Starting phenix.real_space_refine on Mon Aug 25 20:47:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqx_47117/08_2025/9dqx_47117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqx_47117/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9dqx_47117/08_2025/9dqx_47117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqx_47117/08_2025/9dqx_47117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dqx_47117/08_2025/9dqx_47117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqx_47117/08_2025/9dqx_47117.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.41, per 1000 atoms: 0.21 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: 2.17 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.25 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: 5.57 Time building geometry restraints manager: 3.00 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 502)) selection = (chain 'E' and (resid 1 through 117 or resid 120 through 502)) selection = (chain 'H' and (resid 1 through 117 or resid 120 through 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.280 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.730 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.015 0.001 ARG F 124 TYR 0.029 0.002 TYR C 27 PHE 0.044 0.002 PHE E 280 TRP 0.060 0.002 TRP A 409 HIS 0.019 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00370 (31692) covalent geometry : angle 0.87224 (43141) SS BOND : bond 0.00441 ( 56) SS BOND : angle 2.14381 ( 112) hydrogen bonds : bond 0.12398 ( 1026) hydrogen bonds : angle 6.96231 ( 2733) link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 1.81443 ( 36) *********************** 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 : 1.176 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: 0.7810 (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: 0.7824 (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: 0.7392 (mmt-90) 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: 0.7812 (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: 0.7625 (mtt90) REVERT: J 318 LEU cc_start: 0.7676 (tp) cc_final: 0.7376 (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: 0.5386 (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: 0.7724 (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: 0.7753 (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: 0.8056 (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: 0.7760 (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: 0.7119 (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: 0.4424 (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: 0.6499 (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: 0.1922 time to fit residues: 371.5941 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 : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 overall best weight: 2.1542 ------------------------------------------------------------------------------- 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 ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS D 196 ASN D 228 ASN D 319 GLN D 327 HIS D 386 HIS G 59 GLN G 175 HIS A 43 ASN A 100 ASN A 139 ASN A 246 ASN E 218 ASN H 174 HIS H 218 ASN H 256 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 96 HIS B 153 HIS B 157 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.146833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130981 restraints weight = 54094.423| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.96 r_work: 0.3449 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31760 Z= 0.162 Angle : 0.660 16.693 43289 Z= 0.336 Chirality : 0.047 0.239 4873 Planarity : 0.005 0.069 5520 Dihedral : 6.081 76.668 4563 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 2.37 % Allowed : 11.02 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.13), residues: 3963 helix: 1.54 (0.24), residues: 420 sheet: -0.30 (0.16), residues: 1105 loop : -1.37 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 34 TYR 0.029 0.002 TYR A 308 PHE 0.021 