Starting phenix.real_space_refine on Wed May 28 12:23:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqx_47117/05_2025/9dqx_47117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqx_47117/05_2025/9dqx_47117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dqx_47117/05_2025/9dqx_47117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqx_47117/05_2025/9dqx_47117.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqx_47117/05_2025/9dqx_47117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqx_47117/05_2025/9dqx_47117.cif" } resolution = 3.4 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= 0.013 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 19564 2.51 5 N 5322 2.21 5 O 5822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 30900 Number of models: 1 Model: "" Number of chains: 20 Chain: "J" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "K" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3174 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 27, 'TRANS': 376} Chain breaks: 1 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1188 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "D" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "G" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "E" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 27, 'TRANS': 378} Chain: "H" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 27, 'TRANS': 378} Chain: "B" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 27, 'TRANS': 378} 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: "I" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain breaks: 2 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: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "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: "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: "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 Time building chain proxies: 17.57, per 1000 atoms: 0.57 Number of scatterers: 30900 At special positions: 0 Unit cell: (185.5, 196.1, 156.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 5822 8.00 N 5322 7.00 C 19564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.02 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.04 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.02 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=2.04 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 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=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 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=2.04 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 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=2.03 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.04 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=2.04 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 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 245 " " NAG B 501 " - " ASN B 196 " " NAG B 502 " - " ASN B 318 " " NAG D 501 " - " ASN D 245 " " NAG E 501 " - " ASN E 196 " " NAG E 502 " - " ASN E 318 " " NAG G 501 " - " ASN G 245 " " NAG H 501 " - " ASN H 196 " " NAG H 502 " - " ASN H 318 " " NAG J 501 " - " ASN J 245 " " NAG K 501 " - " ASN K 196 " " NAG K 502 " - " ASN K 318 " Time building additional restraints: 6.87 Conformation dependent library (CDL) restraints added in 3.7 seconds 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7372 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 96 sheets defined 12.0% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.574A pdb=" N MET J 242 " --> pdb=" O SER J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 255 Processing helix chain 'J' and resid 256 through 259 removed outlier: 3.989A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 256 through 259' Processing helix chain 'J' and resid 403 through 437 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 removed outlier: 3.603A pdb=" N ILE K 355 " --> pdb=" O TRP K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 398 Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.545A pdb=" N GLY D 258 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 4.328A 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 403 through 437 Processing helix chain 'G' and resid 111 through 116 removed outlier: 4.369A pdb=" N THR G 115 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE G 116 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.864A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 289 through 293 Processing helix chain 'G' and resid 397 through 402 removed outlier: 3.782A pdb=" N VAL G 402 " --> pdb=" O PHE G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 437 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.924A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.612A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 437 Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.755A pdb=" N GLY E 194 " --> pdb=" O PRO E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 226 removed outlier: 3.525A pdb=" N GLN E 225 " --> pdb=" O LYS E 222 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS E 226 " --> pdb=" O ALA E 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 222 through 226' 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 removed outlier: 3.638A pdb=" N LEU E 402 " --> pdb=" O THR E 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.856A pdb=" N GLY H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 363 through 402 Proline residue: H 399 - end of helix Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.568A pdb=" N GLY B 194 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.775A pdb=" N HIS B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 403 Proline residue: B 399 - end of helix removed outlier: 3.852A pdb=" N ALA B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 11 Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 49 through 53 removed outlier: 3.910A pdb=" N ALA I 52 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL I 53 " --> pdb=" O LEU I 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 49 through 53' Processing sheet with id=AA1, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.974A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 15 through 20 removed outlier: 5.247A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS J 49 " --> pdb=" O HIS J 118 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS J 118 " --> pdb=" O CYS J 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 140 through 147 removed outlier: 7.654A pdb=" N HIS J 118 " --> pdb=" O CYS J 49 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N CYS J 49 " --> pdb=" O HIS J 118 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL J 47 " --> pdb=" O VAL J 120 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU J 45 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER J 35 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ARG J 134 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL J 33 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ILE J 31 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 59 through 62 Processing sheet with id=AA5, first strand: chain 'J' and resid 87 through 88 removed outlier: 3.543A pdb=" N MET J 88 " --> pdb=" O GLY J 91 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY J 91 " --> pdb=" O MET J 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'J' and resid 203 through 205 Processing sheet with id=AA7, first strand: chain 'J' and resid 219 through 221 Processing sheet with id=AA8, first strand: chain 'J' and resid 296 through 304 removed outlier: 4.415A pdb=" N GLU J 298 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 306 through 307 removed outlier: 6.678A pdb=" N CYS J 306 " --> pdb=" O LYS J 381 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'K' and resid 14 through 16 Processing sheet with id=AB3, first strand: chain 'K' and resid 31 through 35 removed outlier: 6.586A pdb=" N GLN K 46 " --> pdb=" O GLU K 32 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL K 34 " --> pdb=" O ARG K 44 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG K 44 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE K 100 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HIS K 96 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU K 102 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG K 92 " --> pdb=" O GLN K 104 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE K 85 " --> pdb=" O CYS K 91 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG K 93 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 11.340A pdb=" N LEU K 83 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP K 109 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 63 through 67 Processing sheet with id=AB5, first strand: chain 'K' and resid 150 through 155 Processing sheet with id=AB6, first strand: chain 'K' and resid 237 through 238 removed outlier: 6.395A pdb=" N ILE K 257 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR K 165 " --> pdb=" O LEU K 255 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU K 255 " --> pdb=" O TYR K 165 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR K 167 " --> pdb=" O GLY K 253 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLY K 253 " --> pdb=" O THR K 167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 180 through 183 removed outlier: 3.689A pdb=" N ILE K 189 " --> pdb=" O THR K 215 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR K 215 " --> pdb=" O ILE K 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 207 through 211 Processing sheet with id=AB9, first strand: chain 'K' and resid 275 through 278 Processing sheet with id=AC1, first strand: chain 'L' and resid 44 through 45 removed outlier: 4.643A pdb=" N GLY L 26 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU L 20 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N TYR L 27 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 96 through 98 Processing sheet with id=AC3, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.136A pdb=" N ALA L 127 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER L 142 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.604A pdb=" N ILE D 280 " --> pdb=" O HIS D 3 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 12 through 19 removed outlier: 5.915A pdb=" N ILE D 13 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL D 33 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D 35 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 128 " --> pdb=" O THR D 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 44 through 49 removed outlier: 6.710A pdb=" N ALA D 121 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N VAL D 47 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA D 119 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.672A pdb=" N GLN D 59 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN D 100 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY D 82 " --> pdb=" O ASN D 100 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN D 102 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL D 80 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER D 104 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS D 78 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA D 106 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR D 76 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA D 74 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AC9, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AD1, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD2, first strand: chain 'D' and resid 260 through 262 Processing sheet with id=AD3, first strand: chain 'D' and resid 302 through 304 removed outlier: 3.621A pdb=" N SER D 315 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA D 348 " --> pdb=" O ALA D 322 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG D 324 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 346 " --> pdb=" O ARG D 324 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY D 326 " --> pdb=" O THR D 344 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR D 344 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 331 through 332 Processing sheet with id=AD5, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AD6, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.955A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 12 through 19 removed outlier: 5.999A pdb=" N ILE G 13 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL G 33 " --> pdb=" O ILE G 13 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 140 through 147 removed outlier: 3.955A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS G 123 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS G 44 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N HIS G 125 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N THR G 42 " --> pdb=" O HIS G 125 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA G 127 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU G 129 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU G 38 " --> pdb=" O LEU G 129 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 59 through 62 Processing sheet with id=AE1, first strand: chain 'G' and resid 87 through 88 removed outlier: 3.805A pdb=" N MET G 88 " --> pdb=" O GLY G 91 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 91 " --> pdb=" O MET G 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AE3, first strand: chain 'G' and resid 219 through 221 Processing sheet with id=AE4, first strand: chain 'G' and resid 296 through 303 removed outlier: 3.767A pdb=" N GLU G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.582A pdb=" N THR G 344 " --> pdb=" O CYS G 328 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 337 through 339 Processing sheet with id=AE7, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.608A pdb=" N THR H 275 " --> pdb=" O HIS H 286 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 387 through 388 removed outlier: 7.498A pdb=" N LEU H 285 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N PHE H 319 " --> pdb=" O LEU H 285 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU H 287 " --> pdb=" O ARG H 317 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ARG H 317 " --> pdb=" O LEU H 287 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA H 289 " --> pdb=" O THR H 315 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR H 315 " --> pdb=" O ALA H 289 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG H 291 " --> pdb=" O GLY H 313 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLY H 313 " --> pdb=" O ARG H 291 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 2 through 8 removed outlier: 4.025A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 12 through 19 removed outlier: 5.652A pdb=" N ILE A 13 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL A 33 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 36 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS A 130 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 38 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS A 44 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 122 