D 306 CYS cc_start: 0.7444 (t) cc_final: 0.7015 (t) REVERT: D 308 TYR cc_start: 0.8590 (p90) cc_final: 0.8373 (p90) REVERT: D 320 TYR cc_start: 0.7889 (p90) cc_final: 0.7304 (p90) REVERT: D 404 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8009 (ttpt) REVERT: E 63 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8139 (ttmm) REVERT: E 70 ASP cc_start: 0.7037 (p0) cc_final: 0.6659 (p0) REVERT: E 72 ASP cc_start: 0.7618 (p0) cc_final: 0.6957 (p0) REVERT: E 76 LYS cc_start: 0.8694 (mttt) cc_final: 0.8349 (mtmm) REVERT: E 127 GLU cc_start: 0.8042 (tt0) cc_final: 0.7766 (tt0) REVERT: E 138 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7400 (tm-30) REVERT: E 139 GLU cc_start: 0.7767 (tp30) cc_final: 0.7022 (tp30) REVERT: E 162 SER cc_start: 0.8500 (t) cc_final: 0.8189 (m) REVERT: E 177 LYS cc_start: 0.8534 (pttp) cc_final: 0.8247 (ttpp) REVERT: E 178 SER cc_start: 0.8796 (t) cc_final: 0.8588 (t) REVERT: E 182 GLU cc_start: 0.7597 (tt0) cc_final: 0.7253 (tt0) REVERT: E 195 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7556 (mmpt) REVERT: E 217 MET cc_start: 0.7069 (mmt) cc_final: 0.6628 (mmp) REVERT: E 248 ASP cc_start: 0.8292 (t0) cc_final: 0.7885 (t0) REVERT: E 250 SER cc_start: 0.8690 (m) cc_final: 0.8279 (m) REVERT: E 324 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7976 (mt-10) REVERT: E 391 LYS cc_start: 0.8654 (tppp) cc_final: 0.8378 (tppp) REVERT: F 6 MET cc_start: 0.4437 (tpt) cc_final: 0.4131 (tpt) REVERT: F 78 GLN cc_start: 0.8294 (mp10) cc_final: 0.8048 (mp10) REVERT: F 99 ASN cc_start: 0.7971 (m-40) cc_final: 0.7495 (m-40) REVERT: F 149 LYS cc_start: 0.8541 (mppt) cc_final: 0.8294 (mppt) REVERT: G 2 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7549 (mt-10) REVERT: G 99 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6714 (tm-30) REVERT: G 114 CYS cc_start: 0.7588 (m) cc_final: 0.7338 (m) REVERT: G 134 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7969 (ttp80) REVERT: G 246 ASN cc_start: 0.7912 (m-40) cc_final: 0.7612 (m-40) REVERT: G 292 GLU cc_start: 0.8221 (mp0) cc_final: 0.7737 (mp0) REVERT: G 298 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6865 (tm-30) REVERT: G 327 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7595 (m-70) REVERT: G 341 GLU cc_start: 0.7992 (mp0) cc_final: 0.7686 (mp0) REVERT: G 393 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8701 (mttm) REVERT: G 404 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7975 (ttpt) REVERT: H 25 CYS cc_start: 0.7106 (p) cc_final: 0.6793 (p) REVERT: H 60 ASP cc_start: 0.8079 (t0) cc_final: 0.7792 (t0) REVERT: H 78 ASP cc_start: 0.8228 (t0) cc_final: 0.7982 (t0) REVERT: H 129 LYS cc_start: 0.8418 (tptt) cc_final: 0.8201 (tmtt) REVERT: H 131 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7686 (mtm180) REVERT: H 239 ASN cc_start: 0.7990 (p0) cc_final: 0.7695 (p0) REVERT: H 281 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.8001 (mttm) REVERT: H 393 ARG cc_start: 0.6357 (tpt170) cc_final: 0.5968 (tpt170) REVERT: I 62 ASP cc_start: 0.7940 (m-30) cc_final: 0.7638 (m-30) REVERT: I 118 ILE cc_start: 0.8755 (mt) cc_final: 0.8524 (mp) REVERT: J 2 GLU cc_start: 0.7833 (pp20) cc_final: 0.7535 (pp20) REVERT: J 30 GLU cc_start: 0.7780 (pp20) cc_final: 0.7229 (pp20) REVERT: J 61 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7671 (ttpt) REVERT: J 75 ASP cc_start: 0.8014 (t0) cc_final: 0.7322 (t0) REVERT: J 102 GLN cc_start: 0.8841 (tt0) cc_final: 0.8593 (tt0) REVERT: J 114 CYS cc_start: 0.7392 (m) cc_final: 0.7151 (m) REVERT: J 116 ILE cc_start: 0.8922 (mp) cc_final: 0.8659 (mm) REVERT: J 125 HIS cc_start: 0.7830 (m90) cc_final: 0.7534 (m170) REVERT: J 149 ASN cc_start: 0.8656 (p0) cc_final: 0.8383 (p0) REVERT: J 174 ASP cc_start: 0.8248 (m-30) cc_final: 0.8042 (m-30) REVERT: J 191 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7823 (mm-30) REVERT: J 195 MET cc_start: 0.7664 (ptt) cc_final: 0.7260 (mtm) REVERT: J 241 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7881 (mm-30) REVERT: J 289 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8129 (mmm160) REVERT: J 292 GLU cc_start: 0.8128 (mp0) cc_final: 0.7740 (mp0) REVERT: J 295 THR cc_start: 0.8543 (p) cc_final: 0.8260 (p) REVERT: J 306 CYS cc_start: 0.7308 (t) cc_final: 0.6964 (t) REVERT: J 397 GLU cc_start: 0.7634 (mp0) cc_final: 0.7338 (mp0) REVERT: J 402 VAL cc_start: 0.8707 (t) cc_final: 0.8449 (t) REVERT: J 408 ASN cc_start: 0.8426 (m-40) cc_final: 0.8203 (m-40) REVERT: J 433 MET cc_start: 0.6722 (mmm) cc_final: 0.6403 (mmm) REVERT: K 20 ARG cc_start: 0.7509 (mtt-85) cc_final: 0.7133 (mtt180) REVERT: K 37 GLU cc_start: 0.7655 (mp0) cc_final: 0.7211 (mp0) REVERT: K 60 ASP cc_start: 0.7907 (t0) cc_final: 0.7615 (t0) REVERT: K 139 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7339 (tm-30) REVERT: K 146 GLN cc_start: 0.8641 (tt0) cc_final: 0.8348 (tt0) REVERT: K 181 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7844 (ttmm) REVERT: K 347 ASP cc_start: 0.7626 (t70) cc_final: 0.7235 (t70) REVERT: K 393 ARG cc_start: 0.8589 (ttt-90) cc_final: 0.7577 (tpm170) REVERT: L 64 GLU cc_start: 0.7778 (mp0) cc_final: 0.7510 (mp0) REVERT: L 83 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8610 (mttm) REVERT: M 57 ASP cc_start: 0.7650 (m-30) cc_final: 0.7087 (m-30) REVERT: A 114 CYS cc_start: 0.7513 (m) cc_final: 0.7239 (m) REVERT: A 202 ASP cc_start: 0.7544 (m-30) cc_final: 0.7155 (m-30) REVERT: A 218 ASP cc_start: 0.7680 (t0) cc_final: 0.7387 (t70) REVERT: A 240 TYR cc_start: 0.8406 (t80) cc_final: 0.8001 (t80) REVERT: A 292 GLU cc_start: 0.8066 (mp0) cc_final: 0.7582 (mp0) REVERT: A 327 HIS cc_start: 0.7974 (m90) cc_final: 0.7683 (t70) REVERT: A 341 GLU cc_start: 0.7800 (mp0) cc_final: 0.7485 (mp0) REVERT: B 60 ASP cc_start: 0.7756 (t0) cc_final: 0.7362 (t0) REVERT: B 70 ASP cc_start: 0.6702 (p0) cc_final: 0.6463 (p0) REVERT: B 81 GLU cc_start: 0.7874 (mp0) cc_final: 0.7629 (mp0) REVERT: B 82 LYS cc_start: 0.8438 (mtpp) cc_final: 0.7827 (mtpt) REVERT: B 157 ARG cc_start: 0.8505 (tpp80) cc_final: 0.8267 (tpp-160) REVERT: B 159 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8503 (ptpt) REVERT: B 199 TYR cc_start: 0.6390 (p90) cc_final: 0.6146 (p90) REVERT: B 217 MET cc_start: 0.7544 (mmp) cc_final: 0.6823 (mmt) REVERT: B 266 CYS cc_start: 0.7943 (p) cc_final: 0.7599 (p) REVERT: B 303 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: B 324 GLU cc_start: 0.8006 (mp0) cc_final: 0.7774 (mp0) REVERT: B 357 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8155 (mt) REVERT: C 11 GLU cc_start: 0.7219 (tt0) cc_final: 0.7002 (tt0) REVERT: C 37 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8829 (ptmm) REVERT: C 64 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 155 ASP cc_start: 0.7545 (m-30) cc_final: 0.7309 (m-30) outliers start: 106 outliers final: 62 residues processed: 997 average time/residue: 1.3619 time to fit residues: 1625.9909 Evaluate side-chains 995 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 925 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 153 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 137 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 411 optimal weight: 7.9990 chunk 363 optimal weight: 3.9990 chunk 412 optimal weight: 1.9990 chunk 395 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 164 optimal weight: 0.4980 chunk 54 optimal weight: 9.9990 chunk 256 optimal weight: 5.