0.002 PHE K 134 TRP 0.027 0.001 TRP B 279 HIS 0.011 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00356 (31692) covalent geometry : angle 0.65383 (43141) SS BOND : bond 0.00633 ( 56) SS BOND : angle 1.77076 ( 112) hydrogen bonds : bond 0.03442 ( 1026) hydrogen bonds : angle 5.60031 ( 2733) link_NAG-ASN : bond 0.00252 ( 12) link_NAG-ASN : angle 1.58275 ( 36) *********************** 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 1293 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1213 time to evaluate : 1.219 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: J 9 ASN cc_start: 0.8370 (t0) cc_final: 0.7886 (t0) REVERT: J 24 TYR cc_start: 0.6785 (m-80) cc_final: 0.6360 (m-80) REVERT: J 49 CYS cc_start: 0.7695 (p) cc_final: 0.7412 (p) REVERT: J 61 LYS cc_start: 0.7983 (tmmt) cc_final: 0.7411 (ttpt) REVERT: J 75 ASP cc_start: 0.7812 (t0) cc_final: 0.7590 (t0) REVERT: J 130 LYS cc_start: 0.7891 (tttp) cc_final: 0.7624 (tppt) REVERT: J 180 ARG cc_start: 0.8451 (ttt-90) cc_final: 0.8222 (ttt-90) REVERT: J 234 THR cc_start: 0.7902 (p) cc_final: 0.7675 (t) REVERT: J 289 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7667 (mtt90) REVERT: J 318 LEU cc_start: 0.7593 (tp) cc_final: 0.7103 (tp) REVERT: J 319 GLN cc_start: 0.7348 (tp40) cc_final: 0.7131 (tp40) REVERT: J 395 ASP cc_start: 0.7452 (t0) cc_final: 0.7144 (t0) REVERT: K 4 ASP cc_start: 0.7465 (t0) cc_final: 0.7249 (t0) REVERT: K 6 PHE cc_start: 0.8088 (m-80) cc_final: 0.7602 (m-80) REVERT: K 7 THR cc_start: 0.8497 (t) cc_final: 0.8203 (p) REVERT: K 25 CYS cc_start: 0.6070 (t) cc_final: 0.5678 (t) REVERT: K 37 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7545 (mm-30) REVERT: K 55 GLN cc_start: 0.8453 (tt0) cc_final: 0.8219 (tt0) REVERT: K 60 ASP cc_start: 0.7189 (t0) cc_final: 0.6750 (t0) REVERT: K 77 GLU cc_start: 0.8042 (pt0) cc_final: 0.7668 (pt0) REVERT: K 127 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7328 (mm-30) REVERT: K 152 CYS cc_start: 0.7236 (p) cc_final: 0.6804 (p) REVERT: K 159 LYS cc_start: 0.8746 (pttm) cc_final: 0.8466 (pttm) REVERT: K 181 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6588 (tm-30) REVERT: K 195 LYS cc_start: 0.8434 (mppt) cc_final: 0.8182 (mppt) REVERT: K 222 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8286 (mmtt) REVERT: K 254 LYS cc_start: 0.8260 (mtmm) cc_final: 0.8015 (mttm) REVERT: K 324 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7627 (mt-10) REVERT: K 391 LYS cc_start: 0.8818 (tttm) cc_final: 0.8332 (tttm) REVERT: K 395 ASP cc_start: 0.8173 (m-30) cc_final: 0.7736 (m-30) REVERT: L 19 MET cc_start: 0.6814 (mmp) cc_final: 0.6609 (mmp) REVERT: L 57 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7946 (mtmm) REVERT: L 80 THR cc_start: 0.8170 (t) cc_final: 0.7895 (m) REVERT: D 61 LYS cc_start: 0.7596 (pptt) cc_final: 0.7345 (ptmm) REVERT: D 76 TYR cc_start: 0.8016 (t80) cc_final: 0.7685 (t80) REVERT: D 99 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6134 (tm-30) REVERT: D 160 LYS cc_start: 0.8086 (tmmt) cc_final: 0.7691 (tmmt) REVERT: D 230 HIS cc_start: 0.7908 (t70) cc_final: 0.7687 (t70) REVERT: D 249 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8128 (mmm160) REVERT: D 307 ILE cc_start: 0.7628 (mt) cc_final: 0.7373 (mm) REVERT: D 320 TYR cc_start: 0.7601 (p90) cc_final: 0.7335 (p90) REVERT: D 365 PHE cc_start: 0.8282 (p90) cc_final: 0.7926 (p90) REVERT: D 388 ILE cc_start: 0.8526 (tp) cc_final: 0.8139 (mm) REVERT: D 430 CYS cc_start: 0.8223 (p) cc_final: 0.8021 (p) REVERT: G 15 TYR cc_start: 0.7867 (t80) cc_final: 0.7516 (t80) REVERT: G 76 TYR cc_start: 0.8233 (t80) cc_final: 0.7463 (t80) REVERT: G 81 PHE cc_start: 0.7414 (m-10) cc_final: 0.7139 (m-10) REVERT: G 105 GLU cc_start: 0.7344 (tt0) cc_final: 0.6905 (tt0) REVERT: G 174 ASP cc_start: 0.8022 (m-30) cc_final: 0.7646 (m-30) REVERT: G 218 ASP cc_start: 0.8133 (t0) cc_final: 0.7615 (t0) REVERT: G 241 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7641 (mm-30) REVERT: G 246 ASN