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR A 46 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 12 through 19 removed outlier: 5.652A pdb=" N ILE A 13 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL A 33 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 36 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS A 130 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU A 38 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS A 44 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 122 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR A 46 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N VAL A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 59 through 62 Processing sheet with id=AF4, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.596A pdb=" N GLY A 91 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AF6, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AF7, first strand: chain 'A' and resid 260 through 262 Processing sheet with id=AF8, first strand: chain 'A' and resid 296 through 303 removed outlier: 3.755A pdb=" N THR A 317 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AG1, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AG2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AG3, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AG4, first strand: chain 'E' and resid 31 through 35 removed outlier: 6.929A pdb=" N GLN E 46 " --> pdb=" O GLU E 32 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL E 34 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG E 44 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE E 100 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N HIS E 96 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU E 102 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 63 through 67 Processing sheet with id=AG6, first strand: chain 'E' and resid 83 through 86 removed outlier: 4.221A pdb=" N ASP E 109 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AG8, first strand: chain 'E' and resid 237 through 238 removed outlier: 6.363A pdb=" N ILE E 257 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR E 165 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU E 255 " --> pdb=" O TYR E 165 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR E 167 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY E 253 " --> pdb=" O THR E 167 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 180 through 183 Processing sheet with id=AH1, first strand: chain 'E' and resid 207 through 211 Processing sheet with id=AH2, first strand: chain 'E' and resid 275 through 279 removed outlier: 3.505A pdb=" N TRP E 279 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 14 through 16 Processing sheet with id=AH4, first strand: chain 'H' and resid 31 through 35 removed outlier: 6.724A pdb=" N GLN H 46 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL H 34 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG H 44 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE H 100 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS H 96 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU H 102 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 50 through 53 removed outlier: 12.310A pdb=" N GLN H 50 " --> pdb=" O THR H 62 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N THR H 62 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY H 52 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 83 through 86 removed outlier: 3.757A pdb=" N SER H 110 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYS H 128 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR H 112 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL H 126 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N SER H 114 " --> pdb=" O CYS H 124 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N CYS H 124 " --> pdb=" O SER H 114 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AH8, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=AH9, first strand: chain 'H' and resid 180 through 183 Processing sheet with id=AI1, first strand: chain 'H' and resid 207 through 211 Processing sheet with id=AI2, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AI3, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.897A pdb=" N GLN B 46 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL B 34 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE B 100 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N HIS B 96 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 102 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 50 through 53 removed outlier: 3.686A pdb=" N GLN B 50 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 63 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.309A pdb=" N ASP B 109 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'B' and resid 150 through 155 Processing sheet with id=AI7, first strand: chain 'B' and resid 237 through 238 removed outlier: 3.985A pdb=" N GLY B 164 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AI9, first strand: chain 'B' and resid 207 through 211 Processing sheet with id=AJ1, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.700A pdb=" N THR B 275 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 24 through 27 removed outlier: 4.288A pdb=" N GLY F 26 " --> pdb=" O ILE F 18 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AJ4, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AJ5, first strand: chain 'F' and resid 103 through 105 Processing sheet with id=AJ6, first strand: chain 'F' and resid 117 through 118 removed outlier: 3.757A pdb=" N ALA F 127 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'I' and resid 24 through 27 removed outlier: 6.695A pdb=" N ILE I 18 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'I' and resid 29 through 31 Processing sheet with id=AJ9, first strand: chain 'I' and resid 87 through 90 removed outlier: 8.281A pdb=" N ALA I 94 " --> pdb=" O PRO I 105 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'I' and resid 117 through 118 Processing sheet with id=AK2, first strand: chain 'C' and resid 24 through 27 removed outlier: 3.746A pdb=" N GLY C 26 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AK4, first strand: chain 'C' and resid 56 through 58 Processing sheet with id=AK5, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AK6, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.891A pdb=" N ALA C 127 " --> pdb=" O ILE C 118 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 128 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 144 " --> pdb=" O ILE C 128 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2733 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: 14.19 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9991 1.35 - 1.47: 8022 1.47 - 1.60: 13431 1.60 - 1.73: 0 1.73 - 1.86: 248 Bond restraints: 31692 Sorted by residual: bond pdb=" C CYS J 328 " pdb=" N PRO J 329 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.44e-02 4.82e+03 4.72e+00 bond pdb=" CB CYS J 62 " pdb=" SG CYS J 62 " ideal model delta sigma weight residual 1.808 1.862 -0.054 3.30e-02 9.18e+02 2.63e+00 bond pdb=" N THR A 53 " pdb=" CA THR A 53 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.59e+00 bond pdb=" CB ASP F 62 " pdb=" CG ASP F 62 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.50e+00 bond pdb=" CB ASP C 62 " pdb=" CG ASP C 62 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.49e+00 ... (remaining 31687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 42000 2.44 - 4.88: 986 4.88 - 7.31: 122 7.31 - 9.75: 25 9.75 - 12.19: 8 Bond angle restraints: 43141 Sorted by residual: angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 112.90 106.58 6.32 9.60e-01 1.09e+00 4.33e+01 angle pdb=" C CYS G 94 " pdb=" N PHE G 95 " pdb=" CA PHE G 95 " ideal model delta sigma weight residual 120.28 125.97 -5.69 1.34e+00 5.57e-01 1.80e+01 angle pdb=" C GLU L 98 " pdb=" N ASN L 99 " pdb=" CA ASN L 99 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TRP E 279 " pdb=" N PHE E 280 " pdb=" CA PHE E 280 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET I 8 " pdb=" CG MET I 8 " pdb=" SD MET I 8 " ideal model delta sigma weight residual 112.70 124.64 -11.94 3.00e+00 1.11e-01 1.58e+01 ... (remaining 43136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 17603 17.83 - 35.66: 1252 35.66 - 53.50: 248 53.50 - 71.33: 49 71.33 - 89.16: 17 Dihedral angle restraints: 19169 sinusoidal: 7654 harmonic: 11515 Sorted by residual: dihedral pdb=" CB CYS H 16 " pdb=" SG CYS H 16 " pdb=" SG CYS H 124 " pdb=" CB CYS H 124 " ideal model delta sinusoidal sigma weight residual 93.00 177.85 -84.85 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS H 152 " pdb=" SG CYS H 152 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual 93.00 175.77 -82.77 1 1.00e+01 1.00e-02 8.39e+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 93.00 169.53 -76.53 1 1.00e+01 1.00e-02 7.36e+01 ... (remaining 19166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3996 0.069 - 0.138: 768 0.138 - 0.207: 93 0.207 - 0.275: 14 0.275 - 0.344: 2 Chirality restraints: 4873 Sorted by residual: chirality pdb=" CB ILE F 18 " pdb=" CA ILE F 18 " pdb=" CG1 ILE F 18 " pdb=" CG2 ILE F 18 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 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 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL K 268 " pdb=" CA VAL K 268 " pdb=" CG1 VAL K 268 " pdb=" CG2 VAL K 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4870 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 409 " -0.019 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP A 409 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 409 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 409 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 409 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 409 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 409 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 409 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 409 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 409 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 279 " -0.017 2.00e-02 2.50e+03 1.98e-02 9.83e+00 pdb=" CG TRP B 279 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 279 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 279 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 279 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 279 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " -0.277 9.50e-02 1.11e+02 1.24e-01 9.53e+00 pdb=" NE ARG B 137 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " -0.009 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1990 2.74 - 3.28: 29856 3.28 - 3.82: 50293 3.82 - 4.36: 58306 4.36 - 4.90: 101694 Nonbonded interactions: 242139 Sorted by model distance: nonbonded pdb=" OG SER K 86 " pdb=" OG1 THR K 112 " model vdw 2.196 3.040 nonbonded pdb=" OG SER H 79 " pdb=" OE1 GLU H 81 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OE1 GLN B 341 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASN K 405 " pdb=" OH TYR L 79 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 57 " pdb=" O SER B 240 " model vdw 2.228 3.040 ... (remaining 242134 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' and (resid 1 through 117 or resid 120 through 406 or resid 501 throug \ h 502)) selection = (chain 'E' and (resid 1 through 117 or resid 120 through 406 or resid 501 throug \ h 502)) selection = (chain 'H' and (resid 1 through 117 or resid 120 through 406 or resid 501 throug \ h 502)) selection = chain 'K' } ncs_group { reference = (chain 'C' and (resid 6 through 132 or resid 137 through 140 or resid 142 throug \ h 163)) selection = (chain 'F' and (resid 6 through 132 or resid 137 through 140 or resid 142 throug \ h 163)) selection = (chain 'I' and (resid 6 through 132 or resid 137 through 163)) selection = (chain 'L' and (resid 6 through 140 or resid 142 through 163)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.050 Extract box with map and model: 1.210 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 67.900 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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 0.054 31760 Z= 0.179 Angle : 0.879 12.188 43289 Z= 0.466 Chirality : 0.055 0.344 4873 Planarity : 0.007 0.124 5520 Dihedral : 12.538 89.162 11629 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.44 (0.13), residues: 3963 helix: 0.48 (0.23), residues: 426 sheet: -0.31 (0.16), residues: 1128 loop : -1.61 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 409 HIS 0.019 0.001 HIS B 73 PHE 0.044 0.002 PHE E 280 TYR 0.029 0.002 TYR C 27 ARG 0.015 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 1.81443 ( 36) hydrogen bonds : bond 0.12398 ( 1026) hydrogen bonds : angle 6.96231 ( 2733) SS BOND : bond 0.00441 ( 56) SS BOND : angle 2.14381 ( 112) covalent geometry : bond 0.00370 (31692) covalent geometry : angle 0.87224 (43141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1252 time to evaluate : 3.578 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: 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: J 9 ASN cc_start: 0.8023 (t160) cc_final: 0.7812 (t0) REVERT: J 49 CYS cc_start: 0.7447 (p) cc_final: 0.7102 (p) REVERT: J 61 LYS cc_start: 0.7997 (tmmt) cc_final: 0.7536 (tmmt) REVERT: J 75 ASP cc_start: 0.8024 (t0) cc_final: 0.7823 (t0) REVERT: J 101 THR cc_start: 0.7271 (m) cc_final: 0.6990 (m) REVERT: J 143 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7608 (mmt90) REVERT: J 175 HIS cc_start: 0.8126 (t70) cc_final: 0.7713 (t70) REVERT: J 180 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.8096 (ttt180) REVERT: J 186 ASN cc_start: 0.8487 (m-40) cc_final: 0.8196 (m-40) REVERT: J 227 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8087 (mtmm) REVERT: J 264 GLU cc_start: 0.8097 (tt0) cc_final: 0.7811 (tt0) REVERT: J 271 CYS cc_start: 0.6720 (m) cc_final: 0.6346 (m) REVERT: J 289 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7624 (mtt90) REVERT: J 318 LEU cc_start: 0.7676 (tp) cc_final: 0.7375 (tp) REVERT: J 395 ASP cc_start: 0.7263 (t0) cc_final: 0.6936 (t0) REVERT: J 406 SER cc_start: 0.8518 (t) cc_final: 0.7876 (p) REVERT: K 7 THR cc_start: 0.8536 (t) cc_final: 0.8277 (p) REVERT: K 25 CYS cc_start: 0.6021 (t) cc_final: 0.5387 (t) REVERT: K 36 ASP cc_start: 0.7270 (p0) cc_final: 0.7036 (p0) REVERT: K 37 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7584 (mm-30) REVERT: K 55 GLN cc_start: 0.8359 (tt0) cc_final: 0.8088 (tt0) REVERT: K 60 ASP cc_start: 0.7112 (t0) cc_final: 0.6833 (t0) REVERT: K 77 GLU cc_start: 0.8068 (pt0) cc_final: 0.7676 (pt0) REVERT: K 82 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8010 (mmmt) REVERT: K 152 CYS cc_start: 0.7124 (p) cc_final: 0.6629 (p) REVERT: K 156 ASP cc_start: 0.8155 (t0) cc_final: 0.7747 (t0) REVERT: K 158 LEU cc_start: 0.8688 (mp) cc_final: 0.8422 (mp) REVERT: K 159 LYS cc_start: 0.8786 (pttm) cc_final: 0.8491 (pttm) REVERT: K 181 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6652 (tm-30) REVERT: K 222 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8290 (mmtt) REVERT: K 324 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7656 (mt-10) REVERT: K 391 LYS cc_start: 0.8739 (tttm) cc_final: 0.8274 (tttm) REVERT: K 393 ARG cc_start: 0.8651 (ttt180) cc_final: 0.7383 (tpt170) REVERT: K 395 ASP cc_start: 0.8265 (m-30) cc_final: 0.7780 (m-30) REVERT: K 397 LEU cc_start: 0.8577 (mm) cc_final: 0.8335 (mm) REVERT: L 57 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7961 (mtmm) REVERT: L 79 TYR cc_start: 0.7313 (p90) cc_final: 0.7084 (p90) REVERT: D 37 GLU cc_start: 0.7272 (mp0) cc_final: 0.6979 (mp0) REVERT: D 99 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6387 (tm-30) REVERT: D 160 LYS cc_start: 0.8113 (tmmt) cc_final: 0.7723 (tmmt) REVERT: D 230 HIS cc_start: 0.7872 (t70) cc_final: 0.7632 (t70) REVERT: D 257 PHE cc_start: 0.8871 (m-80) cc_final: 0.8594 (m-80) REVERT: D 273 TYR cc_start: 0.8096 (p90) cc_final: 0.7678 (p90) REVERT: D 320 TYR cc_start: 0.7309 (p90) cc_final: 0.7097 (p90) REVERT: D 373 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7754 (mmtm) REVERT: D 387 ILE cc_start: 0.8691 (mm) cc_final: 0.8015 (tp) REVERT: D 388 ILE cc_start: 0.8325 (tp) cc_final: 0.8055 (mm) REVERT: D 409 TRP cc_start: 0.7170 (m100) cc_final: 0.6866 (m100) REVERT: D 430 CYS cc_start: 0.8143 (p) cc_final: 0.7937 (p) REVERT: D 433 MET cc_start: 0.8274 (ttm) cc_final: 0.8058 (ttm) REVERT: G 15 TYR cc_start: 0.7774 (t80) cc_final: 0.7342 (t80) REVERT: G 30 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7131 (mm-30) REVERT: G 67 GLU cc_start: 0.6787 (tp30) cc_final: 0.6580 (tp30) REVERT: G 76 TYR cc_start: 0.8190 (t80) cc_final: 0.7759 (t80) REVERT: G 105 GLU cc_start: 0.7300 (tt0) cc_final: 0.7051 (tt0) REVERT: G 139 ASN cc_start: 0.7366 (m110) cc_final: 0.7133 (m110) REVERT: G 174 ASP cc_start: 0.7980 (m-30) cc_final: 0.7758 (m-30) REVERT: G 218 ASP cc_start: 0.7937 (t0) cc_final: 0.7536 (t0) REVERT: G 241 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 244 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8023 (mtmt) REVERT: G 264 GLU cc_start: 0.7528 (mp0) cc_final: 0.7094 (mp0) REVERT: G 311 ASP cc_start: 0.7355 (t0) cc_final: 0.7050 (t0) REVERT: G 324 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7688 (ptm-80) REVERT: G 341 GLU cc_start: 0.7400 (mp0) cc_final: 0.7085 (mp0) REVERT: A 52 HIS cc_start: 0.7886 (t-90) cc_final: 0.7638 (t-170) REVERT: A 136 VAL cc_start: 0.8340 (p) cc_final: 0.7997 (m) REVERT: A 203 ILE cc_start: 0.8570 (tt) cc_final: 0.8033 (pt) REVERT: A 234 THR cc_start: 0.8212 (m) cc_final: 0.7908 (t) REVERT: A 298 GLU cc_start: 0.6698 (tp30) cc_final: 0.6455 (tp30) REVERT: A 323 ASN cc_start: 0.8469 (p0) cc_final: 0.8203 (p0) REVERT: A 353 THR cc_start: 0.7362 (m) cc_final: 0.7118 (t) REVERT: A 386 HIS cc_start: 0.7776 (m-70) cc_final: 0.7516 (m-70) REVERT: A 388 ILE cc_start: 0.8254 (tp) cc_final: 0.7906 (tp) REVERT: A 430 CYS cc_start: 0.8374 (m) cc_final: 0.8106 (m) REVERT: A 434 LEU cc_start: 0.8694 (mm) cc_final: 0.8489 (mm) REVERT: E 27 SER cc_start: 0.8606 (t) cc_final: 0.8356 (t) REVERT: E 36 ASP cc_start: 0.7566 (p0) cc_final: 0.7257 (p0) REVERT: E 76 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8130 (mmtt) REVERT: E 109 ASP cc_start: 0.7537 (m-30) cc_final: 0.7116 (m-30) REVERT: E 129 LYS cc_start: 0.8393 (tppt) cc_final: 0.7892 (tppt) REVERT: E 131 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7420 (mmt-90) REVERT: E 139 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7225 (mt-10) REVERT: E 162 SER cc_start: 0.8867 (t) cc_final: 0.8627 (t) REVERT: E 195 LYS cc_start: 0.8320 (mttt) cc_final: 0.8110 (mttt) REVERT: E 250 SER cc_start: 0.8638 (m) cc_final: 0.8297 (t) REVERT: E 254 LYS cc_start: 0.8240 (mttt) cc_final: 0.7829 (mttm) REVERT: E 278 LYS cc_start: 0.8334 (mmtp) cc_final: 0.7770 (mmtp) REVERT: E 354 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7108 (mt-10) REVERT: E 391 LYS cc_start: 0.8313 (mptt) cc_final: 0.7915 (mptt) REVERT: E 393 ARG cc_start: 0.5124 (tpt170) cc_final: 0.4425 (tpt170) REVERT: H 60 ASP cc_start: 0.7830 (t0) cc_final: 0.7361 (t0) REVERT: H 77 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7808 (mm-30) REVERT: H 94 LEU cc_start: 0.8542 (mt) cc_final: 0.8319 (mt) REVERT: H 159 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8440 (ptpp) REVERT: H 161 THR cc_start: 0.7863 (p) cc_final: 0.7660 (p) REVERT: H 168 MET cc_start: 0.7448 (mtp) cc_final: 0.7075 (mtp) REVERT: H 179 TYR cc_start: 0.7585 (m-10) cc_final: 0.7341 (m-10) REVERT: H 393 ARG cc_start: 0.6112 (tpt170) cc_final: 0.5540 (tpt170) REVERT: H 405 ASN cc_start: 0.7452 (m-40) cc_final: 0.7150 (m-40) REVERT: B 76 LYS cc_start: 0.7961 (tppp) cc_final: 0.7472 (tppp) REVERT: B 80 MET cc_start: 0.7798 (ttt) cc_final: 0.7571 (ttt) REVERT: B 97 LYS cc_start: 0.7844 (tttp) cc_final: 0.7455 (tttp) REVERT: B 102 LEU cc_start: 0.8322 (tp) cc_final: 0.7996 (tt) REVERT: B 159 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8071 (ptpt) REVERT: B 265 VAL cc_start: 0.8830 (t) cc_final: 0.8355 (p) REVERT: B 281 LYS cc_start: 0.8158 (mttt) cc_final: 0.7832 (mttt) REVERT: B 391 LYS cc_start: 0.8742 (tttm) cc_final: 0.8293 (tttm) REVERT: B 393 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6270 (tpp80) REVERT: F 8 MET cc_start: 0.7384 (mmp) cc_final: 0.7153 (mmp) REVERT: F 19 MET cc_start: 0.7153 (mmp) cc_final: 0.6926 (mmm) REVERT: F 44 LYS cc_start: 0.7577 (pptt) cc_final: 0.7187 (pptt) REVERT: F 56 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7961 (ptpp) REVERT: F 101 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6722 (ttt180) REVERT: F 124 ARG cc_start: 0.6711 (ttp-110) cc_final: 0.6500 (ttp-110) REVERT: I 25 ASN cc_start: 0.6547 (t0) cc_final: 0.6273 (t0) REVERT: I 64 GLU cc_start: 0.7272 (mp0) cc_final: 0.6624 (mp0) REVERT: I 78 GLN cc_start: 0.8125 (mp-120) cc_final: 0.7892 (mp-120) REVERT: I 111 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8261 (mtpp) REVERT: C 37 LYS cc_start: 0.8490 (tmmt) cc_final: 0.8214 (tmmt) outliers start: 0 outliers final: 0 residues processed: 1252 average time/residue: 0.4508 time to fit residues: 860.0337 Evaluate side-chains 1170 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1170 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN J 100 ASN K 50 GLN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS D 196 ASN D 228 ASN D 319 GLN D 327 HIS G 59 GLN G 175 HIS G 345 HIS A 43 ASN A 100 ASN A 246 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN H 174 HIS H 218 ASN H 256 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 153 HIS B 157 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 361 HIS ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119058 restraints weight = 56012.768| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.90 r_work: 0.3350 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 31760 Z= 0.262 Angle : 0.715 16.926 43289 Z= 0.369 Chirality : 0.049 0.266 4873 Planarity : 0.006 0.058 5520 Dihedral : 6.312 77.144 4563 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % Rotamer: Outliers : 2.61 % Allowed : 11.49 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.19 (0.13), residues: 3963 helix: 1.60 (0.24), residues: 414 sheet: -0.45 (0.15), residues: 1197 loop : -1.46 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 279 HIS 0.014 0.001 HIS B 73 PHE 0.024 0.002 PHE K 134 TYR 0.030 0.002 TYR A 308 ARG 0.009 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 12) link_NAG-ASN : angle 1.86914 ( 36) hydrogen bonds : bond 0.03829 ( 1026) hydrogen bonds : angle 5.71446 ( 2733) SS BOND : bond 0.00424 ( 56) SS BOND : angle 2.01975 ( 112) covalent geometry : bond 0.00563 (31692) covalent geometry : angle 0.70672 (43141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1223 time to evaluate : 3.302 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8430 (t0) cc_final: 0.7904 (t0) REVERT: J 49 CYS cc_start: 0.7608 (p) cc_final: 0.7369 (p) REVERT: J 50 LYS cc_start: 0.8291 (tttm) cc_final: 0.8015 (tttm) REVERT: J 61 LYS cc_start: 0.8020 (tmmt) cc_final: 0.7563 (ttpt) REVERT: J 130 LYS cc_start: 0.7920 (tttp) cc_final: 0.7641 (tppt) REVERT: J 180 ARG cc_start: 0.8561 (ttt-90) cc_final: 0.8357 (ttt-90) REVERT: J 191 GLU cc_start: 0.4683 (tt0) cc_final: 0.3857 (mt-10) REVERT: J 234 THR cc_start: 0.7953 (p) cc_final: 0.7711 (t) REVERT: J 271 CYS cc_start: 0.6616 (m) cc_final: 0.6311 (m) REVERT: J 289 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7590 (mtt90) REVERT: J 292 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7857 (mt-10) REVERT: J 318 LEU cc_start: 0.7653 (tp) cc_final: 0.7179 (tp) REVERT: K 4 ASP cc_start: 0.7587 (t0) cc_final: 0.7369 (t0) REVERT: K 7 THR cc_start: 0.8526 (t) cc_final: 0.8238 (p) REVERT: K 55 GLN cc_start: 0.8491 (tt0) cc_final: 0.8257 (tt0) REVERT: K 60 ASP cc_start: 0.7386 (t0) cc_final: 0.6787 (t0) REVERT: K 77 GLU cc_start: 0.8012 (pt0) cc_final: 0.7648 (pt0) REVERT: K 82 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8329 (mtpt) REVERT: K 127 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7391 (mm-30) REVERT: K 138 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7094 (mm-30) REVERT: K 152 CYS cc_start: 0.7274 (p) cc_final: 0.6883 (p) REVERT: K 156 ASP cc_start: 0.8180 (t0) cc_final: 0.7727 (t0) REVERT: K 158 LEU cc_start: 0.8696 (mp) cc_final: 0.8310 (mp) REVERT: K 159 LYS cc_start: 0.8768 (pttm) cc_final: 0.8455 (pttm) REVERT: K 176 TYR cc_start: 0.8046 (m-80) cc_final: 0.7770 (m-80) REVERT: K 181 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6584 (tm-30) REVERT: K 195 LYS cc_start: 0.8433 (mppt) cc_final: 0.8154 (mppt) REVERT: K 222 LYS cc_start: 0.8536 (mmtt) cc_final: 0.8322 (mmtt) REVERT: K 324 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7655 (mt-10) REVERT: K 354 GLU cc_start: 0.7647 (mp0) cc_final: 0.7372 (mp0) REVERT: K 391 LYS cc_start: 0.8778 (tttm) cc_final: 0.8311 (tttm) REVERT: K 395 ASP cc_start: 0.8199 (m-30) cc_final: 0.7768 (m-30) REVERT: L 57 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7992 (mtmm) REVERT: D 61 LYS cc_start: 0.7697 (pptt) cc_final: 0.7467 (ptmm) REVERT: D 76 TYR cc_start: 0.8223 (t80) cc_final: 0.7940 (t80) REVERT: D 99 GLU cc_start: 0.6873 (tm-30) cc_final: 0.6204 (tm-30) REVERT: D 160 LYS cc_start: 0.8122 (tmmt) cc_final: 0.7737 (tmmt) REVERT: D 230 HIS cc_start: 0.7975 (t70) cc_final: 0.7713 (t70) REVERT: D 257 PHE cc_start: 0.9041 (m-80) cc_final: 0.8827 (m-80) REVERT: D 270 ASN cc_start: 0.7915 (m110) cc_final: 0.7620 (m110) REVERT: D 307 ILE cc_start: 0.7724 (mt) cc_final: 0.7430 (mp) REVERT: D 320 TYR cc_start: 0.7745 (p90) cc_final: 0.7427 (p90) REVERT: D 323 ASN cc_start: 0.8141 (p0) cc_final: 0.7882 (p0) REVERT: D 365 PHE cc_start: 0.8268 (p90) cc_final: 0.7954 (p90) REVERT: D 373 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7851 (mmtm) REVERT: D 390 GLU cc_start: 0.7569 (pm20) cc_final: 0.7291 (pm20) REVERT: D 430 CYS cc_start: 0.8232 (p) cc_final: 0.8011 (p) REVERT: G 174 ASP cc_start: 0.7988 (m-30) cc_final: 0.7609 (m-30) REVERT: G 218 ASP cc_start: 0.8238 (t0) cc_final: 0.7689 (t0) REVERT: G 241 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7572 (mm-30) REVERT: G 246 ASN cc_start: 0.7609 (t0) cc_final: 0.7292 (t0) REVERT: G 343 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8179 (m) REVERT: G 404 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7900 (ttmm) REVERT: A 50 LYS cc_start: 0.8108 (tttp) cc_final: 0.7744 (ttpp) REVERT: A 87 PHE cc_start: 0.7866 (t80) cc_final: 0.7491 (t80) REVERT: A 88 MET cc_start: 0.7742 (mtp) cc_final: 0.7519 (mtp) REVERT: A 202 ASP cc_start: 0.7529 (p0) cc_final: 0.7305 (p0) REVERT: A 263 VAL cc_start: 0.8169 (m) cc_final: 0.7944 (p) REVERT: A 298 GLU cc_start: 0.6936 (tp30) cc_final: 0.6670 (tp30) REVERT: A 321 LYS cc_start: 0.8363 (pptt) cc_final: 0.8123 (pptt) REVERT: A 323 ASN cc_start: 0.8668 (p0) cc_final: 0.8356 (p0) REVERT: A 373 LYS cc_start: 0.8434 (mptt) cc_final: 0.8160 (mptt) REVERT: A 430 CYS cc_start: 0.8477 (m) cc_final: 0.8245 (m) REVERT: E 34 VAL cc_start: 0.8946 (t) cc_final: 0.8496 (m) REVERT: E 36 ASP cc_start: 0.7640 (p0) cc_final: 0.7273 (p0) REVERT: E 76 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8172 (mmtt) REVERT: E 129 LYS cc_start: 0.8563 (tppt) cc_final: 0.8178 (tppt) REVERT: E 131 ARG cc_start: 0.8033 (mmt90) cc_final: 0.7648 (mmt180) REVERT: E 139 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7177 (mt-10) REVERT: E 168 MET cc_start: 0.7586 (tmm) cc_final: 0.7366 (tmm) REVERT: E 229 TYR cc_start: 0.7593 (p90) cc_final: 0.7204 (p90) REVERT: E 254 LYS cc_start: 0.8099 (mttt) cc_final: 0.7749 (mttt) REVERT: E 277 THR cc_start: 0.8444 (m) cc_final: 0.7923 (p) REVERT: E 393 ARG cc_start: 0.5463 (tpt170) cc_final: 0.4702 (tpt170) REVERT: E 394 ARG cc_start: 0.7702 (ptm-80) cc_final: 0.7460 (ptm-80) REVERT: H 60 ASP cc_start: 0.7940 (t0) cc_final: 0.7425 (t0) REVERT: H 65 ARG cc_start: 0.8635 (ptm-80) cc_final: 0.7807 (ptm-80) REVERT: H 105 CYS cc_start: 0.6882 (m) cc_final: 0.6658 (m) REVERT: H 141 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7679 (mt) REVERT: H 179 TYR cc_start: 0.7769 (m-10) cc_final: 0.7422 (m-10) REVERT: H 224 LYS cc_start: 0.8141 (ptmm) cc_final: 0.7904 (ptmm) REVERT: H 347 ASP cc_start: 0.7574 (t0) cc_final: 0.6904 (t0) REVERT: H 393 ARG cc_start: 0.5897 (tpt170) cc_final: 0.5325 (tpt170) REVERT: H 394 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7759 (ttp-110) REVERT: B 76 LYS cc_start: 0.7961 (tppp) cc_final: 0.7504 (tppp) REVERT: B 97 LYS cc_start: 0.8118 (tttp) cc_final: 0.7849 (tttp) REVERT: B 159 LYS cc_start: 0.8473 (ptpt) cc_final: 0.8114 (ptpt) REVERT: B 224 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7147 (tmtt) REVERT: B 254 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7394 (mtpt) REVERT: B 265 VAL cc_start: 0.9065 (t) cc_final: 0.8589 (p) REVERT: B 276 VAL cc_start: 0.8755 (t) cc_final: 0.8436 (m) REVERT: B 281 LYS cc_start: 0.8285 (mttt) cc_final: 0.7968 (mttt) REVERT: B 354 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 362 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8302 (mmm-85) REVERT: F 8 MET cc_start: 0.7483 (mmp) cc_final: 0.7229 (mmp) REVERT: F 19 MET cc_start: 0.6659 (mmp) cc_final: 0.5913 (mmp) REVERT: F 44 LYS cc_start: 0.7910 (pptt) cc_final: 0.7626 (pptt) REVERT: F 56 LYS cc_start: 0.8284 (ptpp) cc_final: 0.7914 (ptpp) REVERT: F 60 MET cc_start: 0.7992 (mmt) cc_final: 0.7760 (mmt) REVERT: F 101 ARG cc_start: 0.7285 (ttt180) cc_final: 0.7084 (ttt180) REVERT: F 120 ASP cc_start: 0.8021 (p0) cc_final: 0.7639 (p0) REVERT: F 124 ARG cc_start: 0.6567 (ttp-110) cc_final: 0.5389 (ttp-110) REVERT: I 37 LYS cc_start: 0.8269 (ptmm) cc_final: 0.7160 (ptmm) REVERT: I 44 LYS cc_start: 0.7990 (tptt) cc_final: 0.7738 (tptt) REVERT: I 49 GLN cc_start: 0.7779 (tm-30) cc_final: 0.7570 (tm-30) REVERT: I 64 GLU cc_start: 0.7199 (mp0) cc_final: 0.6595 (mp0) REVERT: I 101 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6488 (mmm-85) REVERT: I 111 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8408 (mtpp) REVERT: C 37 LYS cc_start: 0.8623 (tmmt) cc_final: 0.8310 (tmmt) REVERT: C 106 ARG cc_start: 0.8057 (ppt170) cc_final: 0.7800 (ppt170) outliers start: 88 outliers final: 57 residues processed: 1249 average time/residue: 0.4620 time to fit residues: 880.5554 Evaluate side-chains 