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS D 186 ASN E 21 HIS E 146 GLN E 286 HIS ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 246 ASN J 396 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.137769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118302 restraints weight = 50031.472| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.16 r_work: 0.3355 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34387 Z= 0.176 Angle : 0.616 11.832 46859 Z= 0.312 Chirality : 0.047 0.348 5246 Planarity : 0.005 0.096 6004 Dihedral : 5.232 70.484 4985 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 3.78 % Allowed : 16.54 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4291 helix: 1.61 (0.24), residues: 440 sheet: 0.19 (0.15), residues: 1256 loop : -0.65 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 163 HIS 0.005 0.001 HIS K 174 PHE 0.019 0.001 PHE H 134 TYR 0.021 0.001 TYR F 97 ARG 0.009 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 16) link_NAG-ASN : angle 3.06413 ( 48) hydrogen bonds : bond 0.03177 ( 1070) hydrogen bonds : angle 4.79635 ( 2922) SS BOND : bond 0.00302 ( 80) SS BOND : angle 1.52037 ( 160) covalent geometry : bond 0.00407 (34291) covalent geometry : angle 0.60284 (46651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 954 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8355 (t80) cc_final: 0.7857 (t80) REVERT: D 30 GLU cc_start: 0.7469 (pp20) cc_final: 0.7184 (pp20) REVERT: D 99 GLU cc_start: 0.7950 (tp30) cc_final: 0.7630 (tp30) REVERT: D 101 THR cc_start: 0.8430 (m) cc_final: 0.8082 (m) REVERT: D 102 GLN cc_start: 0.8892 (tt0) cc_final: 0.8628 (tt0) REVERT: D 202 ASP cc_start: 0.7737 (m-30) cc_final: 0.7402 (m-30) REVERT: D 260 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8304 (mtpm) REVERT: D 298 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6669 (tm-30) REVERT: D 306 CYS cc_start: 0.7468 (t) cc_final: 0.7058 (t) REVERT: D 320 TYR cc_start: 0.8024 (p90) cc_final: 0.7459 (p90) REVERT: D 393 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8813 (mmtt) REVERT: E 20 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7391 (ttt180) REVERT: E 63 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8191 (ttmm) REVERT: E 70 ASP cc_start: 0.6867 (p0) cc_final: 0.6465 (p0) REVERT: E 72 ASP cc_start: 0.7550 (p0) cc_final: 0.6836 (p0) REVERT: E 76 LYS cc_start: 0.8712 (mttt) cc_final: 0.8338 (mtmm) REVERT: E 81 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: E 127 GLU cc_start: 0.8053 (tt0) cc_final: 0.7766 (tt0) REVERT: E 138 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7286 (tm-30) REVERT: E 139 GLU cc_start: 0.7784 (tp30) cc_final: 0.6944 (tp30) REVERT: E 162 SER cc_start: 0.8511 (t) cc_final: 0.8208 (m) REVERT: E 177 LYS cc_start: 0.8565 (pttp) cc_final: 0.8289 (ttpp) REVERT: E 178 SER cc_start: 0.8822 (t) cc_final: 0.8612 (t) REVERT: E 182 GLU cc_start: 0.7606 (tt0) cc_final: 0.7268 (tt0) REVERT: E 217 MET cc_start: 0.7284 (mmt) cc_final: 0.6740 (mmp) REVERT: E 248 ASP cc_start: 0.8283 (t0) cc_final: 0.7878 (t0) REVERT: E 250 SER cc_start: 0.8718 (m) cc_final: 0.8294 (m) REVERT: E 324 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7999 (mt-10) REVERT: E 391 LYS cc_start: 0.8663 (tppp) cc_final: 0.8388 (tppp) REVERT: F 6 MET cc_start: 0.4595 (tpt) cc_final: 0.4271 (tpt) REVERT: F 78 GLN cc_start: 0.8303 (mp10) cc_final: 0.8065 (mp10) REVERT: F 99 ASN cc_start: 0.8015 (m-40) cc_final: 0.7567 (m-40) REVERT: F 149 LYS cc_start: 0.8555 (mppt) cc_final: 0.8332 (mppt) REVERT: G 75 ASP cc_start: 0.8255 (t0) cc_final: 0.7919 (t0) REVERT: G 99 GLU cc_start: 0.7479 (tm-30) cc_final: 0.6671 (tm-30) REVERT: G 114 CYS cc_start: 0.7546 (m) cc_final: 0.7298 (m) REVERT: G 246 ASN cc_start: 0.7949 (m-40) cc_final: 0.7655 (m-40) REVERT: G 292 GLU cc_start: 0.8231 (mp0) cc_final: 0.7668 (mp0) REVERT: G 298 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6925 (tm-30) REVERT: G 327 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7597 (m-70) REVERT: G 341 GLU cc_start: 0.8008 (mp0) cc_final: 0.7686 (mp0) REVERT: G 393 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8744 (mttm) REVERT: G 395 ASP cc_start: 0.7715 (t70) cc_final: 0.7210 (t70) REVERT: G 404 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7974 (ttpt) REVERT: H 25 CYS cc_start: 0.7090 (p) cc_final: 0.6760 (p) REVERT: H 60 ASP cc_start: 0.7992 (t0) cc_final: 0.7688 (t0) REVERT: H 78 ASP cc_start: 0.8236 (t0) cc_final: 0.7993 (t0) REVERT: H 129 LYS cc_start: 0.8427 (tptt) cc_final: 0.8195 (tmtt) REVERT: H 131 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7682 (mtm180) REVERT: H 239 ASN cc_start: 0.8028 (p0) cc_final: 0.7708 (p0) REVERT: H 281 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8010 (mttm) REVERT: H 393 ARG cc_start: 0.6457 (tpt170) cc_final: 0.5061 (ttm170) REVERT: H 408 VAL cc_start: 0.7205 (t) cc_final: 0.6894 (m) REVERT: I 118 ILE cc_start: 0.8795 (mt) cc_final: 0.8574 (mp) REVERT: J 2 GLU cc_start: 0.7844 (pp20) cc_final: 0.7527 (pp20) REVERT: J 30 GLU cc_start: 0.7763 (pp20) cc_final: 0.7225 (pp20) REVERT: J 61 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7707 (ttpt) REVERT: J 75 ASP cc_start: 0.8107 (t0) cc_final: 0.7373 (t0) REVERT: J 102 GLN cc_start: 0.8854 (tt0) cc_final: 0.8637 (tt0) REVERT: J 114 CYS cc_start: 0.7414 (m) cc_final: 0.7188 (m) REVERT: J 116 ILE cc_start: 0.8962 (mp) cc_final: 0.8708 (mm) REVERT: J 125 HIS cc_start: 0.7844 (m90) cc_final: 0.7524 (m170) REVERT: J 149 ASN cc_start: 0.8693 (p0) cc_final: 0.8424 (p0) REVERT: J 174 ASP cc_start: 0.8250 (m-30) cc_final: 0.8050 (m-30) REVERT: J 191 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7822 (mm-30) REVERT: J 195 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7357 (mtm) REVERT: J 212 ASP cc_start: 0.7864 (t0) cc_final: 0.7528 (t0) REVERT: J 241 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7962 (mm-30) REVERT: J 289 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8193 (mmm160) REVERT: J 292 GLU cc_start: 0.8128 (mp0) cc_final: 0.7758 (mp0) REVERT: J 295 THR cc_start: 0.8500 (p) cc_final: 0.8236 (p) REVERT: J 306 CYS cc_start: 0.7320 (t) cc_final: 0.6980 (t) REVERT: J 397 GLU cc_start: 0.7622 (mp0) cc_final: 0.7326 (mp0) REVERT: J 402 VAL cc_start: 0.8723 (t) cc_final: 0.8469 (t) REVERT: J 408 ASN cc_start: 0.8452 (m-40) cc_final: 0.8242 (m-40) REVERT: J 433 MET cc_start: 0.6745 (mmm) cc_final: 0.6416 (mmm) REVERT: K 37 GLU cc_start: 0.7698 (mp0) cc_final: 0.7259 (mp0) REVERT: K 60 ASP cc_start: 0.7905 (t0) cc_final: 0.7630 (t0) REVERT: K 139 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7382 (tm-30) REVERT: K 146 GLN cc_start: 0.8675 (tt0) cc_final: 0.8393 (tt0) REVERT: K 181 LYS cc_start: 0.8363 (ttpp) cc_final: 0.7817 (ttmm) REVERT: K 347 ASP cc_start: 0.7619 (t70) cc_final: 0.7244 (t70) REVERT: K 393 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.7587 (tpm170) REVERT: M 57 ASP cc_start: 0.7710 (m-30) cc_final: 0.7124 (m-30) REVERT: A 105 GLU cc_start: 0.8163 (tp30) cc_final: 0.7901 (mm-30) REVERT: A 202 ASP cc_start: 0.7559 (m-30) cc_final: 0.7189 (m-30) REVERT: A 218 ASP cc_start: 0.7698 (t0) cc_final: 0.7419 (t70) REVERT: A 240 TYR cc_start: 0.8426 (t80) cc_final: 0.8026 (t80) REVERT: A 289 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7764 (mtp85) REVERT: A 291 SER cc_start: 0.8646 (OUTLIER) cc_final: 0.8000 (p) REVERT: A 292 GLU cc_start: 0.8146 (mp0) cc_final: 0.7494 (mp0) REVERT: A 341 GLU cc_start: 0.7787 (mp0) cc_final: 0.7459 (mp0) REVERT: A 379 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: B 60 ASP cc_start: 0.7725 (t0) cc_final: 0.7320 (t0) REVERT: B 70 ASP cc_start: 0.6743 (p0) cc_final: 0.6485 (p0) REVERT: B 80 MET cc_start: 0.8507 (ttp) cc_final: 0.8268 (ttp) REVERT: B 81 GLU cc_start: 0.7913 (mp0) cc_final: 0.7688 (mp0) REVERT: B 82 LYS cc_start: 0.8532 (mtpp) cc_final: 0.7879 (mtpt) REVERT: B 112 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8270 (p) REVERT: B 157 ARG cc_start: 0.8520 (tpp80) cc_final: 0.8267 (tpp-160) REVERT: B 159 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8527 (ptpt) REVERT: B 199 TYR cc_start: 0.6365 (p90) cc_final: 0.6008 (p90) REVERT: B 217 MET cc_start: 0.7565 (mmp) cc_final: 0.6833 (mmt) REVERT: B 303 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: B 357 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8210 (mt) REVERT: C 11 GLU cc_start: 0.7239 (tt0) cc_final: 0.7009 (tt0) REVERT: C 37 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8780 (ptmm) REVERT: C 64 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7541 (mt-10) REVERT: C 155 ASP cc_start: 0.7554 (m-30) cc_final: 0.7322 (m-30) REVERT: P 79 CYS cc_start: 0.0832 (OUTLIER) cc_final: -0.1725 (t) outliers start: 139 outliers final: 96 residues processed: 1010 average time/residue: 1.3502 time to fit residues: 1625.9716 Evaluate side-chains 1056 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 946 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 36 MET Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 77 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 208 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS E 21 HIS E 286 HIS F 23 GLN ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN H 332 ASN J 52 HIS J 186 ASN J 204 GLN J 228 ASN J 396 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS A 362 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.135959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.116522 restraints weight = 50180.646| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.16 r_work: 0.3320 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 34387 Z= 0.247 Angle : 0.671 12.328 46859 Z= 0.341 Chirality : 0.049 0.346 5246 Planarity : 0.005 0.090 6004 Dihedral : 5.461 66.436 4985 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 93.99 % Rotamer: Outliers : 4.19 % Allowed : 17.22 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4291 helix: 1.40 (0.24), residues: 448 sheet: 0.21 (0.15), residues: 1212 loop : -0.72 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 163 HIS 0.006 0.001 HIS E 333 PHE 0.022 0.002 PHE H 134 TYR 0.023 0.002 TYR A 308 ARG 0.010 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 16) link_NAG-ASN : angle 3.00829 ( 48) hydrogen bonds : bond 0.03437 ( 1070) hydrogen bonds : angle 4.91425 ( 2922) SS BOND : bond 0.00403 ( 80) SS BOND : angle 1.91507 ( 160) covalent geometry : bond 0.00566 (34291) covalent geometry : angle 0.65606 (46651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 965 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8434 (t80) cc_final: 0.7959 (t80) REVERT: D 30 GLU cc_start: 0.7556 (pp20) cc_final: 0.7219 (pp20) REVERT: D 75 ASP cc_start: 0.8392 (t0) cc_final: 0.8027 (t0) REVERT: D 99 GLU cc_start: 0.7979 (tp30) cc_final: 0.7600 (tp30) REVERT: D 101 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8105 (m) REVERT: D 102 GLN cc_start: 0.8953 (tt0) cc_final: 0.8706 (tt0) REVERT: D 202 ASP cc_start: 0.7733 (m-30) cc_final: 0.7372 (m-30) REVERT: D 260 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8305 (mtpp) REVERT: D 298 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6711 (tm-30) REVERT: D 306 CYS cc_start: 0.7552 (t) cc_final: 0.7172 (t) REVERT: D 320 TYR cc_start: 0.8053 (p90) cc_final: 0.7463 (p90) REVERT: D 393 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8787 (mmtt) REVERT: E 20 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7388 (ttt180) REVERT: E 70 ASP cc_start: 0.6717 (p0) cc_final: 0.6300 (p0) REVERT: E 72 ASP cc_start: 0.7519 (p0) cc_final: 0.6778 (p0) REVERT: E 76 LYS cc_start: 0.8741 (mttt) cc_final: 0.8313 (mtmm) REVERT: E 81 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: E 127 GLU cc_start: 0.8015 (tt0) cc_final: 0.7695 (tt0) REVERT: E 138 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7354 (tm-30) REVERT: E 139 GLU cc_start: 0.7814 (tp30) cc_final: 0.7174 (tp30) REVERT: E 162 SER cc_start: 0.8515 (t) cc_final: 0.8209 (m) REVERT: E 177 LYS cc_start: 0.8542 (pttp) cc_final: 0.8260 (ttpp) REVERT: E 178 SER cc_start: 0.8839 (t) cc_final: 0.8631 (t) REVERT: E 182 GLU cc_start: 0.7696 (tt0) cc_final: 0.7373 (tt0) REVERT: E 195 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7936 (mtpp) REVERT: E 217 MET cc_start: 0.7521 (mmt) cc_final: 0.7053 (mmp) REVERT: E 248 ASP cc_start: 0.8305 (t0) cc_final: 0.7915 (t0) REVERT: E 250 SER cc_start: 0.8725 (m) cc_final: 0.8294 (m) REVERT: E 324 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8072 (mt-10) REVERT: E 391 LYS cc_start: 0.8680 (tppp) cc_final: 0.8396 (tppp) REVERT: F 6 MET cc_start: 0.4501 (tpt) cc_final: 0.4228 (tpt) REVERT: F 30 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7174 (t) REVERT: F 78 GLN cc_start: 0.8396 (mp10) cc_final: 0.8145 (mp10) REVERT: F 99 ASN cc_start: 0.8117 (m-40) cc_final: 0.7669 (m-40) REVERT: F 149 LYS cc_start: 0.8575 (mppt) cc_final: 0.8346 (mppt) REVERT: G 5 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8493 (m) REVERT: G 75 ASP cc_start: 0.8196 (t0) cc_final: 0.7894 (t0) REVERT: G 114 CYS cc_start: 0.7579 (m) cc_final: 0.7329 (m) REVERT: G 134 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8049 (ttp80) REVERT: G 246 ASN cc_start: 0.7982 (m-40) cc_final: 0.7663 (m-40) REVERT: G 298 GLU cc_start: 0.7560 (tm-30) cc_final: 0.6977 (tm-30) REVERT: G 327 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7600 (m-70) REVERT: G 341 GLU cc_start: 0.8030 (mp0) cc_final: 0.7674 (mp0) REVERT: G 393 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8780 (mttm) REVERT: G 395 ASP cc_start: 0.7779 (t70) cc_final: 0.7264 (t70) REVERT: G 404 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7963 (ttpt) REVERT: H 20 ARG cc_start: 0.8052 (tpt90) cc_final: 0.7604 (tpt90) REVERT: H 25 CYS cc_start: 0.7049 (p) cc_final: 0.6702 (p) REVERT: H 60 ASP cc_start: 0.8029 (t0) cc_final: 0.7666 (t0) REVERT: H 78 ASP cc_start: 0.8263 (t0) cc_final: 0.8013 (t0) REVERT: H 129 LYS cc_start: 0.8427 (tptt) cc_final: 0.8207 (tmtt) REVERT: H 131 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7752 (mtm180) REVERT: H 217 MET cc_start: 0.6504 (mtm) cc_final: 0.6282 (mtp) REVERT: H 239 ASN cc_start: 0.8103 (p0) cc_final: 0.7802 (p0) REVERT: H 251 VAL cc_start: 0.8593 (t) cc_final: 0.8336 (m) REVERT: H 281 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8104 (mttm) REVERT: H 393 ARG cc_start: 0.6611 (tpt170) cc_final: 0.5207 (ttm170) REVERT: I 118 ILE cc_start: 0.8842 (mt) cc_final: 0.8615 (mp) REVERT: I 135 GLU cc_start: 0.4206 (tp30) cc_final: 0.3987 (tp30) REVERT: J 2 GLU cc_start: 0.7860 (pp20) cc_final: 0.7528 (pp20) REVERT: J 30 GLU cc_start: 0.7766 (pp20) cc_final: 0.7216 (pp20) REVERT: J 45 GLU cc_start: 0.7905 (tp30) cc_final: 0.7524 (tp30) REVERT: J 75 ASP cc_start: 0.8175 (t0) cc_final: 0.7932 (t0) REVERT: J 102 GLN cc_start: 0.8875 (tt0) cc_final: 0.8628 (tt0) REVERT: J 114 CYS cc_start: 0.7373 (m) cc_final: 0.7157 (m) REVERT: J 116 ILE cc_start: 0.8983 (mp) cc_final: 0.8713 (mm) REVERT: J 125 HIS cc_start: 0.7817 (m90) cc_final: 0.7490 (m170) REVERT: J 191 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7633 (mm-30) REVERT: J 195 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7536 (mtm) REVERT: J 212 ASP cc_start: 0.7911 (t0) cc_final: 0.7585 (t0) REVERT: J 241 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7999 (mm-30) REVERT: J 289 ARG cc_start: 0.8489 (mmm-85) cc_final: 0.8203 (mmm160) REVERT: J 292 GLU cc_start: 0.8189 (mp0) cc_final: 0.7764 (mp0) REVERT: J 295 THR cc_start: 0.8460 (p) cc_final: 0.8174 (p) REVERT: J 306 CYS cc_start: 0.7357 (t) cc_final: 0.7038 (t) REVERT: J 397 GLU cc_start: 0.7588 (mp0) cc_final: 0.7253 (mp0) REVERT: J 402 VAL cc_start: 0.8748 (t) cc_final: 0.8480 (t) REVERT: J 410 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8358 (mp) REVERT: J 433 MET cc_start: 0.6778 (mmm) cc_final: 0.6443 (mmm) REVERT: K 37 GLU cc_start: 0.7727 (mp0) cc_final: 0.7309 (mp0) REVERT: K 60 ASP cc_start: 0.7898 (t0) cc_final: 0.7624 (t0) REVERT: K 139 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7391 (tm-30) REVERT: K 146 GLN cc_start: 0.8721 (tt0) cc_final: 0.8464 (tt0) REVERT: K 181 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7795 (ttmm) REVERT: K 342 GLU cc_start: 0.7675 (tt0) cc_final: 0.7390 (tt0) REVERT: K 347 ASP cc_start: 0.7683 (t70) cc_final: 0.7285 (t70) REVERT: K 393 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.7570 (tpm170) REVERT: M 57 ASP cc_start: 0.7734 (m-30) cc_final: 0.7116 (m-30) REVERT: A 202 ASP cc_start: 0.7597 (m-30) cc_final: 0.7235 (m-30) REVERT: A 218 ASP cc_start: 0.7699 (t0) cc_final: 0.7407 (t70) REVERT: A 240 TYR cc_start: 0.8407 (t80) cc_final: 0.7987 (t80) REVERT: A 291 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 292 GLU cc_start: 0.8204 (mp0) cc_final: 0.7520 (mp0) REVERT: A 341 GLU cc_start: 0.7806 (mp0) cc_final: 0.7457 (mp0) REVERT: B 22 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 70 ASP cc_start: 0.6771 (p0) cc_final: 0.6479 (p0) REVERT: B 112 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8293 (p) REVERT: B 159 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8516 (ptpt) REVERT: B 199 TYR cc_start: 0.6462 (p90) cc_final: 0.5999 (p90) REVERT: B 217 MET cc_start: 0.7595 (mmp) cc_final: 0.6913 (mmt) REVERT: B 239 ASN cc_start: 0.8458 (p0) cc_final: 0.8234 (p0) REVERT: B 303 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7851 (mtm-85) REVERT: B 357 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8265 (mt) REVERT: C 37 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8812 (ptmm) REVERT: C 64 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7597 (mt-10) REVERT: C 155 ASP cc_start: 0.7551 (m-30) cc_final: 0.7307 (m-30) REVERT: P 79 CYS cc_start: 0.0839 (OUTLIER) cc_final: -0.1717 (t) outliers start: 154 outliers final: 103 residues processed: 1034 average time/residue: 1.3716 time to fit residues: 1697.7210 Evaluate side-chains 1054 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 934 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 382 optimal weight: 1.9990 chunk 304 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS E 21 HIS E 286 HIS F 92 HIS ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN J 52 HIS J 204 GLN J 228 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS A 362 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116338 restraints weight = 49805.613| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.15 r_work: 0.3332 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 34387 Z= 0.205 Angle : 0.659 13.616 46859 Z= 0.334 Chirality : 0.048 0.342 5246 Planarity : 0.005 0.084 6004 Dihedral : 5.435 61.648 4985 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 3.92 % Allowed : 18.63 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.13), residues: 4291 helix: 1.55 (0.24), residues: 440 sheet: 0.20 (0.15), residues: 1192 loop : -0.75 (0.12), residues: 2659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 163 HIS 0.005 0.001 HIS K 174 PHE 0.022 0.001 PHE H 134 TYR 0.026 0.002 TYR E 199 ARG 0.010 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00542 ( 16) link_NAG-ASN : angle 2.84625 ( 48) hydrogen bonds : bond 0.03279 ( 1070) hydrogen bonds : angle 4.90096 ( 2922) SS BOND : bond 0.00389 ( 80) SS BOND : angle 1.77905 ( 160) covalent geometry : bond 0.00473 (34291) covalent geometry : angle 0.64585 (46651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 941 time to evaluate : 3.