1235 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1175 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 207 SER Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 27 optimal weight: 7.9990 chunk 375 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 314 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 390 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 277 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 ASN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 319 GLN D 327 HIS D 386 HIS D 408 ASN G 139 ASN G 230 HIS G 345 HIS A 43 ASN A 139 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 331 HIS A 345 HIS H 46 GLN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 96 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116450 restraints weight = 56002.587| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.86 r_work: 0.3320 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 31760 Z= 0.307 Angle : 0.736 17.038 43289 Z= 0.379 Chirality : 0.050 0.254 4873 Planarity : 0.006 0.064 5520 Dihedral : 6.169 77.170 4563 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.79 % Favored : 93.11 % Rotamer: Outliers : 4.30 % Allowed : 14.78 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.36 (0.13), residues: 3963 helix: 1.66 (0.24), residues: 419 sheet: -0.75 (0.14), residues: 1266 loop : -1.52 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 279 HIS 0.015 0.002 HIS B 96 PHE 0.027 0.002 PHE E 51 TYR 0.029 0.002 TYR A 308 ARG 0.018 0.001 ARG F 122 Details of bonding type rmsd link_NAG-ASN : bond 0.00410 ( 12) link_NAG-ASN : angle 2.02621 ( 36) hydrogen bonds : bond 0.03987 ( 1026) hydrogen bonds : angle 5.68375 ( 2733) SS BOND : bond 0.00597 ( 56) SS BOND : angle 2.11788 ( 112) covalent geometry : bond 0.00665 (31692) covalent geometry : angle 0.72656 (43141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1212 time to evaluate : 3.608 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8467 (t0) cc_final: 0.7920 (t0) REVERT: J 49 CYS cc_start: 0.7565 (p) cc_final: 0.7351 (p) REVERT: J 50 LYS cc_start: 0.8348 (tttm) cc_final: 0.8106 (tttm) REVERT: J 61 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7435 (ttpt) REVERT: J 99 GLU cc_start: 0.7136 (tt0) cc_final: 0.6488 (tt0) REVERT: J 101 THR cc_start: 0.8010 (m) cc_final: 0.7707 (m) REVERT: J 191 GLU cc_start: 0.5158 (tt0) cc_final: 0.4165 (mt-10) REVERT: J 289 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7693 (mtt90) REVERT: J 318 LEU cc_start: 0.7669 (tp) cc_final: 0.7172 (tp) REVERT: K 7 THR cc_start: 0.8594 (t) cc_final: 0.8330 (p) REVERT: K 18 TYR cc_start: 0.7854 (t80) cc_final: 0.7100 (t80) REVERT: K 25 CYS cc_start: 0.6021 (t) cc_final: 0.5556 (t) REVERT: K 55 GLN cc_start: 0.8519 (tt0) cc_final: 0.8284 (tt0) REVERT: K 60 ASP cc_start: 0.7368 (t0) cc_final: 0.6727 (t0) REVERT: K 77 GLU cc_start: 0.8053 (pt0) cc_final: 0.7679 (pt0) REVERT: K 82 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8487 (mtpt) REVERT: K 133 LYS cc_start: 0.8561 (mtmm) cc_final: 0.8300 (mtmm) REVERT: K 138 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7144 (mm-30) REVERT: K 156 ASP cc_start: 0.8193 (t0) cc_final: 0.7769 (t0) REVERT: K 159 LYS cc_start: 0.8803 (pttm) cc_final: 0.8513 (pttm) REVERT: K 176 TYR cc_start: 0.8262 (m-80) cc_final: 0.7838 (m-80) REVERT: K 181 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6653 (tm-30) REVERT: K 190 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7556 (ttpp) REVERT: K 195 LYS cc_start: 0.8440 (mppt) cc_final: 0.8125 (mppt) REVERT: K 222 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8309 (mmtt) REVERT: K 287 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8515 (pp) REVERT: K 354 GLU cc_start: 0.7782 (mp0) cc_final: 0.7416 (mp0) REVERT: K 391 LYS cc_start: 0.8767 (tttm) cc_final: 0.8298 (tttm) REVERT: K 395 ASP cc_start: 0.8134 (m-30) cc_final: 0.7692 (m-30) REVERT: L 57 LYS cc_start: 0.8287 (mtmm) cc_final: 0.7978 (mtmm) REVERT: D 61 LYS cc_start: 0.7814 (pptt) cc_final: 0.7427 (ptmm) REVERT: D 99 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6139 (tm-30) REVERT: D 114 CYS cc_start: 0.7275 (m) cc_final: 0.6962 (m) REVERT: D 230 HIS cc_start: 0.8067 (t70) cc_final: 0.7858 (t70) REVERT: D 257 PHE cc_start: 0.9105 (m-80) cc_final: 0.8880 (m-80) REVERT: D 270 ASN cc_start: 0.8015 (m110) cc_final: 0.7731 (m110) REVERT: D 308 TYR cc_start: 0.7977 (p90) cc_final: 0.7673 (p90) REVERT: D 364 ASN cc_start: 0.8200 (m-40) cc_final: 0.7962 (m-40) REVERT: D 373 LYS cc_start: 0.8188 (mmtm) cc_final: 0.7905 (mmtm) REVERT: D 390 GLU cc_start: 0.7665 (pm20) cc_final: 0.7281 (pm20) REVERT: D 430 CYS cc_start: 0.8306 (p) cc_final: 0.7963 (p) REVERT: G 30 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6973 (mm-30) REVERT: G 76 TYR cc_start: 0.8409 (t80) cc_final: 0.7433 (t80) REVERT: G 78 CYS cc_start: 0.6559 (p) cc_final: 0.6294 (p) REVERT: G 105 GLU cc_start: 0.7383 (tt0) cc_final: 0.6907 (tt0) REVERT: G 174 ASP cc_start: 0.7956 (m-30) cc_final: 0.7447 (m-30) REVERT: G 218 ASP cc_start: 0.8229 (t0) cc_final: 0.7679 (t0) REVERT: G 241 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7539 (mm-30) REVERT: G 246 ASN cc_start: 0.7620 (t0) cc_final: 0.6897 (t0) REVERT: G 343 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8255 (m) REVERT: G 346 VAL cc_start: 0.7828 (t) cc_final: 0.7386 (m) REVERT: G 404 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7840 (ttmm) REVERT: A 9 ASN cc_start: 0.8016 (p0) cc_final: 0.7706 (p0) REVERT: A 50 LYS cc_start: 0.8204 (tttp) cc_final: 0.7805 (ttpt) REVERT: A 188 ASP cc_start: 0.7920 (t0) cc_final: 0.7596 (t0) REVERT: A 242 MET cc_start: 0.8491 (tpp) cc_final: 0.8069 (tpp) REVERT: A 263 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 323 ASN cc_start: 0.8755 (p0) cc_final: 0.8385 (p0) REVERT: A 373 LYS cc_start: 0.8423 (mptt) cc_final: 0.8135 (mptt) REVERT: E 36 ASP cc_start: 0.7644 (p0) cc_final: 0.7321 (p0) REVERT: E 76 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8245 (mmtt) REVERT: E 127 GLU cc_start: 0.7659 (tp30) cc_final: 0.7300 (tp30) REVERT: E 129 LYS cc_start: 0.8612 (tppt) cc_final: 0.8388 (tppt) REVERT: E 131 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7786 (mmt180) REVERT: E 139 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7117 (mt-10) REVERT: E 162 SER cc_start: 0.8821 (t) cc_final: 0.8575 (t) REVERT: E 168 MET cc_start: 0.7666 (tmm) cc_final: 0.7344 (tmm) REVERT: E 254 LYS cc_start: 0.8233 (mttt) cc_final: 0.7911 (mttt) REVERT: E 277 THR cc_start: 0.8455 (m) cc_final: 0.7911 (p) REVERT: E 278 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8333 (mtpp) REVERT: E 324 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 393 ARG cc_start: 0.5544 (tpt170) cc_final: 0.4965 (tpt170) REVERT: E 394 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.7488 (ptm-80) REVERT: H 60 ASP cc_start: 0.7980 (t0) cc_final: 0.7465 (t0) REVERT: H 65 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.7983 (ptm-80) REVERT: H 131 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7504 (mmt-90) REVERT: H 168 MET cc_start: 0.7512 (mtp) cc_final: 0.6828 (mmm) REVERT: H 224 LYS cc_start: 0.8207 (ptmm) cc_final: 0.7976 (ptmm) REVERT: H 347 ASP cc_start: 0.7541 (t0) cc_final: 0.6893 (t0) REVERT: H 393 ARG cc_start: 0.5871 (tpt170) cc_final: 0.5392 (tpt170) REVERT: H 394 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7748 (ttp-110) REVERT: H 397 LEU cc_start: 0.8283 (mm) cc_final: 0.8012 (mm) REVERT: B 76 LYS cc_start: 0.7966 (tppp) cc_final: 0.7513 (tppp) REVERT: B 94 LEU cc_start: 0.8686 (mm) cc_final: 0.8465 (mp) REVERT: B 97 LYS cc_start: 0.8208 (tttp) cc_final: 0.7972 (tttp) REVERT: B 159 LYS cc_start: 0.8451 (ptpt) cc_final: 0.8184 (ptpt) REVERT: B 206 TYR cc_start: 0.7561 (t80) cc_final: 0.7270 (t80) REVERT: B 225 GLN cc_start: 0.6174 (tm-30) cc_final: 0.5796 (tm-30) REVERT: B 239 ASN cc_start: 0.7470 (p0) cc_final: 0.7267 (t0) REVERT: B 254 LYS cc_start: 0.7723 (mtpt) cc_final: 0.7244 (mtpt) REVERT: B 265 VAL cc_start: 0.9184 (t) cc_final: 0.8756 (p) REVERT: B 276 VAL cc_start: 0.8769 (t) cc_final: 0.8439 (m) REVERT: B 281 LYS cc_start: 0.8356 (mttt) cc_final: 0.8049 (mttt) REVERT: B 347 ASP cc_start: 0.8025 (t0) cc_final: 0.7575 (t70) REVERT: B 354 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 362 ARG cc_start: 0.8496 (mmm-85) cc_final: 0.8218 (mmm-85) REVERT: F 8 MET cc_start: 0.7520 (mmp) cc_final: 0.7259 (mmp) REVERT: F 14 LYS cc_start: 0.7196 (OUTLIER) cc_final: 0.6837 (ptmm) REVERT: F 19 MET cc_start: 0.6832 (mmp) cc_final: 0.6298 (mmp) REVERT: F 56 LYS cc_start: 0.8344 (ptpp) cc_final: 0.7821 (ptpp) REVERT: F 60 MET cc_start: 0.8009 (mmt) cc_final: 0.7785 (mmt) REVERT: F 97 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4679 (m-80) REVERT: F 101 ARG cc_start: 0.7357 (ttt180) cc_final: 0.6916 (ttt180) REVERT: F 111 LYS cc_start: 0.8731 (mttt) cc_final: 0.8371 (mttt) REVERT: F 122 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6411 (ttp80) REVERT: I 29 CYS cc_start: 0.8175 (m) cc_final: 0.7945 (m) REVERT: I 44 LYS cc_start: 0.8250 (tptt) cc_final: 0.7987 (tptt) REVERT: I 49 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7532 (tm-30) REVERT: I 101 ARG cc_start: 0.6974 (mmm-85) cc_final: 0.6499 (mmm-85) REVERT: I 111 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8410 (mtpp) REVERT: I 128 ILE cc_start: 0.8864 (mp) cc_final: 0.8659 (mt) REVERT: C 55 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7092 (mm) REVERT: C 64 GLU cc_start: 0.7016 (tt0) cc_final: 0.6016 (tt0) REVERT: C 106 ARG cc_start: 0.8197 (ppt170) cc_final: 0.7939 (ppt170) outliers start: 145 outliers final: 96 residues processed: 1261 average time/residue: 0.4758 time to fit residues: 916.9805 Evaluate side-chains 1275 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1172 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 242 MET Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 396 CYS Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 380 CYS Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 48 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 316 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 388 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 272 HIS ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 204 GLN D 327 HIS G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 HIS H 96 HIS B 96 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN ** C 96 GLN ** 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 = 0.3734 r_free = 0.3734 target = 0.140372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123362 restraints weight = 56178.953| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.90 r_work: 0.3342 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31760 Z= 0.196 Angle : 0.684 17.001 43289 Z= 0.347 Chirality : 0.048 0.252 4873 Planarity : 0.005 0.073 5520 Dihedral : 5.844 78.571 4563 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.28 % Favored : 93.67 % Rotamer: Outliers : 4.53 % Allowed : 17.06 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.23 (0.13), residues: 3963 helix: 1.86 (0.24), residues: 412 sheet: -0.62 (0.15), residues: 1226 loop : -1.46 (0.12), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 279 HIS 0.011 0.001 HIS J 331 PHE 0.024 0.002 PHE E 51 TYR 0.027 0.002 TYR A 308 ARG 0.008 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 12) link_NAG-ASN : angle 1.67760 ( 36) hydrogen bonds : bond 0.03488 ( 1026) hydrogen bonds : angle 5.50317 ( 2733) SS BOND : bond 0.00429 ( 56) SS BOND : angle 2.07352 ( 112) covalent geometry : bond 0.00434 (31692) covalent geometry : angle 0.67495 (43141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1196 time to evaluate : 3.353 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: 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: J 9 ASN cc_start: 0.8445 (t0) cc_final: 0.7864 (t0) REVERT: J 49 CYS cc_start: 0.7586 (p) cc_final: 0.7350 (p) REVERT: J 50 LYS cc_start: 0.8334 (tttm) cc_final: 0.7881 (tttp) REVERT: J 61 LYS cc_start: 0.7838 (tmmt) cc_final: 0.7361 (ttpt) REVERT: J 99 GLU cc_start: 0.7132 (tt0) cc_final: 0.6542 (tt0) REVERT: J 101 THR cc_start: 0.7984 (m) cc_final: 0.7689 (m) REVERT: J 130 LYS cc_start: 0.7773 (tttp) cc_final: 0.7521 (tppt) REVERT: J 134 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: J 191 GLU cc_start: 0.5132 (tt0) cc_final: 0.3965 (mt-10) REVERT: J 234 THR cc_start: 0.8063 (p) cc_final: 0.7810 (t) REVERT: J 271 CYS cc_start: 0.6716 (m) cc_final: 0.6494 (m) REVERT: J 282 ILE cc_start: 0.8639 (mt) cc_final: 0.8205 (tp) REVERT: J 289 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7620 (mtt90) REVERT: J 318 LEU cc_start: 0.7663 (tp) cc_final: 0.7109 (tp) REVERT: K 7 THR cc_start: 0.8559 (t) cc_final: 0.8306 (p) REVERT: K 18 TYR cc_start: 0.7821 (t80) cc_final: 0.7046 (t80) REVERT: K 55 GLN cc_start: 0.8418 (tt0) cc_final: 0.8187 (tt0) REVERT: K 60 ASP cc_start: 0.7324 (t0) cc_final: 0.6676 (t0) REVERT: K 77 GLU cc_start: 0.8072 (pt0) cc_final: 0.7700 (pt0) REVERT: K 82 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8416 (mtpt) REVERT: K 109 ASP cc_start: 0.7767 (m-30) cc_final: 0.7544 (t0) REVERT: K 133 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8258 (mtmm) REVERT: K 138 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7068 (mm-30) REVERT: K 152 CYS cc_start: 0.7280 (p) cc_final: 0.6961 (p) REVERT: K 156 ASP cc_start: 0.8220 (t0) cc_final: 0.7792 (t0) REVERT: K 158 LEU cc_start: 0.8720 (mp) cc_final: 0.8171 (mp) REVERT: K 159 LYS cc_start: 0.8797 (pttm) cc_final: 0.8518 (pttm) REVERT: K 176 TYR cc_start: 0.8289 (m-80) cc_final: 0.7894 (m-80) REVERT: K 181 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6730 (tm-30) REVERT: K 190 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7564 (ttpp) REVERT: K 195 LYS cc_start: 0.8412 (mppt) cc_final: 0.8093 (mppt) REVERT: K 222 LYS cc_start: 0.8565 (mmtt) cc_final: 0.8323 (mmtt) REVERT: K 287 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8542 (pp) REVERT: K 324 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7733 (mt-10) REVERT: K 354 GLU cc_start: 0.7681 (mp0) cc_final: 0.7269 (mp0) REVERT: K 395 ASP cc_start: 0.8110 (m-30) cc_final: 0.7828 (m-30) REVERT: L 57 LYS cc_start: 0.8248 (mtmm) cc_final: 0.7920 (mtmm) REVERT: L 80 THR cc_start: 0.8308 (t) cc_final: 0.7970 (m) REVERT: D 46 TYR cc_start: 0.8394 (p90) cc_final: 0.8037 (p90) REVERT: D 61 LYS cc_start: 0.7755 (pptt) cc_final: 0.7450 (ptmm) REVERT: D 99 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6129 (tm-30) REVERT: D 189 PHE cc_start: 0.8743 (p90) cc_final: 0.8280 (p90) REVERT: D 230 HIS cc_start: 0.8045 (t70) cc_final: 0.7828 (t70) REVERT: D 270 ASN cc_start: 0.7964 (m110) cc_final: 0.7698 (m110) REVERT: D 308 TYR cc_start: 0.7805 (p90) cc_final: 0.7487 (p90) REVERT: D 323 ASN cc_start: 0.8206 (p0) cc_final: 0.8006 (p0) REVERT: D 364 ASN cc_start: 0.8219 (m-40) cc_final: 0.7986 (m-40) REVERT: D 382 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8355 (Cg_exo) REVERT: D 390 GLU cc_start: 0.7604 (pm20) cc_final: 0.7090 (pm20) REVERT: G 30 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6969 (mm-30) REVERT: G 76 TYR cc_start: 0.8366 (t80) cc_final: 0.7699 (t80) REVERT: G 174 ASP cc_start: 0.7922 (m-30) cc_final: 0.7141 (m-30) REVERT: G 218 ASP cc_start: 0.8160 (t0) cc_final: 0.7626 (t0) REVERT: G 237 VAL cc_start: 0.8623 (p) cc_final: 0.8369 (m) REVERT: G 241 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7570 (mm-30) REVERT: G 246 ASN cc_start: 0.7597 (t0) cc_final: 0.6926 (t0) REVERT: G 343 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8245 (m) REVERT: G 404 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7886 (ttmm) REVERT: A 9 ASN cc_start: 0.7855 (p0) cc_final: 0.7567 (p0) REVERT: A 50 LYS cc_start: 0.8189 (tttp) cc_final: 0.7783 (ttpt) REVERT: A 87 PHE cc_start: 0.7991 (t80) cc_final: 0.7496 (t80) REVERT: A 188 ASP cc_start: 0.7954 (t0) cc_final: 0.7630 (t0) REVERT: A 202 ASP cc_start: 0.7580 (p0) cc_final: 0.7275 (p0) REVERT: A 263 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 311 ASP cc_start: 0.7903 (t0) cc_final: 0.7700 (t0) REVERT: A 320 TYR cc_start: 0.8081 (p90) cc_final: 0.7309 (p90) REVERT: A 373 LYS cc_start: 0.8415 (mptt) cc_final: 0.8131 (mptt) REVERT: E 36 ASP cc_start: 0.7650 (p0) cc_final: 0.7293 (p0) REVERT: E 76 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8222 (mmtt) REVERT: E 127 GLU cc_start: 0.7668 (tp30) cc_final: 0.7465 (tp30) REVERT: E 129 LYS cc_start: 0.8629 (tppt) cc_final: 0.8356 (tppt) REVERT: E 131 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7772 (mmt-90) REVERT: E 139 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7109 (mt-10) REVERT: E 162 SER cc_start: 0.8850 (t) cc_final: 0.8605 (t) REVERT: E 168 MET cc_start: 0.7618 (tmm) cc_final: 0.7378 (tmm) REVERT: E 195 LYS cc_start: 0.8233 (mttt) cc_final: 0.8033 (mttt) REVERT: E 254 LYS cc_start: 0.8218 (mttt) cc_final: 0.7919 (mttt) REVERT: E 277 THR cc_start: 0.8452 (m) cc_final: 0.7930 (p) REVERT: E 278 LYS cc_start: 0.8627 (mmtp) cc_final: 0.8252 (mtpp) REVERT: E 324 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7819 (mt-10) REVERT: E 393 ARG cc_start: 0.5390 (tpt170) cc_final: 0.4843 (tpt170) REVERT: E 394 ARG cc_start: 0.7688 (ptm-80) cc_final: 0.7460 (ptm-80) REVERT: H 60 ASP cc_start: 0.7957 (t0) cc_final: 0.7423 (t0) REVERT: H 131 ARG cc_start: 0.8149 (mmt-90) cc_final: 0.7567 (mmt-90) REVERT: H 179 TYR cc_start: 0.7693 (m-10) cc_final: 0.7451 (m-10) REVERT: H 224 LYS cc_start: 0.8219 (ptmm) cc_final: 0.7978 (ptmm) REVERT: H 347 ASP cc_start: 0.7524 (t0) cc_final: 0.6877 (t0) REVERT: H 393 ARG cc_start: 0.5863 (tpt170) cc_final: 0.5114 (tpt170) REVERT: H 394 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7782 (ttp-110) REVERT: H 397 LEU cc_start: 0.8294 (mm) cc_final: 0.8027 (mm) REVERT: B 76 LYS cc_start: 0.7978 (tppp) cc_final: 0.7521 (tppp) REVERT: B 77 GLU cc_start: 0.7746 (tt0) cc_final: 0.7519 (tt0) REVERT: B 94 LEU cc_start: 0.8677 (mm) cc_final: 0.8465 (mp) REVERT: B 159 LYS cc_start: 0.8452 (ptpt) cc_final: 0.8227 (ptpt) REVERT: B 206 TYR cc_start: 0.7544 (t80) cc_final: 0.7237 (t80) REVERT: B 225 GLN cc_start: 0.6158 (tm-30) cc_final: 0.5715 (tm-30) REVERT: B 254 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7555 (mtpt) REVERT: B 265 VAL cc_start: 0.9165 (t) cc_final: 0.8713 (p) REVERT: B 272 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7550 (t-90) REVERT: B 281 LYS cc_start: 0.8399 (mttt) cc_final: 0.8112 (mttt) REVERT: B 354 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 8 MET cc_start: 0.7481 (mmp) cc_final: 0.7229 (mmp) REVERT: F 19 MET cc_start: 0.6989 (mmp) cc_final: 0.6686 (mmp) REVERT: F 56 LYS cc_start: 0.8380 (ptpp) cc_final: 0.7886 (ptpp) REVERT: F 60 MET cc_start: 0.8033 (mmt) cc_final: 0.7802 (mmt) REVERT: F 88 TYR cc_start: 0.6306 (m-80) cc_final: 0.6015 (m-80) REVERT: F 96 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.5990 (mm110) REVERT: F 111 LYS cc_start: 0.8638 (mttt) cc_final: 0.8278 (mttt) REVERT: I 8 MET cc_start: 0.8035 (mmm) cc_final: 0.7830 (mmm) REVERT: I 14 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7657 (mmtp) REVERT: I 44 LYS cc_start: 0.8228 (tptt) cc_final: 0.7960 (tptt) REVERT: I 49 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7548 (tm-30) REVERT: I 101 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6497 (mmm-85) REVERT: I 111 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8422 (mtpp) REVERT: I 128 ILE cc_start: 0.8963 (mp) cc_final: 0.8716 (mt) REVERT: C 37 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8285 (tmmt) REVERT: C 55 LEU cc_start: 0.8022 (mm) cc_final: 0.6961 (mm) REVERT: C 106 ARG cc_start: 0.8118 (ppt170) cc_final: 0.7846 (ppt170) outliers start: 153 outliers final: 114 residues processed: 1249 average time/residue: 0.4649 time to fit residues: 883.2382 Evaluate side-chains 1284 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1165 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 354 optimal weight: 7.9990 chunk 37 optimal weight: 30.0000 chunk 290 optimal weight: 0.0870 chunk 377 optimal weight: 9.9990 chunk 380 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 211 optimal weight: 0.0770 overall best weight: 3.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 33 ASN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 204 GLN D 327 HIS G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 331 HIS A 345 HIS E 50 GLN H 96 HIS ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3721 r_free = 0.3721 target = 0.134886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118199 restraints weight = 55558.933| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.84 r_work: 0.3363 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31760 Z= 0.198 Angle : 0.679 17.653 43289 Z= 0.344 Chirality : 0.048 0.289 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.706 78.151 4563 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.56 % Favored : 93.39 % Rotamer: Outliers : 5.07 % Allowed : 17.98 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.16 (0.13), residues: 3963 helix: 1.99 (0.24), residues: 412 sheet: -0.51 (0.15), residues: 1183 loop : -1.46 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 279 HIS 0.019 0.001 HIS D 327 PHE 0.021 0.002 PHE E 51 TYR 0.031 0.002 TYR A 308 ARG 0.013 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 1.67670 ( 36) hydrogen bonds : bond 0.03418 ( 1026) hydrogen bonds : angle 5.41700 ( 2733) SS BOND : bond 0.00463 ( 56) SS BOND : angle 2.09148 ( 112) covalent geometry : bond 0.00440 (31692) covalent geometry : angle 0.66968 (43141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1198 time to evaluate : 3.358 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: 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: J 9 ASN cc_start: 0.8425 (t0) cc_final: 0.7871 (t0) REVERT: J 49 CYS cc_start: 0.7551 (p) cc_final: 0.7314 (p) REVERT: J 50 LYS cc_start: 0.8322 (tttm) cc_final: 0.7856 (tttp) REVERT: J 99 GLU cc_start: 0.7092 (tt0) cc_final: 0.6506 (tt0) REVERT: J 101 THR cc_start: 0.7984 (m) cc_final: 0.7674 (m) REVERT: J 130 LYS cc_start: 0.7801 (tttp) cc_final: 0.7581 (tttp) REVERT: J 134 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7829 (ttm-80) REVERT: J 180 ARG cc_start: 0.8597 (ttt-90) cc_final: 0.8248 (ttt-90) REVERT: J 191 GLU cc_start: 0.4830 (tt0) cc_final: 0.3814 (mt-10) REVERT: J 234 THR cc_start: 0.8053 (p) cc_final: 0.7790 (t) REVERT: J 282 ILE cc_start: 0.8637 (mt) cc_final: 0.8219 (tp) REVERT: J 289 ARG cc_start: 0.7859 (mtt90) cc_final: 0.7538 (mtt90) REVERT: J 318 LEU cc_start: 0.7665 (tp) cc_final: 0.7108 (tp) REVERT: K 7 THR cc_start: 0.8533 (t) cc_final: 0.8264 (p) REVERT: K 18 TYR cc_start: 0.7800 (t80) cc_final: 0.6988 (t80) REVERT: K 25 CYS cc_start: 0.5607 (t) cc_final: 0.5292 (t) REVERT: K 55 GLN cc_start: 0.8344 (tt0) cc_final: 0.8120 (tt0) REVERT: K 60 ASP cc_start: 0.7289 (t0) cc_final: 0.6641 (t0) REVERT: K 77 GLU cc_start: 0.8063 (pt0) cc_final: 0.7734 (pt0) REVERT: K 82 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8359 (mtpt) REVERT: K 109 ASP cc_start: 0.7734 (m-30) cc_final: 0.7497 (t0) REVERT: K 133 LYS cc_start: 0.8502 (mtmm) cc_final: 0.8255 (mtmm) REVERT: K 138 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6975 (mm-30) REVERT: K 152 CYS cc_start: 0.7219 (p) cc_final: 0.6921 (p) REVERT: K 156 ASP cc_start: 0.8225 (t0) cc_final: 0.7802 (t0) REVERT: K 158 LEU cc_start: 0.8724 (mp) cc_final: 0.8154 (mp) REVERT: K 159 LYS cc_start: 0.8763 (pttm) cc_final: 0.8482 (pttm) REVERT: K 176 TYR cc_start: 0.8275 (m-80) cc_final: 0.7902 (m-80) REVERT: K 181 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6715 (tm-30) REVERT: K 195 LYS cc_start: 0.8440 (mppt) cc_final: 0.8120 (mppt) REVERT: K 222 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8301 (mmtt) REVERT: K 287 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8559 (pp) REVERT: K 324 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7740 (mt-10) REVERT: K 354 GLU cc_start: 0.7637 (mp0) cc_final: 0.7171 (mp0) REVERT: K 395 ASP cc_start: 0.8042 (m-30) cc_final: 0.7784 (m-30) REVERT: L 57 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7832 (mtmm) REVERT: L 80 THR cc_start: 0.8273 (t) cc_final: 0.7928 (m) REVERT: D 61 LYS cc_start: 0.7752 (pptt) cc_final: 0.7132 (ptmm) REVERT: D 76 TYR cc_start: 0.8346 (t80) cc_final: 0.7886 (t80) REVERT: D 99 GLU cc_start: 0.6770 (tm-30) cc_final: 0.6050 (tm-30) REVERT: D 270 ASN cc_start: 0.7996 (m110) cc_final: 0.7735 (m110) REVERT: D 320 TYR cc_start: 0.7910 (p90) cc_final: 0.7625 (p90) REVERT: D 323 ASN cc_start: 0.8205 (p0) cc_final: 0.7931 (p0) REVERT: D 364 ASN cc_start: 0.8225 (m-40) cc_final: 0.8002 (m-40) REVERT: D 390 GLU cc_start: 0.7597 (pm20) cc_final: 0.7224 (pm20) REVERT: G 30 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6906 (mm-30) REVERT: G 76 TYR cc_start: 0.8371 (t80) cc_final: 0.7628 (t80) REVERT: G 174 ASP cc_start: 0.7839 (m-30) cc_final: 0.7317 (m-30) REVERT: G 218 ASP cc_start: 0.8167 (t0) cc_final: 0.7646 (t0) REVERT: G 237 VAL cc_start: 0.8626 (p) cc_final: 0.8388 (m) REVERT: G 241 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7583 (mm-30) REVERT: G 246 ASN cc_start: 0.7632 (t0) cc_final: 0.6966 (t0) REVERT: G 308 TYR cc_start: 0.8707 (p90) cc_final: 0.8471 (p90) REVERT: G 343 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8231 (m) REVERT: G 346 VAL cc_start: 0.7781 (t) cc_final: 0.7389 (m) REVERT: G 404 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7866 (ttmm) REVERT: A 9 ASN cc_start: 0.7959 (p0) cc_final: 0.7666 (p0) REVERT: A 20 GLU cc_start: 0.7437 (tt0) cc_final: 0.7211 (tt0) REVERT: A 188 ASP cc_start: 0.7910 (t0) cc_final: 0.7599 (t0) REVERT: A 202 ASP cc_start: 0.7466 (p0) cc_final: 0.7220 (p0) REVERT: A 263 VAL cc_start: 0.8136 (m) cc_final: 0.7925 (p) REVERT: A 320 TYR cc_start: 0.8078 (p90) cc_final: 0.7306 (p90) REVERT: A 373 LYS cc_start: 0.8418 (mptt) cc_final: 0.8125 (mptt) REVERT: E 36 ASP cc_start: 0.7626 (p0) cc_final: 0.7291 (p0) REVERT: E 76 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8250 (mmtt) REVERT: E 129 LYS cc_start: 0.8639 (tppt) cc_final: 0.8377 (tppt) REVERT: E 131 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7766 (mmt180) REVERT: E 162 SER cc_start: 0.8847 (t) cc_final: 0.8611 (t) REVERT: E 168 MET cc_start: 0.7614 (tmm) cc_final: 0.7367 (tmm) REVERT: E 254 LYS cc_start: 0.8264 (mttt) cc_final: 0.7986 (mttt) REVERT: E 277 THR cc_start: 0.8500 (m) cc_final: 0.8024 (p) REVERT: E 278 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8321 (mtpp) REVERT: E 324 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 339 TRP cc_start: 0.8312 (m-90) cc_final: 0.8058 (m-90) REVERT: E 393 ARG cc_start: 0.5391 (tpt170) cc_final: 0.4872 (tpt170) REVERT: E 394 ARG cc_start: 0.7623 (ptm-80) cc_final: 0.7400 (ptm-80) REVERT: H 60 ASP cc_start: 0.7971 (t0) cc_final: 0.7444 (t0) REVERT: H 80 MET cc_start: 0.8656 (tpp) cc_final: 0.8410 (tpp) REVERT: H 131 ARG cc_start: 0.8081 (mmt-90) cc_final: 0.7585 (mmt-90) REVERT: H 224 LYS cc_start: 0.8238 (ptmm) cc_final: 0.7990 (ptmm) REVERT: H 342 GLU cc_start: 0.7072 (pm20) cc_final: 0.6687 (pm20) REVERT: H 347 ASP cc_start: 0.7513 (t0) cc_final: 0.6885 (t0) REVERT: H 393 ARG cc_start: 0.5943 (tpt170) cc_final: 0.5170 (tpt170) REVERT: H 394 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7747 (ttp-110) REVERT: H 397 LEU cc_start: 0.8336 (mm) cc_final: 0.8077 (mm) REVERT: B 67 MET cc_start: 0.7127 (mmm) cc_final: 0.6274 (mmm) REVERT: B 76 LYS cc_start: 0.7935 (tppp) cc_final: 0.7503 (tppp) REVERT: B 77 GLU cc_start: 0.7628 (tt0) cc_final: 0.7348 (tt0) REVERT: B 129 LYS cc_start: 0.8809 (tptt) cc_final: 0.8592 (tptt) REVERT: B 206 TYR cc_start: 0.7463 (t80) cc_final: 0.7122 (t80) REVERT: B 225 GLN cc_start: 0.6586 (tm-30) cc_final: 0.6029 (tm-30) REVERT: B 265 VAL cc_start: 0.9175 (t) cc_final: 0.8729 (p) REVERT: B 272 HIS cc_start: 0.8173 (OUTLIER) cc_final: 0.7566 (t-90) REVERT: B 281 LYS cc_start: 0.8430 (mttt) cc_final: 0.8142 (mttt) REVERT: B 354 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 8 MET cc_start: 0.7189 (mmp) cc_final: 0.6953 (mmp) REVERT: F 19 MET cc_start: 0.6656 (mmp) cc_final: 0.6412 (mmp) REVERT: F 56 LYS cc_start: 0.8324 (ptpp) cc_final: 0.7825 (ptpp) REVERT: F 60 MET cc_start: 0.7996 (mmt) cc_final: 0.7789 (mmt) REVERT: F 88 TYR cc_start: 0.6128 (m-80) cc_final: 0.5261 (m-80) REVERT: F 97 TYR cc_start: 0.5497 (OUTLIER) cc_final: 0.4909 (m-80) REVERT: F 101 ARG cc_start: 0.7093 (ttt180) cc_final: 0.6772 (ttt180) REVERT: F 111 LYS cc_start: 0.8643 (mttt) cc_final: 0.8311 (mttt) REVERT: I 8 MET cc_start: 0.7939 (mmm) cc_final: 0.7691 (mmm) REVERT: I 14 LYS cc_start: 0.8051 (mmtp) cc_final: 0.7831 (mmtp) REVERT: I 44 LYS cc_start: 0.8202 (tptt) cc_final: 0.7981 (tptt) REVERT: I 49 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7491 (tm-30) REVERT: I 111 LYS cc_start: 0.8617 (mtpp) cc_final: 0.8411 (mtpp) REVERT: I 128 ILE cc_start: 0.8966 (mp) cc_final: 0.8745 (mm) REVERT: C 37 LYS cc_start: 0.8420 (tmmt) cc_final: 0.8218 (tmmt) REVERT: C 55 LEU cc_start: 0.7998 (mm) cc_final: 0.7602 (mt) REVERT: C 106 ARG cc_start: 0.8067 (ppt170) cc_final: 0.7784 (ppt170) outliers start: 171 outliers final: 132 residues processed: 1259 average time/residue: 0.4524 time to fit residues: 868.6877 Evaluate side-chains 1301 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1165 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 259 CYS Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 242 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 334 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 91 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 276 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 339 optimal weight: 6.