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8413 (t80) cc_final: 0.7950 (t80) REVERT: D 30 GLU cc_start: 0.7553 (pp20) cc_final: 0.7230 (pp20) REVERT: D 75 ASP cc_start: 0.8390 (t0) cc_final: 0.8050 (t0) REVERT: D 99 GLU cc_start: 0.7890 (tp30) cc_final: 0.7536 (tp30) REVERT: D 101 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8136 (m) REVERT: D 102 GLN cc_start: 0.8959 (tt0) cc_final: 0.8691 (tt0) REVERT: D 202 ASP cc_start: 0.7724 (m-30) cc_final: 0.7393 (m-30) REVERT: D 242 MET cc_start: 0.8270 (mmm) cc_final: 0.8063 (mmm) REVERT: D 260 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8324 (mtpp) REVERT: D 298 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6715 (tm-30) REVERT: D 306 CYS cc_start: 0.7494 (t) cc_final: 0.7117 (t) REVERT: D 320 TYR cc_start: 0.8032 (p90) cc_final: 0.7420 (p90) REVERT: D 393 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8806 (mmtt) REVERT: E 20 ARG cc_start: 0.7799 (ttt180) cc_final: 0.7424 (ttt180) REVERT: E 70 ASP cc_start: 0.6682 (p0) cc_final: 0.6235 (p0) REVERT: E 72 ASP cc_start: 0.7499 (p0) cc_final: 0.6746 (p0) REVERT: E 76 LYS cc_start: 0.8699 (mttt) cc_final: 0.8290 (mtmm) REVERT: E 81 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: E 127 GLU cc_start: 0.8028 (tt0) cc_final: 0.7694 (tt0) REVERT: E 138 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7382 (tm-30) REVERT: E 139 GLU cc_start: 0.7830 (tp30) cc_final: 0.7152 (tp30) REVERT: E 162 SER cc_start: 0.8512 (t) cc_final: 0.8197 (m) REVERT: E 177 LYS cc_start: 0.8522 (pttp) cc_final: 0.8248 (ttpp) REVERT: E 178 SER cc_start: 0.8755 (t) cc_final: 0.8544 (t) REVERT: E 182 GLU cc_start: 0.7715 (tt0) cc_final: 0.7404 (tt0) REVERT: E 195 LYS cc_start: 0.8207 (mmmm) cc_final: 0.7950 (mtpp) REVERT: E 217 MET cc_start: 0.7575 (mmt) cc_final: 0.6987 (mmp) REVERT: E 248 ASP cc_start: 0.8296 (t0) cc_final: 0.7917 (t0) REVERT: E 250 SER cc_start: 0.8746 (m) cc_final: 0.8307 (m) REVERT: E 391 LYS cc_start: 0.8658 (tppp) cc_final: 0.8369 (tppp) REVERT: F 6 MET cc_start: 0.4547 (tpt) cc_final: 0.4261 (tpt) REVERT: F 30 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7202 (t) REVERT: F 78 GLN cc_start: 0.8424 (mp10) cc_final: 0.8173 (mp10) REVERT: F 99 ASN cc_start: 0.8120 (m-40) cc_final: 0.7674 (m-40) REVERT: F 149 LYS cc_start: 0.8551 (mppt) cc_final: 0.8310 (mppt) REVERT: G 5 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8495 (m) REVERT: G 114 CYS cc_start: 0.7587 (m) cc_final: 0.7355 (m) REVERT: G 134 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8086 (ttp80) REVERT: G 246 ASN cc_start: 0.7992 (m-40) cc_final: 0.7679 (m-40) REVERT: G 298 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6938 (tm-30) REVERT: G 327 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7617 (m-70) REVERT: G 341 GLU cc_start: 0.8030 (mp0) cc_final: 0.7688 (mp0) REVERT: G 393 LYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8773 (mttm) REVERT: G 395 ASP cc_start: 0.7814 (t70) cc_final: 0.7329 (t70) REVERT: G 404 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8008 (ttpt) REVERT: H 20 ARG cc_start: 0.8041 (tpt90) cc_final: 0.7593 (tpt90) REVERT: H 25 CYS cc_start: 0.7030 (p) cc_final: 0.6687 (p) REVERT: H 60 ASP cc_start: 0.8019 (t0) cc_final: 0.7673 (t0) REVERT: H 78 ASP cc_start: 0.8255 (t0) cc_final: 0.7999 (t0) REVERT: H 129 LYS cc_start: 0.8429 (tptt) cc_final: 0.8198 (tmtt) REVERT: H 131 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7748 (mtm180) REVERT: H 239 ASN cc_start: 0.8122 (p0) cc_final: 0.7884 (p0) REVERT: H 250 SER cc_start: 0.8559 (m) cc_final: 0.8310 (p) REVERT: H 251 VAL cc_start: 0.8594 (t) cc_final: 0.8323 (m) REVERT: H 281 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8096 (mttm) REVERT: H 393 ARG cc_start: 0.6337 (tpt170) cc_final: 0.4995 (ttm170) REVERT: I 118 ILE cc_start: 0.8847 (mt) cc_final: 0.8612 (mp) REVERT: J 2 GLU cc_start: 0.7889 (pp20) cc_final: 0.7568 (pp20) REVERT: J 30 GLU cc_start: 0.7747 (pp20) cc_final: 0.7213 (pp20) REVERT: J 45 GLU cc_start: 0.7892 (tp30) cc_final: 0.7518 (tp30) REVERT: J 75 ASP cc_start: 0.8232 (t0) cc_final: 0.7963 (t0) REVERT: J 102 GLN cc_start: 0.8871 (tt0) cc_final: 0.8606 (tt0) REVERT: J 114 CYS cc_start: 0.7360 (m) cc_final: 0.7153 (m) REVERT: J 116 ILE cc_start: 0.8944 (mp) cc_final: 0.8682 (mm) REVERT: J 125 HIS cc_start: 0.7808 (m90) cc_final: 0.7476 (m170) REVERT: J 191 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7629 (mm-30) REVERT: J 212 ASP cc_start: 0.7914 (t0) cc_final: 0.7587 (t0) REVERT: J 241 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7991 (mm-30) REVERT: J 289 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8220 (mmm160) REVERT: J 292 GLU cc_start: 0.8160 (mp0) cc_final: 0.7806 (mp0) REVERT: J 295 THR cc_start: 0.8465 (p) cc_final: 0.8192 (p) REVERT: J 306 CYS cc_start: 0.7344 (t) cc_final: 0.7006 (t) REVERT: J 311 ASP cc_start: 0.7536 (t0) cc_final: 0.7327 (t0) REVERT: J 397 GLU cc_start: 0.7588 (mp0) cc_final: 0.7227 (mp0) REVERT: J 402 VAL cc_start: 0.8746 (t) cc_final: 0.8478 (t) REVERT: J 433 MET cc_start: 0.6755 (mmm) cc_final: 0.6426 (mmm) REVERT: K 37 GLU cc_start: 0.7697 (mp0) cc_final: 0.7284 (mp0) REVERT: K 60 ASP cc_start: 0.7907 (t0) cc_final: 0.7624 (t0) REVERT: K 139 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7412 (tm-30) REVERT: K 146 GLN cc_start: 0.8719 (tt0) cc_final: 0.8451 (tt0) REVERT: K 181 LYS cc_start: 0.8338 (ttpp) cc_final: 0.7791 (ttmm) REVERT: K 342 GLU cc_start: 0.7661 (tt0) cc_final: 0.7325 (tt0) REVERT: K 347 ASP cc_start: 0.7710 (t70) cc_final: 0.7333 (t70) REVERT: K 393 ARG cc_start: 0.8603 (ttt-90) cc_final: 0.7550 (tpm170) REVERT: L 83 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8660 (mttp) REVERT: M 57 ASP cc_start: 0.7700 (m-30) cc_final: 0.7076 (m-30) REVERT: A 76 TYR cc_start: 0.7761 (t80) cc_final: 0.7560 (t80) REVERT: A 105 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 202 ASP cc_start: 0.7568 (m-30) cc_final: 0.7198 (m-30) REVERT: A 218 ASP cc_start: 0.7695 (t0) cc_final: 0.7409 (t70) REVERT: A 240 TYR cc_start: 0.8411 (t80) cc_final: 0.7999 (t80) REVERT: A 241 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7726 (mm-30) REVERT: A 262 GLU cc_start: 0.7560 (mp0) cc_final: 0.7297 (mp0) REVERT: A 291 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8015 (p) REVERT: A 292 GLU cc_start: 0.8219 (mp0) cc_final: 0.7522 (mp0) REVERT: A 341 GLU cc_start: 0.7826 (mp0) cc_final: 0.7464 (mp0) REVERT: B 22 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8766 (p) REVERT: B 70 ASP cc_start: 0.6768 (p0) cc_final: 0.6489 (p0) REVERT: B 112 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 159 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8524 (ptpt) REVERT: B 199 TYR cc_start: 0.6415 (p90) cc_final: 0.6045 (p90) REVERT: B 217 MET cc_start: 0.7588 (mmp) cc_final: 0.7001 (mmt) REVERT: B 239 ASN cc_start: 0.8448 (p0) cc_final: 0.8187 (p0) REVERT: B 303 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: B 357 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8226 (mt) REVERT: C 37 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8799 (pptt) REVERT: C 64 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7636 (mt-10) REVERT: C 155 ASP cc_start: 0.7545 (m-30) cc_final: 0.7306 (m-30) REVERT: P 79 CYS cc_start: 0.1016 (OUTLIER) cc_final: -0.1540 (t) outliers start: 144 outliers final: 106 residues processed: 1008 average time/residue: 1.3518 time to fit residues: 1642.3780 Evaluate side-chains 1064 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 943 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 11 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 156 optimal weight: 0.0020 chunk 158 optimal weight: 6.9990 chunk 142 optimal weight: 0.4980 chunk 396 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 HIS F 23 GLN ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 ASN J 9 ASN J 204 GLN J 246 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.118986 restraints weight = 50119.359| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.17 r_work: 0.3363 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34387 Z= 0.121 Angle : 0.629 13.784 46859 Z= 0.317 Chirality : 0.046 0.331 5246 Planarity : 0.005 0.076 6004 Dihedral : 5.232 59.931 4985 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 2.94 % Allowed : 19.86 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 4291 helix: 1.69 (0.24), residues: 440 sheet: 0.13 (0.15), residues: 1224 loop : -0.67 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 409 HIS 0.005 0.001 HIS L 40 PHE 0.019 0.001 PHE H 134 TYR 0.018 0.001 TYR I 79 ARG 0.010 0.000 ARG A 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00558 ( 16) link_NAG-ASN : angle 2.70890 ( 48) hydrogen bonds : bond 0.03032 ( 1070) hydrogen bonds : angle 4.80290 ( 2922) SS BOND : bond 0.00288 ( 80) SS BOND : angle 1.50507 ( 160) covalent geometry : bond 0.00278 (34291) covalent geometry : angle 0.61763 (46651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 948 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7494 (pp20) cc_final: 0.7210 (pp20) REVERT: D 75 ASP cc_start: 0.8446 (t0) cc_final: 0.8111 (t0) REVERT: D 99 GLU cc_start: 0.8014 (tp30) cc_final: 0.7606 (tp30) REVERT: D 101 THR cc_start: 0.8424 (m) cc_final: 0.8085 (m) REVERT: D 102 GLN cc_start: 0.8932 (tt0) cc_final: 0.8678 (tt0) REVERT: D 135 ILE cc_start: 0.8552 (mt) cc_final: 0.8134 (tt) REVERT: D 202 ASP cc_start: 0.7748 (m-30) cc_final: 0.7395 (m-30) REVERT: D 298 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6709 (tm-30) REVERT: D 306 CYS cc_start: 0.7376 (t) cc_final: 0.6975 (t) REVERT: D 320 TYR cc_start: 0.7903 (p90) cc_final: 0.7440 (p90) REVERT: D 393 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8814 (mmtt) REVERT: E 70 ASP cc_start: 0.6687 (p0) cc_final: 0.6223 (p0) REVERT: E 72 ASP cc_start: 0.7454 (p0) cc_final: 0.6725 (p0) REVERT: E 76 LYS cc_start: 0.8703 (mttt) cc_final: 0.8394 (mtmt) REVERT: E 81 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: E 127 GLU cc_start: 0.8043 (tt0) cc_final: 0.7726 (tt0) REVERT: E 138 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 139 GLU cc_start: 0.7818 (tp30) cc_final: 0.6978 (tp30) REVERT: E 162 SER cc_start: 0.8538 (t) cc_final: 0.8180 (m) REVERT: E 177 LYS cc_start: 0.8495 (pttp) cc_final: 0.8232 (ttpp) REVERT: E 178 SER cc_start: 0.8738 (t) cc_final: 0.8526 (t) REVERT: E 182 GLU cc_start: 0.7631 (tt0) cc_final: 0.7280 (tt0) REVERT: E 195 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7578 (mmpt) REVERT: E 217 MET cc_start: 0.7474 (mmt) cc_final: 0.6877 (mmp) REVERT: E 248 ASP cc_start: 0.8250 (t0) cc_final: 0.7904 (t0) REVERT: E 250 SER cc_start: 0.8729 (m) cc_final: 0.8275 (m) REVERT: E 391 LYS cc_start: 0.8638 (tppp) cc_final: 0.8352 (tppp) REVERT: F 6 MET cc_start: 0.4570 (tpt) cc_final: 0.4256 (tpt) REVERT: F 30 VAL cc_start: 0.7579 (OUTLIER) cc_final: 0.7192 (t) REVERT: F 78 GLN cc_start: 0.8387 (mp10) cc_final: 0.8167 (mp10) REVERT: F 99 ASN cc_start: 0.7980 (m-40) cc_final: 0.7544 (m-40) REVERT: F 149 LYS cc_start: 0.8461 (mppt) cc_final: 0.8215 (mppt) REVERT: G 5 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8477 (m) REVERT: G 114 CYS cc_start: 0.7612 (m) cc_final: 0.7383 (m) REVERT: G 134 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8029 (ttp80) REVERT: G 246 ASN cc_start: 0.7944 (m-40) cc_final: 0.7646 (m-40) REVERT: G 267 ARG cc_start: 0.8502 (pmt170) cc_final: 0.8177 (pmt170) REVERT: G 292 GLU cc_start: 0.8239 (mp0) cc_final: 0.7704 (mp0) REVERT: G 298 GLU cc_start: 0.7460 (tm-30) cc_final: 0.6872 (tm-30) REVERT: G 327 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.7470 (m90) REVERT: G 341 GLU cc_start: 0.8000 (mp0) cc_final: 0.7663 (mp0) REVERT: G 393 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8726 (mttm) REVERT: G 395 ASP cc_start: 0.7925 (t70) cc_final: 0.7454 (t70) REVERT: G 404 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8055 (ttpt) REVERT: H 20 ARG cc_start: 0.8012 (tpt90) cc_final: 0.7564 (tpt90) REVERT: H 25 CYS cc_start: 0.7134 (p) cc_final: 0.6790 (p) REVERT: H 60 ASP cc_start: 0.8021 (t0) cc_final: 0.7721 (t0) REVERT: H 78 ASP cc_start: 0.8215 (t0) cc_final: 0.7957 (t0) REVERT: H 129 LYS cc_start: 0.8447 (tptt) cc_final: 0.8211 (tmtt) REVERT: H 131 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7740 (mtm180) REVERT: H 189 ILE cc_start: 0.8138 (pp) cc_final: 0.7928 (pp) REVERT: H 239 ASN cc_start: 0.8010 (p0) cc_final: 0.7746 (p0) REVERT: H 250 SER cc_start: 0.8506 (m) cc_final: 0.8246 (p) REVERT: H 281 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8048 (mttp) REVERT: H 393 ARG cc_start: 0.6212 (tpt170) cc_final: 0.4855 (ttm170) REVERT: H 408 VAL cc_start: 0.7321 (t) cc_final: 0.7060 (m) REVERT: I 47 ASN cc_start: 0.8277 (t0) cc_final: 0.8005 (t0) REVERT: I 118 ILE cc_start: 0.8820 (mt) cc_final: 0.8592 (mp) REVERT: J 2 GLU cc_start: 0.7864 (pp20) cc_final: 0.7561 (pp20) REVERT: J 30 GLU cc_start: 0.7791 (pp20) cc_final: 0.7254 (pp20) REVERT: J 75 ASP cc_start: 0.8193 (t0) cc_final: 0.7934 (t0) REVERT: J 102 GLN cc_start: 0.8839 (tt0) cc_final: 0.8616 (tt0) REVERT: J 114 CYS cc_start: 0.7338 (m) cc_final: 0.7134 (m) REVERT: J 116 ILE cc_start: 0.8931 (mp) cc_final: 0.8672 (mm) REVERT: J 125 HIS cc_start: 0.7828 (m90) cc_final: 0.7530 (m170) REVERT: J 191 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7812 (mm-30) REVERT: J 212 ASP cc_start: 0.7899 (t0) cc_final: 0.7589 (t0) REVERT: J 241 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8007 (mm-30) REVERT: J 289 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8250 (mmm160) REVERT: J 292 GLU cc_start: 0.8155 (mp0) cc_final: 0.7803 (mp0) REVERT: J 295 THR cc_start: 0.8512 (p) cc_final: 0.8274 (p) REVERT: J 306 CYS cc_start: 0.7342 (t) cc_final: 0.6999 (t) REVERT: J 311 ASP cc_start: 0.7477 (t0) cc_final: 0.7260 (t0) REVERT: J 397 GLU cc_start: 0.7575 (mp0) cc_final: 0.7238 (mp0) REVERT: J 402 VAL cc_start: 0.8706 (t) cc_final: 0.8452 (t) REVERT: J 433 MET cc_start: 0.6734 (mmm) cc_final: 0.6449 (mmm) REVERT: K 37 GLU cc_start: 0.7678 (mp0) cc_final: 0.7191 (mp0) REVERT: K 139 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7398 (tm-30) REVERT: K 146 GLN cc_start: 0.8701 (tt0) cc_final: 0.8444 (tt0) REVERT: K 181 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7791 (ttmm) REVERT: K 342 GLU cc_start: 0.7683 (tt0) cc_final: 0.7409 (tt0) REVERT: K 347 ASP cc_start: 0.7659 (t70) cc_final: 0.7293 (t70) REVERT: K 393 ARG cc_start: 0.8574 (ttt-90) cc_final: 0.7481 (tpm170) REVERT: L 83 LYS cc_start: 0.8838 (mtpp) cc_final: 0.8615 (mttp) REVERT: M 57 ASP cc_start: 0.7613 (m-30) cc_final: 0.6969 (m-30) REVERT: A 202 ASP cc_start: 0.7550 (m-30) cc_final: 0.7167 (m-30) REVERT: A 218 ASP cc_start: 0.7661 (t0) cc_final: 0.7345 (t70) REVERT: A 240 TYR cc_start: 0.8444 (t80) cc_final: 0.8001 (t80) REVERT: A 241 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7747 (mm-30) REVERT: A 262 GLU cc_start: 0.7535 (mp0) cc_final: 0.7274 (mp0) REVERT: A 292 GLU cc_start: 0.8199 (mp0) cc_final: 0.7660 (mp0) REVERT: A 341 GLU cc_start: 0.7809 (mp0) cc_final: 0.7443 (mp0) REVERT: A 362 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7950 (mm110) REVERT: A 379 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7451 (mm-30) REVERT: B 60 ASP cc_start: 0.7773 (t0) cc_final: 0.7403 (t0) REVERT: B 70 ASP cc_start: 0.6654 (p0) cc_final: 0.6419 (p0) REVERT: B 82 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8255 (mtmt) REVERT: B 157 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8226 (tpp-160) REVERT: B 199 TYR cc_start: 0.6469 (p90) cc_final: 0.6157 (p90) REVERT: B 217 MET cc_start: 0.7542 (mmp) cc_final: 0.6965 (mmt) REVERT: B 239 ASN cc_start: 0.8390 (p0) cc_final: 0.8156 (p0) REVERT: B 303 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7804 (mtm-85) REVERT: B 357 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 37 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8824 (ptmm) REVERT: C 64 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7518 (mt-10) REVERT: C 124 ARG cc_start: 0.8358 (mtm180) cc_final: 0.8133 (mtp180) REVERT: C 155 ASP cc_start: 0.7509 (m-30) cc_final: 0.7277 (m-30) REVERT: P 79 CYS cc_start: 0.0901 (OUTLIER) cc_final: -0.1539 (t) outliers start: 108 outliers final: 83 residues processed: 997 average time/residue: 1.3252 time to fit residues: 1588.6298 Evaluate side-chains 1018 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 924 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 46 optimal weight: 4.9990 chunk 342 optimal weight: 0.9980 chunk 239 optimal weight: 4.9990 chunk 336 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 360 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 213 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 400 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS E 286 HIS ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 327 HIS K 21 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.118853 restraints weight = 50047.593| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.15 r_work: 0.3362 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 34387 Z= 0.134 Angle : 0.638 13.263 46859 Z= 0.322 Chirality : 0.047 0.333 5246 Planarity : 0.005 0.076 6004 Dihedral : 5.184 59.203 4985 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.27 % Rotamer: Outliers : 2.91 % Allowed : 20.10 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4291 helix: 1.71 (0.24), residues: 440 sheet: 0.15 (0.15), residues: 1224 loop : -0.65 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 163 HIS 0.005 0.001 HIS K 21 PHE 0.023 0.001 PHE H 134 TYR 0.018 0.001 TYR B 53 ARG 0.010 0.000 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 16) link_NAG-ASN : angle 2.67006 ( 48) hydrogen bonds : bond 0.03062 ( 1070) hydrogen bonds : angle 4.76375 ( 2922) SS BOND : bond 0.00365 ( 80) SS BOND : angle 1.75705 ( 160) covalent geometry : bond 0.00315 (34291) covalent geometry : angle 0.62573 (46651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 943 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8334 (t80) cc_final: 0.7808 (t80) REVERT: D 30 GLU cc_start: 0.7491 (pp20) cc_final: 0.7219 (pp20) REVERT: D 75 ASP cc_start: 0.8446 (t0) cc_final: 0.8074 (t0) REVERT: D 99 GLU cc_start: 0.8002 (tp30) cc_final: 0.7577 (tp30) REVERT: D 101 THR cc_start: 0.8419 (m) cc_final: 0.8085 (m) REVERT: D 102 GLN cc_start: 0.8942 (tt0) cc_final: 0.8702 (tt0) REVERT: D 135 ILE cc_start: 0.8529 (mt) cc_final: 0.8119 (tt) REVERT: D 202 ASP cc_start: 0.7752 (m-30) cc_final: 0.7391 (m-30) REVERT: D 298 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6731 (tm-30) REVERT: D 306 CYS cc_start: 0.7395 (t) cc_final: 0.6976 (t) REVERT: D 320 TYR cc_start: 0.7891 (p90) cc_final: 0.7335 (p90) REVERT: D 393 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8796 (mmtt) REVERT: E 70 ASP cc_start: 0.6696 (p0) cc_final: 0.6237 (p0) REVERT: E 72 ASP cc_start: 0.7433 (p0) cc_final: 0.6698 (p0) REVERT: E 76 LYS cc_start: 0.8723 (mttt) cc_final: 0.8403 (mtmt) REVERT: E 81 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: E 127 GLU cc_start: 0.8061 (tt0) cc_final: 0.7736 (tt0) REVERT: E 138 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7534 (tm-30) REVERT: E 139 GLU cc_start: 0.7765 (tp30) cc_final: 0.7161 (tp30) REVERT: E 162 SER cc_start: 0.8501 (t) cc_final: 0.8185 (m) REVERT: E 177 LYS cc_start: 0.8512 (pttp) cc_final: 0.8253 (ttpp) REVERT: E 178 SER cc_start: 0.8795 (t) cc_final: 0.8579 (t) REVERT: E 182 GLU cc_start: 0.7674 (tt0) cc_final: 0.7289 (tt0) REVERT: E 195 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7891 (mtpp) REVERT: E 217 MET cc_start: 0.7470 (mmt) cc_final: 0.6873 (mmp) REVERT: E 248 ASP cc_start: 0.8275 (t0) cc_final: 0.7938 (t0) REVERT: E 250 SER cc_start: 0.8738 (m) cc_final: 0.8288 (m) REVERT: E 391 LYS cc_start: 0.8655 (tppp) cc_final: 0.8377 (tppp) REVERT: F 6 MET cc_start: 0.4454 (tpt) cc_final: 0.4180 (tpt) REVERT: F 30 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7214 (t) REVERT: F 99 ASN cc_start: 0.7989 (m-40) cc_final: 0.7552 (m-40) REVERT: F 149 LYS cc_start: 0.8455 (mppt) cc_final: 0.8210 (mppt) REVERT: G 5 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8553 (p) REVERT: G 75 ASP cc_start: 0.8247 (t0) cc_final: 0.7942 (t0) REVERT: G 114 CYS cc_start: 0.7537 (m) cc_final: 0.7313 (m) REVERT: G 134 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8004 (ttp80) REVERT: G 246 ASN cc_start: 0.7959 (m-40) cc_final: 0.7668 (m-40) REVERT: G 267 ARG cc_start: 0.8505 (pmt170) cc_final: 