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 33 ASN K 332 ASN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 204 GLN D 230 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.133979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117340 restraints weight = 55960.488| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.84 r_work: 0.3359 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31760 Z= 0.232 Angle : 0.699 18.039 43289 Z= 0.354 Chirality : 0.048 0.313 4873 Planarity : 0.005 0.053 5520 Dihedral : 5.719 76.959 4563 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.81 % Favored : 93.14 % Rotamer: Outliers : 5.36 % Allowed : 19.25 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.17 (0.13), residues: 3963 helix: 2.01 (0.25), residues: 412 sheet: -0.51 (0.15), residues: 1160 loop : -1.47 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 279 HIS 0.009 0.001 HIS J 331 PHE 0.024 0.002 PHE E 51 TYR 0.030 0.002 TYR A 308 ARG 0.014 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 12) link_NAG-ASN : angle 1.76488 ( 36) hydrogen bonds : bond 0.03499 ( 1026) hydrogen bonds : angle 5.42082 ( 2733) SS BOND : bond 0.00522 ( 56) SS BOND : angle 2.35032 ( 112) covalent geometry : bond 0.00513 (31692) covalent geometry : angle 0.68772 (43141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1182 time to evaluate : 3.244 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8420 (t0) cc_final: 0.7867 (t0) REVERT: J 49 CYS cc_start: 0.7535 (p) cc_final: 0.7288 (p) REVERT: J 50 LYS cc_start: 0.8327 (tttm) cc_final: 0.7851 (tttp) REVERT: J 61 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7456 (ttpt) REVERT: J 63 CYS cc_start: 0.5974 (OUTLIER) cc_final: 0.5549 (m) REVERT: J 96 CYS cc_start: 0.6268 (t) cc_final: 0.5411 (t) REVERT: J 99 GLU cc_start: 0.7149 (tt0) cc_final: 0.6350 (tt0) REVERT: J 101 THR cc_start: 0.8013 (m) cc_final: 0.7713 (m) REVERT: J 130 LYS cc_start: 0.7872 (tttp) cc_final: 0.7631 (tttp) REVERT: J 134 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7826 (ttm-80) REVERT: J 191 GLU cc_start: 0.4466 (tt0) cc_final: 0.3744 (mt-10) REVERT: J 234 THR cc_start: 0.8069 (p) cc_final: 0.7789 (t) REVERT: J 282 ILE cc_start: 0.8624 (mt) cc_final: 0.8200 (tp) REVERT: J 289 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7553 (mtt90) REVERT: J 318 LEU cc_start: 0.7669 (tp) cc_final: 0.7083 (tp) REVERT: K 4 ASP cc_start: 0.7506 (t0) cc_final: 0.7304 (t0) REVERT: K 7 THR cc_start: 0.8553 (t) cc_final: 0.8256 (p) REVERT: K 18 TYR cc_start: 0.7907 (t80) cc_final: 0.7136 (t80) REVERT: K 60 ASP cc_start: 0.7279 (t0) cc_final: 0.6664 (t0) REVERT: K 77 GLU cc_start: 0.8067 (pt0) cc_final: 0.7739 (pt0) REVERT: K 82 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8382 (mttm) REVERT: K 109 ASP cc_start: 0.7769 (m-30) cc_final: 0.7490 (t0) REVERT: K 127 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7531 (mt-10) REVERT: K 133 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8246 (mtmm) REVERT: K 138 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7072 (mm-30) REVERT: K 156 ASP cc_start: 0.8190 (t0) cc_final: 0.7821 (t0) REVERT: K 158 LEU cc_start: 0.8739 (mp) cc_final: 0.8152 (mp) REVERT: K 159 LYS cc_start: 0.8768 (pttm) cc_final: 0.8498 (pttm) REVERT: K 176 TYR cc_start: 0.8256 (m-80) cc_final: 0.7891 (m-80) REVERT: K 181 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6823 (tm-30) REVERT: K 195 LYS cc_start: 0.8434 (mppt) cc_final: 0.8106 (mppt) REVERT: K 222 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8245 (mmtt) REVERT: K 287 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8570 (pp) REVERT: K 324 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7745 (mt-10) REVERT: K 354 GLU cc_start: 0.7690 (mp0) cc_final: 0.7179 (mp0) REVERT: K 395 ASP cc_start: 0.8017 (m-30) cc_final: 0.7760 (m-30) REVERT: L 57 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7860 (mtmm) REVERT: D 61 LYS cc_start: 0.7805 (pptt) cc_final: 0.7181 (ptmm) REVERT: D 174 ASP cc_start: 0.7914 (t0) cc_final: 0.7683 (t0) REVERT: D 270 ASN cc_start: 0.8007 (m110) cc_final: 0.7736 (m110) REVERT: D 308 TYR cc_start: 0.7824 (p90) cc_final: 0.7575 (p90) REVERT: D 323 ASN cc_start: 0.8305 (p0) cc_final: 0.8084 (p0) REVERT: D 364 ASN cc_start: 0.8228 (m-40) cc_final: 0.7995 (m-40) REVERT: D 390 GLU cc_start: 0.7609 (pm20) cc_final: 0.7059 (pm20) REVERT: G 30 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6946 (mm-30) REVERT: G 76 TYR cc_start: 0.8383 (t80) cc_final: 0.7629 (t80) REVERT: G 80 VAL cc_start: 0.8868 (t) cc_final: 0.8568 (m) REVERT: G 174 ASP cc_start: 0.7863 (m-30) cc_final: 0.7312 (m-30) REVERT: G 218 ASP cc_start: 0.8172 (t0) cc_final: 0.7645 (t0) REVERT: G 237 VAL cc_start: 0.8588 (p) cc_final: 0.8356 (m) REVERT: G 241 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7597 (mm-30) REVERT: G 246 ASN cc_start: 0.7686 (t0) cc_final: 0.7019 (t0) REVERT: G 343 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8243 (m) REVERT: G 346 VAL cc_start: 0.7840 (t) cc_final: 0.7440 (m) REVERT: G 404 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7823 (ttmm) REVERT: A 9 ASN cc_start: 0.7998 (p0) cc_final: 0.7677 (p0) REVERT: A 20 GLU cc_start: 0.7497 (tt0) cc_final: 0.7245 (tt0) REVERT: A 107 TYR cc_start: 0.7777 (p90) cc_final: 0.7406 (p90) REVERT: A 188 ASP cc_start: 0.7906 (t0) cc_final: 0.7614 (t0) REVERT: A 202 ASP cc_start: 0.7494 (p0) cc_final: 0.7269 (p0) REVERT: E 36 ASP cc_start: 0.7605 (p0) cc_final: 0.7256 (p0) REVERT: E 76 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8222 (mmtt) REVERT: E 131 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7813 (mmt-90) REVERT: E 162 SER cc_start: 0.8872 (t) cc_final: 0.8633 (t) REVERT: E 168 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7330 (tmm) REVERT: E 200 GLU cc_start: 0.7277 (tt0) cc_final: 0.6859 (tt0) REVERT: E 254 LYS cc_start: 0.8263 (mttt) cc_final: 0.7996 (mttt) REVERT: E 277 THR cc_start: 0.8527 (m) cc_final: 0.8021 (p) REVERT: E 278 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8259 (mtpp) REVERT: E 324 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7725 (mt-10) REVERT: E 393 ARG cc_start: 0.5495 (tpt170) cc_final: 0.4957 (tpt170) REVERT: H 60 ASP cc_start: 0.7957 (t0) cc_final: 0.7441 (t0) REVERT: H 80 MET cc_start: 0.8713 (tpp) cc_final: 0.8436 (tpp) REVERT: H 87 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7950 (p) REVERT: H 131 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7558 (mmt-90) REVERT: H 141 LEU cc_start: 0.8353 (mt) cc_final: 0.8008 (mt) REVERT: H 224 LYS cc_start: 0.8283 (ptmm) cc_final: 0.7986 (ptmm) REVERT: H 347 ASP cc_start: 0.7474 (t0) cc_final: 0.6833 (t0) REVERT: H 394 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7768 (ttp-110) REVERT: H 397 LEU cc_start: 0.8342 (mm) cc_final: 0.8066 (mm) REVERT: B 76 LYS cc_start: 0.7960 (tppp) cc_final: 0.7537 (tppp) REVERT: B 77 GLU cc_start: 0.7654 (tt0) cc_final: 0.7381 (tt0) REVERT: B 129 LYS cc_start: 0.8784 (tptt) cc_final: 0.8566 (tptt) REVERT: B 206 TYR cc_start: 0.7549 (t80) cc_final: 0.7169 (t80) REVERT: B 225 GLN cc_start: 0.6551 (tm-30) cc_final: 0.6010 (tm-30) REVERT: B 239 ASN cc_start: 0.7482 (p0) cc_final: 0.7244 (t0) REVERT: B 265 VAL cc_start: 0.9132 (t) cc_final: 0.8710 (p) REVERT: B 272 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7516 (t-90) REVERT: B 281 LYS cc_start: 0.8465 (mttt) cc_final: 0.8189 (mttt) REVERT: B 354 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 56 LYS cc_start: 0.8333 (ptpp) cc_final: 0.7881 (ptpp) REVERT: F 76 THR cc_start: 0.7829 (p) cc_final: 0.7491 (p) REVERT: F 88 TYR cc_start: 0.6369 (m-80) cc_final: 0.5978 (m-80) REVERT: F 97 TYR cc_start: 0.5395 (m-80) cc_final: 0.5008 (m-80) REVERT: F 111 LYS cc_start: 0.8672 (mttt) cc_final: 0.8355 (mttt) REVERT: F 116 ARG cc_start: 0.8305 (mtp180) cc_final: 0.8043 (mtp85) REVERT: I 8 MET cc_start: 0.7967 (mmm) cc_final: 0.7714 (mmm) REVERT: I 44 LYS cc_start: 0.8262 (tptt) cc_final: 0.8045 (tptt) REVERT: I 49 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7459 (tm-30) REVERT: I 111 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8420 (mtpp) REVERT: I 128 ILE cc_start: 0.8970 (mp) cc_final: 0.8731 (mm) REVERT: C 37 LYS cc_start: 0.8463 (tmmt) cc_final: 0.8245 (tmmt) REVERT: C 55 LEU cc_start: 0.8033 (mm) cc_final: 0.7616 (mt) REVERT: C 106 ARG cc_start: 0.8154 (ppt170) cc_final: 0.7863 (ppt170) outliers start: 181 outliers final: 141 residues processed: 1257 average time/residue: 0.4439 time to fit residues: 853.7191 Evaluate side-chains 1320 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1173 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain L residue 8 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 191 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 146 TRP Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 68 optimal weight: 0.6980 chunk 181 optimal weight: 7.9990 chunk 296 optimal weight: 0.6980 chunk 245 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 chunk 384 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS L 92 HIS D 196 ASN D 230 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3729 r_free = 0.3729 target = 0.135460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118675 restraints weight = 55978.611| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.89 r_work: 0.3366 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31760 Z= 0.166 Angle : 0.682 17.747 43289 Z= 0.343 Chirality : 0.048 0.313 4873 Planarity : 0.005 0.051 5520 Dihedral : 5.563 77.944 4563 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 5.12 % Allowed : 20.56 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.08 (0.13), residues: 3963 helix: 2.17 (0.24), residues: 406 sheet: -0.47 (0.15), residues: 1148 loop : -1.40 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 279 HIS 0.012 0.001 HIS D 230 PHE 0.023 0.002 PHE E 51 TYR 0.031 0.002 TYR A 308 ARG 0.012 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 12) link_NAG-ASN : angle 1.54170 ( 36) hydrogen bonds : bond 0.03243 ( 1026) hydrogen bonds : angle 5.32949 ( 2733) SS BOND : bond 0.00479 ( 56) SS BOND : angle 2.16953 ( 112) covalent geometry : bond 0.00377 (31692) covalent geometry : angle 0.67313 (43141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1164 time to evaluate : 3.531 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8372 (t0) cc_final: 0.7854 (t0) REVERT: J 49 CYS cc_start: 0.7625 (p) cc_final: 0.7327 (p) REVERT: J 50 LYS cc_start: 0.8287 (tttm) cc_final: 0.8022 (tttm) REVERT: J 61 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7438 (ttpt) REVERT: J 63 CYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5568 (m) REVERT: J 96 CYS cc_start: 0.6199 (t) cc_final: 0.5306 (t) REVERT: J 99 GLU cc_start: 0.7160 (tt0) cc_final: 0.6307 (tt0) REVERT: J 130 LYS cc_start: 0.7788 (tttp) cc_final: 0.7551 (tttp) REVERT: J 134 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7777 (ttm-80) REVERT: J 180 ARG cc_start: 0.8566 (ttt-90) cc_final: 0.8350 (ttt-90) REVERT: J 191 GLU cc_start: 0.4341 (tt0) cc_final: 0.3646 (mt-10) REVERT: J 234 THR cc_start: 0.7986 (p) cc_final: 0.7714 (t) REVERT: J 282 ILE cc_start: 0.8599 (mt) cc_final: 0.8176 (tp) REVERT: J 289 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7596 (mtt90) REVERT: K 4 ASP cc_start: 0.7534 (t0) cc_final: 0.7302 (t0) REVERT: K 7 THR cc_start: 0.8519 (t) cc_final: 0.8219 (p) REVERT: K 18 TYR cc_start: 0.7719 (t80) cc_final: 0.6922 (t80) REVERT: K 55 GLN cc_start: 0.8325 (tt0) cc_final: 0.8098 (tt0) REVERT: K 60 ASP cc_start: 0.7245 (t0) cc_final: 0.6628 (t0) REVERT: K 77 GLU cc_start: 0.8068 (pt0) cc_final: 0.7724 (pt0) REVERT: K 82 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8320 (mttm) REVERT: K 109 ASP cc_start: 0.7721 (m-30) cc_final: 0.7445 (t0) REVERT: K 127 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7528 (mt-10) REVERT: K 138 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7036 (mm-30) REVERT: K 156 ASP cc_start: 0.8211 (t0) cc_final: 0.7798 (t0) REVERT: K 158 LEU cc_start: 0.8710 (mp) cc_final: 0.8102 (mp) REVERT: K 159 LYS cc_start: 0.8761 (pttm) cc_final: 0.8480 (pttm) REVERT: K 176 TYR cc_start: 0.8256 (m-80) cc_final: 0.7908 (m-80) REVERT: K 181 GLU cc_start: 0.7338 (tm-30) cc_final: 0.6867 (tm-30) REVERT: K 195 LYS cc_start: 0.8415 (mppt) cc_final: 0.8068 (mppt) REVERT: K 222 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8225 (mmtt) REVERT: K 287 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8538 (pp) REVERT: K 324 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7739 (mt-10) REVERT: K 354 GLU cc_start: 0.7708 (mp0) cc_final: 0.7159 (mp0) REVERT: K 395 ASP cc_start: 0.8011 (m-30) cc_final: 0.7749 (m-30) REVERT: D 61 LYS cc_start: 0.7741 (pptt) cc_final: 0.7045 (ptmm) REVERT: D 174 ASP cc_start: 0.7915 (t0) cc_final: 0.7680 (t0) REVERT: D 270 ASN cc_start: 0.8029 (m110) cc_final: 0.7779 (m110) REVERT: D 308 TYR cc_start: 0.7849 (p90) cc_final: 0.7611 (p90) REVERT: D 321 LYS cc_start: 0.8093 (ptpp) cc_final: 0.7827 (mtmm) REVERT: D 323 ASN cc_start: 0.8238 (p0) cc_final: 0.8024 (p0) REVERT: D 364 ASN cc_start: 0.8215 (m-40) cc_final: 0.8009 (m-40) REVERT: D 390 GLU cc_start: 0.7584 (pm20) cc_final: 0.7011 (pm20) REVERT: G 30 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6937 (mm-30) REVERT: G 76 TYR cc_start: 0.8376 (t80) cc_final: 0.7712 (t80) REVERT: G 80 VAL cc_start: 0.8862 (t) cc_final: 0.8536 (m) REVERT: G 174 ASP cc_start: 0.7872 (m-30) cc_final: 0.7309 (m-30) REVERT: G 218 ASP cc_start: 0.8174 (t0) cc_final: 0.7628 (t0) REVERT: G 237 VAL cc_start: 0.8563 (p) cc_final: 0.8347 (m) REVERT: G 241 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7528 (mm-30) REVERT: G 246 ASN cc_start: 0.7651 (t0) cc_final: 0.6982 (t0) REVERT: G 343 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8202 (m) REVERT: G 346 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7471 (m) REVERT: G 404 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7849 (ttmm) REVERT: A 9 ASN cc_start: 0.7735 (p0) cc_final: 0.7404 (p0) REVERT: A 20 GLU cc_start: 0.7509 (tt0) cc_final: 0.7240 (tt0) REVERT: A 107 TYR cc_start: 0.7691 (p90) cc_final: 0.7110 (p90) REVERT: A 186 ASN cc_start: 0.8881 (m-40) cc_final: 0.8629 (m110) REVERT: A 188 ASP cc_start: 0.7942 (t0) cc_final: 0.7645 (t0) REVERT: A 202 ASP cc_start: 0.7428 (p0) cc_final: 0.7193 (p0) REVERT: A 249 ARG cc_start: 0.8694 (mmp-170) cc_final: 0.8442 (mmp80) REVERT: A 320 TYR cc_start: 0.8114 (p90) cc_final: 0.7234 (p90) REVERT: E 34 VAL cc_start: 0.9089 (t) cc_final: 0.8583 (m) REVERT: E 36 ASP cc_start: 0.7568 (p0) cc_final: 0.7280 (p0) REVERT: E 76 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8154 (mmtt) REVERT: E 105 CYS cc_start: 0.7464 (m) cc_final: 0.7127 (m) REVERT: E 131 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7730 (mmt180) REVERT: E 162 SER cc_start: 0.8857 (t) cc_final: 0.8628 (t) REVERT: E 168 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7248 (tmm) REVERT: E 200 GLU cc_start: 0.7303 (tt0) cc_final: 0.6863 (tt0) REVERT: E 254 LYS cc_start: 0.8177 (mttt) cc_final: 0.7913 (mttt) REVERT: E 277 THR cc_start: 0.8523 (m) cc_final: 0.8005 (p) REVERT: E 299 LYS cc_start: 0.8383 (mttt) cc_final: 0.8021 (mtpp) REVERT: E 324 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 393 ARG cc_start: 0.5287 (tpt170) cc_final: 0.4731 (tpt170) REVERT: E 394 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7393 (ttp80) REVERT: H 60 ASP cc_start: 0.7962 (t0) cc_final: 0.7444 (t0) REVERT: H 76 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7559 (ttmt) REVERT: H 80 MET cc_start: 0.8795 (tpp) cc_final: 0.8543 (tpp) REVERT: H 131 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7555 (mmt-90) REVERT: H 141 LEU cc_start: 0.8360 (mt) cc_final: 0.8085 (mt) REVERT: H 224 LYS cc_start: 