0.8190 (pmt170) REVERT: G 292 GLU cc_start: 0.8245 (mp0) cc_final: 0.7711 (mp0) REVERT: G 298 GLU cc_start: 0.7449 (tm-30) cc_final: 0.6855 (tm-30) REVERT: G 327 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7461 (m90) REVERT: G 341 GLU cc_start: 0.8010 (mp0) cc_final: 0.7668 (mp0) REVERT: G 393 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8731 (mttm) REVERT: G 395 ASP cc_start: 0.7917 (t70) cc_final: 0.7458 (t70) REVERT: G 404 LYS cc_start: 0.8381 (ttpt) cc_final: 0.8061 (ttpt) REVERT: H 20 ARG cc_start: 0.8008 (tpt90) cc_final: 0.7571 (tpt90) REVERT: H 25 CYS cc_start: 0.7093 (p) cc_final: 0.6778 (p) REVERT: H 60 ASP cc_start: 0.7993 (t0) cc_final: 0.7689 (t0) REVERT: H 78 ASP cc_start: 0.8208 (t0) cc_final: 0.7952 (t0) REVERT: H 129 LYS cc_start: 0.8451 (tptt) cc_final: 0.8220 (tmtt) REVERT: H 131 ARG cc_start: 0.7979 (mtm180) cc_final: 0.7710 (mtm180) REVERT: H 239 ASN cc_start: 0.8027 (p0) cc_final: 0.7739 (p0) REVERT: H 250 SER cc_start: 0.8475 (m) cc_final: 0.8215 (p) REVERT: H 281 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: H 393 ARG cc_start: 0.6289 (tpt170) cc_final: 0.4920 (ttm170) REVERT: H 408 VAL cc_start: 0.7331 (t) cc_final: 0.7080 (m) REVERT: I 118 ILE cc_start: 0.8815 (mt) cc_final: 0.8590 (mp) REVERT: J 2 GLU cc_start: 0.7896 (pp20) cc_final: 0.7583 (pp20) REVERT: J 30 GLU cc_start: 0.7760 (pp20) cc_final: 0.7220 (pp20) REVERT: J 75 ASP cc_start: 0.8211 (t0) cc_final: 0.7959 (t0) REVERT: J 102 GLN cc_start: 0.8846 (tt0) cc_final: 0.8614 (tt0) REVERT: J 114 CYS cc_start: 0.7328 (m) cc_final: 0.7123 (m) REVERT: J 116 ILE cc_start: 0.8930 (mp) cc_final: 0.8670 (mm) REVERT: J 125 HIS cc_start: 0.7839 (m90) cc_final: 0.7543 (m170) REVERT: J 186 ASN cc_start: 0.8691 (m110) cc_final: 0.8474 (m-40) REVERT: J 191 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7802 (mm-30) REVERT: J 212 ASP cc_start: 0.7903 (t0) cc_final: 0.7595 (t0) REVERT: J 241 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7987 (mm-30) REVERT: J 260 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7789 (tttp) REVERT: J 289 ARG cc_start: 0.8478 (mmm-85) cc_final: 0.8254 (mmm160) REVERT: J 292 GLU cc_start: 0.8143 (mp0) cc_final: 0.7798 (mp0) REVERT: J 295 THR cc_start: 0.8500 (p) cc_final: 0.8278 (p) REVERT: J 306 CYS cc_start: 0.7317 (t) cc_final: 0.6969 (t) REVERT: J 311 ASP cc_start: 0.7448 (t0) cc_final: 0.7222 (t0) REVERT: J 397 GLU cc_start: 0.7583 (mp0) cc_final: 0.7250 (mp0) REVERT: J 402 VAL cc_start: 0.8704 (t) cc_final: 0.8461 (t) REVERT: J 433 MET cc_start: 0.6687 (mmm) cc_final: 0.6386 (mmm) REVERT: K 37 GLU cc_start: 0.7649 (mp0) cc_final: 0.7172 (mp0) REVERT: K 139 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7418 (tm-30) REVERT: K 146 GLN cc_start: 0.8695 (tt0) cc_final: 0.8413 (tt0) REVERT: K 181 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7782 (ttmm) REVERT: K 342 GLU cc_start: 0.7676 (tt0) cc_final: 0.7388 (tt0) REVERT: K 347 ASP cc_start: 0.7624 (t70) cc_final: 0.7264 (t70) REVERT: K 393 ARG cc_start: 0.8578 (ttt-90) cc_final: 0.7477 (tpm170) REVERT: L 83 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8616 (mttp) REVERT: M 57 ASP cc_start: 0.7595 (m-30) cc_final: 0.6970 (m-30) REVERT: A 202 ASP cc_start: 0.7597 (m-30) cc_final: 0.7199 (m-30) REVERT: A 218 ASP cc_start: 0.7631 (t0) cc_final: 0.7337 (t70) REVERT: A 240 TYR cc_start: 0.8436 (t80) cc_final: 0.8039 (t80) REVERT: A 241 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 262 GLU cc_start: 0.7551 (mp0) cc_final: 0.7285 (mp0) REVERT: A 292 GLU cc_start: 0.8164 (mp0) cc_final: 0.7636 (mp0) REVERT: A 341 GLU cc_start: 0.7799 (mp0) cc_final: 0.7438 (mp0) REVERT: A 379 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7389 (mm-30) REVERT: B 60 ASP cc_start: 0.7755 (t0) cc_final: 0.7414 (t0) REVERT: B 70 ASP cc_start: 0.6632 (p0) cc_final: 0.6422 (p0) REVERT: B 112 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 159 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8465 (ptpt) REVERT: B 199 TYR cc_start: 0.6472 (p90) cc_final: 0.6165 (p90) REVERT: B 217 MET cc_start: 0.7535 (mmp) cc_final: 0.6960 (mmt) REVERT: B 239 ASN cc_start: 0.8361 (p0) cc_final: 0.8128 (p0) REVERT: B 303 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7789 (mtm-85) REVERT: B 357 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8126 (mt) REVERT: C 64 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7550 (mt-10) REVERT: C 80 THR cc_start: 0.8599 (m) cc_final: 0.8315 (p) REVERT: C 124 ARG cc_start: 0.8349 (mtm180) cc_final: 0.8079 (mtp180) REVERT: C 155 ASP cc_start: 0.7502 (m-30) cc_final: 0.7275 (m-30) REVERT: P 79 CYS cc_start: 0.0780 (OUTLIER) cc_final: -0.1661 (t) outliers start: 107 outliers final: 87 residues processed: 992 average time/residue: 1.3238 time to fit residues: 1591.2629 Evaluate side-chains 1030 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 931 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 32 THR Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 81 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 393 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 260 LYS Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 105 CYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 121 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 331 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 376 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS E 286 HIS G 3 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 HIS J 9 ASN J 52 HIS J 59 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN J 228 ASN J 327 HIS K 21 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117814 restraints weight = 50272.490| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.14 r_work: 0.3347 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 34387 Z= 0.176 Angle : 0.659 13.131 46859 Z= 0.333 Chirality : 0.048 0.336 5246 Planarity : 0.005 0.076 6004 Dihedral : 5.269 57.305 4985 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 3.05 % Allowed : 19.83 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4291 helix: 1.62 (0.24), residues: 448 sheet: 0.19 (0.15), residues: 1200 loop : -0.68 (0.12), residues: 2643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 163 HIS 0.010 0.001 HIS B 96 PHE 0.026 0.001 PHE H 134 TYR 0.022 0.002 TYR B 53 ARG 0.010 0.001 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00532 ( 16) link_NAG-ASN : angle 2.64614 ( 48) hydrogen bonds : bond 0.03190 ( 1070) hydrogen bonds : angle 4.80176 ( 2922) SS BOND : bond 0.00375 ( 80) SS BOND : angle 1.82374 ( 160) covalent geometry : bond 0.00410 (34291) covalent geometry : angle 0.64647 (46651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34209.91 seconds wall clock time: 587 minutes 22.57 seconds (35242.57 seconds total)