0.8261 (ptmm) cc_final: 0.7918 (ptmm) REVERT: H 347 ASP cc_start: 0.7479 (t0) cc_final: 0.6834 (t0) REVERT: H 397 LEU cc_start: 0.8331 (mm) cc_final: 0.8042 (mm) REVERT: B 67 MET cc_start: 0.7070 (mmm) cc_final: 0.6753 (mmm) REVERT: B 76 LYS cc_start: 0.7936 (tppp) cc_final: 0.7519 (tppp) REVERT: B 77 GLU cc_start: 0.7665 (tt0) cc_final: 0.7315 (tt0) REVERT: B 129 LYS cc_start: 0.8779 (tptt) cc_final: 0.8567 (tptt) REVERT: B 140 TYR cc_start: 0.8377 (p90) cc_final: 0.7973 (p90) REVERT: B 206 TYR cc_start: 0.7600 (t80) cc_final: 0.7207 (t80) REVERT: B 225 GLN cc_start: 0.6542 (tm-30) cc_final: 0.5940 (tm-30) REVERT: B 265 VAL cc_start: 0.9111 (t) cc_final: 0.8672 (p) REVERT: B 272 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7485 (t-90) REVERT: B 281 LYS cc_start: 0.8422 (mttt) cc_final: 0.8108 (mttt) REVERT: B 354 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7540 (mt-10) REVERT: F 56 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7863 (ptpp) REVERT: F 88 TYR cc_start: 0.6178 (m-80) cc_final: 0.5942 (m-80) REVERT: F 97 TYR cc_start: 0.5440 (m-80) cc_final: 0.5156 (m-80) REVERT: F 111 LYS cc_start: 0.8598 (mttt) cc_final: 0.8295 (mttt) REVERT: I 8 MET cc_start: 0.7900 (mmm) cc_final: 0.7574 (mmm) REVERT: I 14 LYS cc_start: 0.8037 (mmtp) cc_final: 0.7811 (mmtp) REVERT: I 25 ASN cc_start: 0.7204 (t0) cc_final: 0.6706 (t0) REVERT: I 44 LYS cc_start: 0.8233 (tptt) cc_final: 0.7999 (tptt) REVERT: I 49 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7486 (tm-30) REVERT: I 111 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8382 (mtpp) REVERT: I 128 ILE cc_start: 0.9006 (mp) cc_final: 0.8789 (mm) REVERT: C 37 LYS cc_start: 0.8492 (tmmt) cc_final: 0.8169 (tmmt) REVERT: C 106 ARG cc_start: 0.8194 (ppt170) cc_final: 0.7904 (ppt170) outliers start: 173 outliers final: 136 residues processed: 1235 average time/residue: 0.4563 time to fit residues: 863.2643 Evaluate side-chains 1306 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1164 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 319 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 252 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 366 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 331 HIS K 50 GLN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 353 HIS K 361 HIS ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 139 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS F 47 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3702 r_free = 0.3702 target = 0.133320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116595 restraints weight = 55931.250| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.88 r_work: 0.3340 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 31760 Z= 0.265 Angle : 0.742 18.645 43289 Z= 0.375 Chirality : 0.050 0.346 4873 Planarity : 0.005 0.051 5520 Dihedral : 5.766 75.497 4563 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 5.15 % Allowed : 20.94 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.21 (0.13), residues: 3963 helix: 2.09 (0.25), residues: 405 sheet: -0.59 (0.15), residues: 1190 loop : -1.49 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 279 HIS 0.013 0.001 HIS D 230 PHE 0.030 0.002 PHE C 16 TYR 0.029 0.002 TYR A 308 ARG 0.011 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 12) link_NAG-ASN : angle 1.84333 ( 36) hydrogen bonds : bond 0.03573 ( 1026) hydrogen bonds : angle 5.44807 ( 2733) SS BOND : bond 0.00558 ( 56) SS BOND : angle 2.44161 ( 112) covalent geometry : bond 0.00584 (31692) covalent geometry : angle 0.73113 (43141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 1180 time to evaluate : 3.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8381 (t0) cc_final: 0.7806 (t0) REVERT: J 49 CYS cc_start: 0.7545 (p) cc_final: 0.7298 (p) REVERT: J 50 LYS cc_start: 0.8306 (tttm) cc_final: 0.8047 (tttm) REVERT: J 61 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7548 (ttpp) REVERT: J 63 CYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5841 (m) REVERT: J 96 CYS cc_start: 0.6209 (t) cc_final: 0.5508 (t) REVERT: J 99 GLU cc_start: 0.7146 (tt0) cc_final: 0.6302 (tt0) REVERT: J 101 THR cc_start: 0.7973 (m) cc_final: 0.7672 (m) REVERT: J 130 LYS cc_start: 0.7847 (tttp) cc_final: 0.7281 (tppt) REVERT: J 134 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7753 (ttm-80) REVERT: J 176 LYS cc_start: 0.8508 (mttt) cc_final: 0.8293 (mttt) REVERT: J 180 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8185 (ttt-90) REVERT: J 191 GLU cc_start: 0.4728 (tt0) cc_final: 0.4023 (mt-10) REVERT: J 282 ILE cc_start: 0.8631 (mt) cc_final: 0.8203 (tp) REVERT: J 289 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7602 (mtt90) REVERT: K 4 ASP cc_start: 0.7585 (t0) cc_final: 0.7379 (t0) REVERT: K 7 THR cc_start: 0.8542 (t) cc_final: 0.8224 (p) REVERT: K 18 TYR cc_start: 0.7802 (t80) cc_final: 0.7073 (t80) REVERT: K 60 ASP cc_start: 0.7290 (t0) cc_final: 0.6621 (t0) REVERT: K 77 GLU cc_start: 0.8050 (pt0) cc_final: 0.7710 (pt0) REVERT: K 82 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8517 (mtpt) REVERT: K 109 ASP cc_start: 0.7761 (m-30) cc_final: 0.7475 (t0) REVERT: K 127 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7576 (mt-10) REVERT: K 138 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7124 (mm-30) REVERT: K 156 ASP cc_start: 0.8204 (t0) cc_final: 0.7787 (t0) REVERT: K 158 LEU cc_start: 0.8731 (mp) cc_final: 0.8139 (mp) REVERT: K 159 LYS cc_start: 0.8762 (pttm) cc_final: 0.8485 (pttm) REVERT: K 176 TYR cc_start: 0.8273 (m-80) cc_final: 0.7906 (m-80) REVERT: K 181 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6888 (tm-30) REVERT: K 195 LYS cc_start: 0.8432 (mppt) cc_final: 0.8093 (mppt) REVERT: K 222 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8231 (mmtt) REVERT: K 354 GLU cc_start: 0.7794 (mp0) cc_final: 0.7268 (mp0) REVERT: K 395 ASP cc_start: 0.8015 (m-30) cc_final: 0.7770 (m-30) REVERT: D 61 LYS cc_start: 0.7849 (pptt) cc_final: 0.7155 (ptmm) REVERT: D 270 ASN cc_start: 0.7935 (m110) cc_final: 0.7697 (m110) REVERT: D 320 TYR cc_start: 0.8110 (p90) cc_final: 0.7756 (p90) REVERT: D 321 LYS cc_start: 0.8192 (ptpp) cc_final: 0.7914 (mtmm) REVERT: D 340 LYS cc_start: 0.8833 (ttmm) cc_final: 0.8509 (ttmm) REVERT: D 364 ASN cc_start: 0.8243 (m-40) cc_final: 0.8009 (m-40) REVERT: D 373 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7891 (mmtm) REVERT: D 390 GLU cc_start: 0.7627 (pm20) cc_final: 0.7054 (pm20) REVERT: G 30 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6939 (mm-30) REVERT: G 76 TYR cc_start: 0.8385 (t80) cc_final: 0.7628 (t80) REVERT: G 80 VAL cc_start: 0.8874 (t) cc_final: 0.8566 (m) REVERT: G 174 ASP cc_start: 0.7891 (m-30) cc_final: 0.7337 (m-30) REVERT: G 218 ASP cc_start: 0.8194 (t0) cc_final: 0.7645 (t0) REVERT: G 237 VAL cc_start: 0.8512 (p) cc_final: 0.8292 (m) REVERT: G 241 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7493 (mm-30) REVERT: G 246 ASN cc_start: 0.7647 (t0) cc_final: 0.6997 (t0) REVERT: G 343 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8229 (m) REVERT: G 346 VAL cc_start: 0.7871 (t) cc_final: 0.7484 (m) REVERT: G 404 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7885 (ttmm) REVERT: A 9 ASN cc_start: 0.8068 (p0) cc_final: 0.7767 (p0) REVERT: A 20 GLU cc_start: 0.7532 (tt0) cc_final: 0.7274 (tt0) REVERT: A 107 TYR cc_start: 0.7849 (p90) cc_final: 0.7390 (p90) REVERT: A 117 ASP cc_start: 0.7200 (t0) cc_final: 0.6762 (t0) REVERT: A 186 ASN cc_start: 0.8891 (m-40) cc_final: 0.8633 (m110) REVERT: A 188 ASP cc_start: 0.7985 (t0) cc_final: 0.7694 (t0) REVERT: A 202 ASP cc_start: 0.7472 (p0) cc_final: 0.7235 (p0) REVERT: A 320 TYR cc_start: 0.8101 (p90) cc_final: 0.7137 (p90) REVERT: A 379 GLU cc_start: 0.6432 (tm-30) cc_final: 0.6227 (tt0) REVERT: E 36 ASP cc_start: 0.7536 (p0) cc_final: 0.7255 (p0) REVERT: E 105 CYS cc_start: 0.7468 (m) cc_final: 0.7147 (m) REVERT: E 131 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7856 (mmt-90) REVERT: E 162 SER cc_start: 0.8878 (t) cc_final: 0.8648 (t) REVERT: E 168 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7345 (tmm) REVERT: E 200 GLU cc_start: 0.7343 (tt0) cc_final: 0.6861 (tt0) REVERT: E 254 LYS cc_start: 0.8128 (mttt) cc_final: 0.7866 (mttt) REVERT: E 277 THR cc_start: 0.8552 (m) cc_final: 0.7996 (p) REVERT: E 278 LYS cc_start: 0.8866 (mttm) cc_final: 0.8474 (mtpp) REVERT: E 281 LYS cc_start: 0.7900 (mptt) cc_final: 0.7664 (mptt) REVERT: E 299 LYS cc_start: 0.8405 (mttt) cc_final: 0.8049 (mtpp) REVERT: E 324 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7833 (mt-10) REVERT: E 393 ARG cc_start: 0.5476 (tpt170) cc_final: 0.5029 (tpt170) REVERT: H 25 CYS cc_start: 0.5852 (t) cc_final: 0.5560 (t) REVERT: H 60 ASP cc_start: 0.7968 (t0) cc_final: 0.7431 (t0) REVERT: H 80 MET cc_start: 0.8841 (tpp) cc_final: 0.8593 (tpp) REVERT: H 131 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7529 (mmt-90) REVERT: H 141 LEU cc_start: 0.8341 (mt) cc_final: 0.8080 (mt) REVERT: H 224 LYS cc_start: 0.8276 (ptmm) cc_final: 0.7956 (ptmm) REVERT: H 347 ASP cc_start: 0.7496 (t0) cc_final: 0.6864 (t0) REVERT: H 394 ARG cc_start: 0.7954 (mtm-85) cc_final: 0.7753 (ttp-110) REVERT: B 18 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.6552 (m-80) REVERT: B 67 MET cc_start: 0.7154 (mmm) cc_final: 0.6684 (mmm) REVERT: B 76 LYS cc_start: 0.7964 (tppp) cc_final: 0.7531 (tppp) REVERT: B 134 PHE cc_start: 0.8598 (p90) cc_final: 0.8251 (p90) REVERT: B 140 TYR cc_start: 0.8444 (p90) cc_final: 0.8048 (p90) REVERT: B 206 TYR cc_start: 0.7675 (t80) cc_final: 0.7248 (t80) REVERT: B 225 GLN cc_start: 0.6437 (tm-30) cc_final: 0.5816 (tm-30) REVERT: B 239 ASN cc_start: 0.7506 (p0) cc_final: 0.7286 (t0) REVERT: B 272 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7522 (t-90) REVERT: B 281 LYS cc_start: 0.8458 (mttt) cc_final: 0.8201 (mttt) REVERT: B 354 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7555 (mt-10) REVERT: F 56 LYS cc_start: 0.8374 (ptpp) cc_final: 0.8054 (ptpp) REVERT: F 97 TYR cc_start: 0.5647 (m-80) cc_final: 0.5368 (m-80) REVERT: F 111 LYS cc_start: 0.8717 (mttt) cc_final: 0.8380 (mttt) REVERT: F 116 ARG cc_start: 0.8408 (mtp180) cc_final: 0.8127 (mtp85) REVERT: I 8 MET cc_start: 0.7942 (mmm) cc_final: 0.7626 (mmm) REVERT: I 49 GLN cc_start: 0.7763 (tm-30) cc_final: 0.7469 (tm-30) REVERT: I 111 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8436 (mtpp) REVERT: I 128 ILE cc_start: 0.8973 (mp) cc_final: 0.8753 (mm) REVERT: C 37 LYS cc_start: 0.8571 (tmmt) cc_final: 0.8212 (tmmt) REVERT: C 106 ARG cc_start: 0.8263 (ppt170) cc_final: 0.8007 (ppt170) outliers start: 174 outliers final: 144 residues processed: 1252 average time/residue: 0.4779 time to fit residues: 917.2164 Evaluate side-chains 1320 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1171 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 372 LYS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 256 HIS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 188 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 19 optimal weight: 0.0050 chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS L 78 GLN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 230 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 386 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS F 47 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3757 r_free = 0.3757 target = 0.142022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125179 restraints weight = 55559.958| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.89 r_work: 0.3373 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31760 Z= 0.139 Angle : 0.705 17.883 43289 Z= 0.353 Chirality : 0.047 0.290 4873 Planarity : 0.005 0.055 5520 Dihedral : 5.528 78.068 4563 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.78 % Favored : 94.17 % Rotamer: Outliers : 4.56 % Allowed : 22.19 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.03 (0.13), residues: 3963 helix: 2.12 (0.24), residues: 405 sheet: -0.43 (0.16), residues: 1111 loop : -1.34 (0.12), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 279 HIS 0.011 0.001 HIS D 230 PHE 0.037 0.002 PHE C 16 TYR 0.031 0.001 TYR A 308 ARG 0.015 0.001 ARG E 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.44441 ( 36) hydrogen bonds : bond 0.03131 ( 1026) hydrogen bonds : angle 5.30255 ( 2733) SS BOND : bond 0.00512 ( 56) SS BOND : angle 2.11401 ( 112) covalent geometry : bond 0.00322 (31692) covalent geometry : angle 0.69657 (43141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1177 time to evaluate : 4.323 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: 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: J 9 ASN cc_start: 0.8260 (t0) cc_final: 0.7809 (t0) REVERT: J 49 CYS cc_start: 0.7603 (p) cc_final: 0.7299 (p) REVERT: J 50 LYS cc_start: 0.8254 (tttm) cc_final: 0.7958 (tttm) REVERT: J 61 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7469 (ttpt) REVERT: J 63 CYS cc_start: 0.5953 (OUTLIER) cc_final: 0.5678 (m) REVERT: J 96 CYS cc_start: 0.6208 (t) cc_final: 0.5571 (t) REVERT: J 99 GLU cc_start: 0.7198 (tt0) cc_final: 0.6338 (tt0) REVERT: J 101 THR cc_start: 0.7938 (m) cc_final: 0.7647 (m) REVERT: J 130 LYS cc_start: 0.7775 (tttp) cc_final: 0.7558 (tttp) REVERT: J 134 ARG cc_start: 0.8129 (ttm-80) cc_final: 0.7707 (ttm-80) REVERT: J 176 LYS cc_start: 0.8499 (mttt) cc_final: 0.8264 (mttt) REVERT: J 180 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8184 (ttt-90) REVERT: J 181 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8819 (mtpp) REVERT: J 191 GLU cc_start: 0.4414 (tt0) cc_final: 0.3653 (mt-10) REVERT: J 234 THR cc_start: 0.7954 (p) cc_final: 0.7711 (t) REVERT: J 282 ILE cc_start: 0.8608 (mt) cc_final: 0.8183 (tp) REVERT: J 289 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7603 (mtt90) REVERT: J 381 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7896 (mtmm) REVERT: K 4 ASP cc_start: 0.7534 (t0) cc_final: 0.7331 (t0) REVERT: K 7 THR cc_start: 0.8552 (t) cc_final: 0.8279 (p) REVERT: K 18 TYR cc_start: 0.7692 (t80) cc_final: 0.6886 (t80) REVERT: K 60 ASP cc_start: 0.7227 (t0) cc_final: 0.6559 (t0) REVERT: K 77 GLU cc_start: 0.8086 (pt0) cc_final: 0.7747 (pt0) REVERT: K 82 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8467 (mtpt) REVERT: K 109 ASP cc_start: 0.7700 (m-30) cc_final: 0.7449 (t0) REVERT: K 138 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7042 (mm-30) REVERT: K 156 ASP cc_start: 0.8185 (t0) cc_final: 0.7778 (t0) REVERT: K 158 LEU cc_start: 0.8712 (mp) cc_final: 0.8096 (mp) REVERT: K 159 LYS cc_start: 0.8752 (pttm) cc_final: 0.8482 (pttm) REVERT: K 176 TYR cc_start: 0.8260 (m-80) cc_final: 0.7912 (m-80) REVERT: K 181 GLU cc_start: 0.7356 (tm-30) cc_final: 0.6865 (tm-30) REVERT: K 195 LYS cc_start: 0.8403 (mppt) cc_final: 0.8057 (mppt) REVERT: K 222 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8177 (mmtt) REVERT: K 353 HIS cc_start: 0.7351 (p90) cc_final: 0.6913 (p-80) REVERT: K 354 GLU cc_start: 0.7700 (mp0) cc_final: 0.7004 (mp0) REVERT: K 395 ASP cc_start: 0.7969 (m-30) cc_final: 0.7735 (m-30) REVERT: D 61 LYS cc_start: 0.7739 (pptt) cc_final: 0.6955 (ptmm) REVERT: D 270 ASN cc_start: 0.7903 (m110) cc_final: 0.7654 (m110) REVERT: D 320 TYR cc_start: 0.7984 (p90) cc_final: 0.7713 (p90) REVERT: D 321 LYS cc_start: 0.8037 (ptpp) cc_final: 0.7714 (mtmm) REVERT: D 373 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7879 (mmtm) REVERT: D 390 GLU cc_start: 0.7566 (pm20) cc_final: 0.6989 (pm20) REVERT: G 30 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6957 (mm-30) REVERT: G 76 TYR cc_start: 0.8363 (t80) cc_final: 0.7740 (t80) REVERT: G 80 VAL cc_start: 0.8816 (t) cc_final: 0.8497 (m) REVERT: G 174 ASP cc_start: 0.7876 (m-30) cc_final: 0.7305 (m-30) REVERT: G 218 ASP cc_start: 0.8129 (t0) cc_final: 0.7578 (t0) REVERT: G 237 VAL cc_start: 0.8549 (p) cc_final: 0.8320 (m) REVERT: G 241 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7514 (mm-30) REVERT: G 246 ASN cc_start: 0.7699 (t0) cc_final: 0.7028 (t0) REVERT: G 343 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8196 (m) REVERT: G 346 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7515 (m) REVERT: G 404 LYS cc_start: 0.8103 (ttmm) cc_final: 0.7831 (ttmm) REVERT: A 9 ASN cc_start: 0.7689 (p0) cc_final: 0.7183 (p0) REVERT: A 20 GLU cc_start: 0.7451 (tt0) cc_final: 0.7177 (tt0) REVERT: A 107 TYR cc_start: 0.7737 (p90) cc_final: 0.7177 (p90) REVERT: A 117 ASP cc_start: 0.7163 (t0) cc_final: 0.6707 (t0) REVERT: A 186 ASN cc_start: 0.8883 (m-40) cc_final: 0.8612 (m110) REVERT: A 188 ASP cc_start: 0.7936 (t0) cc_final: 0.7660 (t0) REVERT: A 217 THR cc_start: 0.8577 (t) cc_final: 0.8322 (p) REVERT: A 234 THR cc_start: 0.7904 (m) cc_final: 0.7689 (m) REVERT: A 249 ARG cc_start: 0.8692 (mmp-170) cc_final: 0.8425 (mmp80) REVERT: E 36 ASP cc_start: 0.7543 (p0) cc_final: 0.7252 (p0) REVERT: E 131 ARG cc_start: 0.8093 (mmt90) cc_final: 0.7846 (mmt180) REVERT: E 162 SER cc_start: 0.8864 (t) cc_final: 0.8650 (t) REVERT: E 168 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7207 (tmm) REVERT: E 200 GLU cc_start: 0.7326 (tt0) cc_final: 0.6882 (tt0) REVERT: E 254 LYS cc_start: 0.8175 (mttt) cc_final: 0.7910 (mttt) REVERT: E 277 THR cc_start: 0.8539 (m) cc_final: 0.8008 (p) REVERT: E 278 LYS cc_start: 0.8776 (mttm) cc_final: 0.8354 (mtpp) REVERT: E 299 LYS cc_start: 0.8391 (mttt) cc_final: 0.8035 (mtpp) REVERT: E 324 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7697 (mt-10) REVERT: E 393 ARG cc_start: 0.5243 (tpt170) cc_final: 0.4676 (tpt170) REVERT: H 25 CYS cc_start: 0.5540 (t) cc_final: 0.5227 (t) REVERT: H 60 ASP cc_start: 0.7930 (t0) cc_final: 0.7433 (t0) REVERT: H 76 LYS cc_start: 0.7650 (ttmm) cc_final: 0.7410 (ttmt) REVERT: H 80 MET cc_start: 0.8803 (tpp) cc_final: 0.8570 (tpp) REVERT: H 141 LEU cc_start: 0.8333 (mt) cc_final: 0.8064 (mt) REVERT: H 179 TYR cc_start: 0.7622 (m-10) cc_final: 0.7395 (m-10) REVERT: H 224 LYS cc_start: 0.8248 (ptmm) cc_final: 0.7949 (ptmm) REVERT: H 347 ASP cc_start: 0.7477 (t0) cc_final: 0.6837 (t0) REVERT: H 393 ARG cc_start: 0.6154 (tpt170) cc_final: 0.5633 (tpt170) REVERT: H 397 LEU cc_start: 0.8369 (mm) cc_final: 0.8084 (mm) REVERT: B 18 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: B 67 MET cc_start: 0.7017 (mmm) cc_final: 0.6467 (mmm) REVERT: B 76 LYS cc_start: 0.7989 (tppp) cc_final: 0.7560 (tppp) REVERT: B 77 GLU cc_start: 0.7675 (tt0) cc_final: 0.7346 (tp30) REVERT: B 140 TYR cc_start: 0.8410 (p90) cc_final: 0.8012 (p90) REVERT: B 206 TYR cc_start: 0.7633 (t80) cc_final: 0.7214 (t80) REVERT: B 225 GLN cc_start: 0.6545 (tm-30) cc_final: 0.5865 (tm-30) REVERT: B 272 HIS cc_start: 0.8135 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: B 281 LYS cc_start: 0.8405 (mttt) cc_final: 0.8071 (mttt) REVERT: B 342 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6671 (pm20) REVERT: B 354 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7515 (mt-10) REVERT: F 56 LYS cc_start: 0.8332 (ptpp) cc_final: 0.8019 (ptpp) REVERT: F 72 MET cc_start: 0.5458 (mtm) cc_final: 0.5094 (mtp) REVERT: F 97 TYR cc_start: 0.5489 (m-80) cc_final: 0.5074 (m-80) REVERT: F 111 LYS cc_start: 0.8589 (mttt) cc_final: 0.8286 (mttt) REVERT: F 116 ARG cc_start: 0.8299 (mtp180) cc_final: 0.8082 (mtp85) REVERT: I 8 MET cc_start: 0.7824 (mmm) cc_final: 0.7478 (mmm) REVERT: I 14 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7572 (mmtp) REVERT: I 25 ASN cc_start: 0.7074 (t0) cc_final: 0.6532 (t0) REVERT: I 49 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7457 (tm-30) REVERT: I 111 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8372 (mtpp) REVERT: I 143 VAL cc_start: 0.8424 (p) cc_final: 0.8174 (m) REVERT: C 37 LYS cc_start: 0.8423 (tmmt) cc_final: 0.7805 (tmmt) REVERT: C 55 LEU cc_start: 0.7908 (mm) cc_final: 0.7362 (mt) REVERT: C 64 GLU cc_start: 0.7076 (tt0) cc_final: 0.5934 (tt0) REVERT: C 106 ARG cc_start: 0.8282 (ppt170) cc_final: 0.8031 (ppt170) outliers start: 154 outliers final: 127 residues processed: 1246 average time/residue: 0.4739 time to fit residues: 903.9463 Evaluate side-chains 1289 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1155 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 78 GLN Chi-restraints excluded: chain L residue 83 LYS Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 192 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 364 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 369 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS L 78 GLN ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 386 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3708 r_free = 0.3708 target = 0.133779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117224 restraints weight = 55736.739| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.83 r_work: 0.3369 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31760 Z= 0.248 Angle : 0.761 18.695 43289 Z= 0.383 Chirality : 0.050 0.332 4873 Planarity : 0.005 0.056 5520 Dihedral : 5.702 75.964 4563 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.17 % Favored : 92.78 % Rotamer: Outliers : 4.41 % Allowed : 22.63 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.14 (0.13), residues: 3963 helix: 2.19 (0.24), residues: 400 sheet: -0.55 (0.15), residues: 1221 loop : -1.44 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 279 HIS 0.009 0.001 HIS H 96 PHE 0.031 0.002 PHE C 16 TYR 0.035 0.002 TYR C 27 ARG 0.012 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 12) link_NAG-ASN : angle 1.78232 ( 36) hydrogen bonds : bond 0.03501 ( 1026) hydrogen bonds : angle 5.36580 ( 2733) SS BOND : bond 0.00633 ( 56) SS BOND : angle 2.62504 ( 112) covalent geometry : bond 0.00552 (31692) covalent geometry : angle 0.74870 (43141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1160 time to evaluate : 3.142 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8338 (t0) cc_final: 0.7840 (t0) REVERT: J 49 CYS cc_start: 0.7585 (p) cc_final: 0.7319 (p) REVERT: J 50 LYS cc_start: 0.8259 (tttm) cc_final: 0.7990 (tttm) REVERT: J 61 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7565 (ttpp) REVERT: J 63 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5917 (m) REVERT: J 96 CYS cc_start: 0.6338 (t) cc_final: 0.5748 (t) REVERT: J 99 GLU cc_start: 0.7252 (tt0) cc_final: 0.6360 (tt0) REVERT: J 101 THR cc_start: 0.7979 (m) cc_final: 0.7673 (m) REVERT: J 130 LYS cc_start: 0.7956 (tttp) cc_final: 0.7739 (tttp) REVERT: J 176 LYS cc_start: 0.8548 (mttt) cc_final: 0.8344 (mttt) REVERT: J 180 ARG cc_start: 0.8598 (ttt-90) cc_final: 0.8216 (ttt-90) REVERT: J 191 GLU cc_start: 0.4747 (tt0) cc_final: 0.4014 (mt-10) REVERT: J 289 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7535 (mtt90) REVERT: K 7 THR cc_start: 0.8508 (t) cc_final: 0.8222 (p) REVERT: K 18 TYR cc_start: 0.7800 (t80) cc_final: 0.7025 (t80) REVERT: K 60 ASP cc_start: 0.7291 (t0) cc_final: 0.6625 (t0) REVERT: K 77 GLU cc_start: 0.8053 (pt0) cc_final: 0.7718 (pt0) REVERT: K 82 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8486 (mtpt) REVERT: K 109 ASP cc_start: 0.7731 (m-30) cc_final: 0.7464 (t0) REVERT: K 138 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7088 (mm-30) REVERT: K 156 ASP cc_start: 0.8144 (t0) cc_final: 0.7770 (t0) REVERT: K 158 LEU cc_start: 0.8786 (mp) cc_final: 0.8235 (mp) REVERT: K 159 LYS cc_start: 0.8714 (pttm) cc_final: 0.8451 (pttm) REVERT: K 176 TYR cc_start: 0.8273 (m-80) cc_final: 0.7919 (m-80) REVERT: K 181 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6907 (tm-30) REVERT: K 195 LYS cc_start: 0.8458 (mppt) cc_final: 0.8126 (mppt) REVERT: K 222 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8203 (mmtt) REVERT: K 354 GLU cc_start: 0.7705 (mp0) cc_final: 0.7126 (mp0) REVERT: K 395 ASP cc_start: 0.8059 (m-30) cc_final: 0.7831 (m-30) REVERT: D 61 LYS cc_start: 0.7867 (pptt) cc_final: 0.7070 (ptmm) REVERT: D 189 PHE cc_start: 0.8671 (p90) cc_final: 0.8324 (p90) REVERT: D 270 ASN cc_start: 0.7992 (m110) cc_final: 0.7718 (m110) REVERT: D 320 TYR cc_start: 0.8081 (p90) cc_final: 0.7524 (p90) REVERT: D 321 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7837 (mtmm) REVERT: D 373 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7872 (mmtm) REVERT: D 390 GLU cc_start: 0.7597 (pm20) cc_final: 0.7046 (pm20) REVERT: G 30 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6920 (mm-30) REVERT: G 76 TYR cc_start: 0.8328 (t80) cc_final: 0.7648 (t80) REVERT: G 80 VAL cc_start: 0.8833 (t) cc_final: 0.8540 (m) REVERT: G 174 ASP cc_start: 0.7916 (m-30) cc_final: 0.7343 (m-30) REVERT: G 218 ASP cc_start: 0.8160 (t0) cc_final: 0.7614 (t0) REVERT: G 237 VAL cc_start: 0.8516 (p) cc_final: 0.8294 (m) REVERT: G 241 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7459 (mm-30) REVERT: G 246 ASN cc_start: 0.7644 (t0) cc_final: 0.6987 (t0) REVERT: G 343 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8228 (m) REVERT: G 346 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7413 (m) REVERT: G 404 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7885 (ttmm) REVERT: A 9 ASN cc_start: 0.7977 (p0) cc_final: 0.7686 (p0) REVERT: A 20 GLU cc_start: 0.7489 (tt0) cc_final: 0.7221 (tt0) REVERT: A 107 TYR cc_start: 0.7847 (p90) cc_final: 0.7411 (p90) REVERT: A 117 ASP cc_start: 0.7106 (t0) cc_final: 0.6651 (t0) REVERT: A 186 ASN cc_start: 0.8867 (m-40) cc_final: 0.8607 (m110) REVERT: A 188 ASP cc_start: 0.7879 (t0) cc_final: 0.7619 (t0) REVERT: E 36 ASP cc_start: 0.7516 (p0) cc_final: 0.7224 (p0) REVERT: E 131 ARG cc_start: 0.8061 (mmt90) cc_final: 0.7737 (mmt180) REVERT: E 162 SER cc_start: 0.8820 (t) cc_final: 0.8607 (t) REVERT: E 168 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7315 (tmm) REVERT: E 200 GLU cc_start: 0.7281 (tt0) cc_final: 0.6809 (tt0) REVERT: E 254 LYS cc_start: 0.8118 (mttt) cc_final: 0.7861 (mttt) REVERT: E 277 THR cc_start: 0.8560 (m) cc_final: 0.8071 (p) REVERT: E 278 LYS cc_start: 0.8786 (mttm) cc_final: 0.8521 (mtpp) REVERT: E 299 LYS cc_start: 0.8419 (mttt) cc_final: 0.8083 (mtpp) REVERT: E 324 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7765 (mt-10) REVERT: E 393 ARG cc_start: 0.5384 (tpt170) cc_final: 0.4939 (tpt170) REVERT: H 25 CYS cc_start: 0.5807 (t) cc_final: 0.5507 (t) REVERT: H 60 ASP cc_start: 0.7965 (t0) cc_final: 0.7450 (t0) REVERT: H 65 ARG cc_start: 0.8707 (ptm-80) cc_final: 0.8058 (ptm-80) REVERT: H 80 MET cc_start: 0.8855 (tpp) cc_final: 0.8604 (tpp) REVERT: H 131 ARG cc_start: 0.8036 (mmt-90) cc_final: 0.7532 (mmt-90) REVERT: H 141 LEU cc_start: 0.8421 (mt) cc_final: 0.8203 (mt) REVERT: H 224 LYS cc_start: 0.8269 (ptmm) cc_final: 0.7997 (ptmm) REVERT: H 347 ASP cc_start: 0.7474 (t0) cc_final: 0.6848 (t0) REVERT: B 18 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: B 36 ASP cc_start: 0.7794 (p0) cc_final: 0.7523 (p0) REVERT: B 67 MET cc_start: 0.7071 (mmm) cc_final: 0.6532 (mmm) REVERT: B 76 LYS cc_start: 0.7989 (tppp) cc_final: 0.7577 (tppp) REVERT: B 77 GLU cc_start: 0.7766 (tt0) cc_final: 0.7513 (tt0) REVERT: B 134 PHE cc_start: 0.8568 (p90) cc_final: 0.8175 (p90) REVERT: B 140 TYR cc_start: 0.8477 (p90) cc_final: 0.8072 (p90) REVERT: B 206 TYR cc_start: 0.7443 (t80) cc_final: 0.7041 (t80) REVERT: B 225 GLN cc_start: 0.6581 (tm-30) cc_final: 0.5895 (tm-30) REVERT: B 239 ASN cc_start: 0.7541 (p0) cc_final: 0.7334 (t0) REVERT: B 272 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: B 281 LYS cc_start: 0.8452 (mttt) cc_final: 0.8188 (mttt) REVERT: B 342 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6670 (pm20) REVERT: B 354 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7540 (mt-10) REVERT: F 56 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7971 (ptpp) REVERT: F 97 TYR cc_start: 0.5728 (m-80) cc_final: 0.5286 (m-80) REVERT: F 111 LYS cc_start: 0.8604 (mttt) cc_final: 0.8308 (mttt) REVERT: F 116 ARG cc_start: 0.8312 (mtp180) cc_final: 0.8057 (mtp85) REVERT: I 8 MET cc_start: 0.7975 (mmm) cc_final: 0.7608 (mmm) REVERT: I 14 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7509 (mmtp) REVERT: I 49 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 37 LYS cc_start: 0.8602 (tmmt) cc_final: 0.7966 (tmmt) REVERT: C 55 LEU cc_start: 0.8087 (mm) cc_final: 0.7758 (mm) REVERT: C 64 GLU cc_start: 0.7306 (tt0) cc_final: 0.6153 (tt0) REVERT: C 106 ARG cc_start: 0.7921 (ppt170) cc_final: 0.7716 (ppt170) outliers start: 149 outliers final: 129 residues processed: 1223 average time/residue: 0.4590 time to fit residues: 855.1678 Evaluate side-chains 1289 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1153 time to evaluate : 3.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 83 LYS Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 LYS Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 386 HIS Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 256 HIS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 6 MET Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 321 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 193 optimal weight: 10.0000 chunk 174 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 363 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 329 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 386 HIS E 50 GLN ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.135558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.118985 restraints weight = 55768.527| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.84 r_work: 0.3366 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31760 Z= 0.166 Angle : 0.735 18.048 43289 Z= 0.368 Chirality : 0.048 0.301 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.598 77.536 4563 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 4.18 % Allowed : 23.13 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.09 (0.13), residues: 3963 helix: 2.07 (0.24), residues: 405 sheet: -0.56 (0.15), residues: 1162 loop : -1.34 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 279 HIS 0.016 0.001 HIS A 386 PHE 0.032 0.002 PHE C 16 TYR 0.031 0.002 TYR C 27 ARG 0.012 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 12) link_NAG-ASN : angle 1.53423 ( 36) hydrogen bonds : bond 0.03259 ( 1026) hydrogen bonds : angle 5.27949 ( 2733) SS BOND : bond 0.00531 ( 56) SS BOND : angle 2.40772 ( 112) covalent geometry : bond 0.00381 (31692) covalent geometry : angle 0.72463 (43141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19569.75 seconds wall clock time: 338 minutes 55.79 seconds (20335.79 seconds total)