cc_start: 0.7604 (t0) cc_final: 0.7266 (t0) REVERT: G 264 GLU cc_start: 0.7550 (mp0) cc_final: 0.7107 (mp0) REVERT: G 341 GLU cc_start: 0.7448 (mp0) cc_final: 0.7087 (mp0) REVERT: G 343 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8113 (m) REVERT: G 404 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7939 (ttmm) REVERT: A 50 LYS cc_start: 0.8085 (tttp) cc_final: 0.7720 (ttpp) REVERT: A 88 MET cc_start: 0.7679 (mtp) cc_final: 0.7460 (mtp) REVERT: A 136 VAL cc_start: 0.8502 (p) cc_final: 0.8157 (m) REVERT: A 202 ASP cc_start: 0.7513 (p0) cc_final: 0.7236 (p0) REVERT: A 263 VAL cc_start: 0.8186 (m) cc_final: 0.7951 (p) REVERT: A 298 GLU cc_start: 0.6930 (tp30) cc_final: 0.6562 (tp30) REVERT: A 320 TYR cc_start: 0.8009 (p90) cc_final: 0.7012 (p90) REVERT: A 323 ASN cc_start: 0.8490 (p0) cc_final: 0.8229 (p0) REVERT: A 387 ILE cc_start: 0.7989 (mm) cc_final: 0.7735 (mm) REVERT: A 388 ILE cc_start: 0.8233 (tp) cc_final: 0.7872 (tp) REVERT: A 430 CYS cc_start: 0.8502 (m) cc_final: 0.8226 (m) REVERT: E 36 ASP cc_start: 0.7655 (p0) cc_final: 0.7306 (p0) REVERT: E 51 PHE cc_start: 0.7894 (m-80) cc_final: 0.7636 (m-80) REVERT: E 76 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8165 (mmtt) REVERT: E 129 LYS cc_start: 0.8505 (tppt) cc_final: 0.8081 (tppt) REVERT: E 131 ARG cc_start: 0.7970 (mmt90) cc_final: 0.7505 (mmt180) REVERT: E 139 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7303 (mt-10) REVERT: E 162 SER cc_start: 0.8828 (t) cc_final: 0.8618 (t) REVERT: E 168 MET cc_start: 0.7482 (tmm) cc_final: 0.7242 (tmm) REVERT: E 169 HIS cc_start: 0.7776 (m-70) cc_final: 0.7437 (m170) REVERT: E 229 TYR cc_start: 0.7561 (p90) cc_final: 0.7207 (p90) REVERT: E 254 LYS cc_start: 0.8162 (mttt) cc_final: 0.7794 (mttm) REVERT: E 393 ARG cc_start: 0.5213 (tpt170) cc_final: 0.4508 (tpt170) REVERT: E 394 ARG cc_start: 0.7697 (ptm-80) cc_final: 0.7461 (ptm-80) REVERT: H 60 ASP cc_start: 0.7849 (t0) cc_final: 0.7345 (t0) REVERT: H 105 CYS cc_start: 0.6766 (m) cc_final: 0.6549 (m) REVERT: H 131 ARG cc_start: 0.8072 (mmt-90) cc_final: 0.7565 (mmt-90) REVERT: H 141 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7605 (mt) REVERT: H 159 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8450 (ptpp) REVERT: H 179 TYR cc_start: 0.7712 (m-10) cc_final: 0.7322 (m-10) REVERT: H 347 ASP cc_start: 0.7587 (t0) cc_final: 0.6937 (t0) REVERT: H 393 ARG cc_start: 0.5776 (tpt170) cc_final: 0.5188 (tpt170) REVERT: B 76 LYS cc_start: 0.7958 (tppp) cc_final: 0.7534 (tppp) REVERT: B 97 LYS cc_start: 0.8006 (tttp) cc_final: 0.7772 (tttp) REVERT: B 159 LYS cc_start: 0.8450 (ptpt) cc_final: 0.8091 (ptpt) REVERT: B 224 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7171 (tmtt) REVERT: B 254 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7356 (mtpt) REVERT: B 265 VAL cc_start: 0.8924 (t) cc_final: 0.8483 (p) REVERT: B 281 LYS cc_start: 0.8317 (mttt) cc_final: 0.7938 (mttt) REVERT: B 300 LEU cc_start: 0.8685 (mp) cc_final: 0.8461 (mt) REVERT: B 354 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 391 LYS cc_start: 0.8778 (tttm) cc_final: 0.8572 (tttm) REVERT: F 8 MET cc_start: 0.7522 (mmp) cc_final: 0.7229 (mmp) REVERT: F 19 MET cc_start: 0.6682 (mmp) cc_final: 0.6147 (mmm) REVERT: F 44 LYS cc_start: 0.7614 (pptt) cc_final: 0.7316 (pptt) REVERT: F 56 LYS cc_start: 0.8233 (ptpp) cc_final: 0.7868 (ptpp) REVERT: F 60 MET cc_start: 0.7934 (mmt) cc_final: 0.7686 (mmt) REVERT: F 101 ARG cc_start: 0.7318 (ttt180) cc_final: 0.6944 (ttt180) REVERT: F 143 VAL cc_start: 0.8339 (t) cc_final: 0.7961 (t) REVERT: I 25 ASN cc_start: 0.7035 (t0) cc_final: 0.6544 (t0) REVERT: I 42 GLU cc_start: 0.7919 (pm20) cc_final: 0.7656 (mp0) REVERT: I 44 LYS cc_start: 0.7843 (tptt) cc_final: 0.7579 (tptt) REVERT: I 64 GLU cc_start: 0.7222 (mp0) cc_final: 0.6627 (mp0) REVERT: I 101 ARG cc_start: 0.6839 (mmm-85) cc_final: 0.6435 (mmm-85) REVERT: I 111 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8318 (mtpp) REVERT: I 126 VAL cc_start: 0.8404 (t) cc_final: 0.8190 (p) REVERT: C 37 LYS cc_start: 0.8595 (tmmt) cc_final: 0.8242 (tmmt) REVERT: C 152 THR cc_start: 0.7245 (p) cc_final: 0.6992 (t) outliers start: 80 outliers final: 57 residues processed: 1234 average time/residue: 0.1891 time to fit residues: 361.2601 Evaluate side-chains 1243 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1183 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 67 MET Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 68 VAL 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 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 280 ILE 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 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 376 CYS Chi-restraints excluded: chain A residue 381 LYS 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 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 329 VAL Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 35 LEU 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 45 ILE 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 321 optimal weight: 5.9990 chunk 218 optimal weight: 0.2980 chunk 298 optimal weight: 0.4980 chunk 178 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN K 174 HIS 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 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN D 327 HIS D 408 ASN G 52 HIS G 139 ASN G 230 HIS A 43 ASN A 204 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN H 96 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.130502 restraints weight = 55968.386| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.96 r_work: 0.3432 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31760 Z= 0.125 Angle : 0.636 16.266 43289 Z= 0.319 Chirality : 0.046 0.197 4873 Planarity : 0.005 0.059 5520 Dihedral : 5.666 79.606 4563 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 2.99 % Allowed : 14.37 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.13), residues: 3963 helix: 1.93 (0.25), residues: 414 sheet: -0.33 (0.15), residues: 1183 loop : -1.26 (0.13), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 122 TYR 0.028 0.001 TYR A 308 PHE 0.019 0.001 PHE K 134 TRP 0.020 0.001 TRP B 279 HIS 0.014 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00285 (31692) covalent geometry : angle 0.62719 (43141) SS BOND : bond 0.00412 ( 56) SS BOND : angle 2.01415 ( 112) hydrogen bonds : bond 0.03211 ( 1026) hydrogen bonds : angle 5.34204 ( 2733) link_NAG-ASN : bond 0.00301 ( 12) link_NAG-ASN : angle 1.43305 ( 36) *********************** 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 1272 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 1171 time to evaluate : 0.734 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: 0.8378 (t0) cc_final: 0.7895 (t0) REVERT: J 24 TYR cc_start: 0.6810 (m-80) cc_final: 0.6396 (m-80) REVERT: J 49 CYS cc_start: 0.7771 (p) cc_final: 0.7563 (p) REVERT: J 61 LYS cc_start: 0.7842 (tmmt) cc_final: 0.7404 (ttpt) REVERT: J 99 GLU cc_start: 0.7071 (tt0) cc_final: 0.6445 (tt0) REVERT: J 130 LYS cc_start: 0.7895 (tttp) cc_final: 0.7638 (tppt) REVERT: J 180 ARG cc_start: 0.8459 (ttt-90) cc_final: 0.8189 (ttt-90) REVERT: J 289 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7562 (mtt90) REVERT: J 318 LEU cc_start: 0.7632 (tp) cc_final: 0.7075 (tp) REVERT: J 319 GLN cc_start: 0.7300 (tp40) cc_final: 0.7035 (tp40) REVERT: J 395 ASP cc_start: 0.7453 (t0) cc_final: 0.7121 (t0) REVERT: K 4 ASP cc_start: 0.7453 (t0) cc_final: 0.7245 (t0) REVERT: K 6 PHE cc_start: 0.8043 (m-80) cc_final: 0.7667 (m-80) REVERT: K 7 THR cc_start: 0.8536 (t) cc_final: 0.8251 (p) REVERT: K 37 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7572 (mm-30) REVERT: K 55 GLN cc_start: 0.8375 (tt0) cc_final: 0.8146 (tt0) REVERT: K 60 ASP cc_start: 0.7150 (t0) cc_final: 0.6700 (t0) REVERT: K 77 GLU cc_start: 0.8039 (pt0) cc_final: 0.7659 (pt0) REVERT: K 128 LYS cc_start: 0.8535 (tptp) cc_final: 0.8328 (mmmt) REVERT: K 152 CYS cc_start: 0.7152 (p) cc_final: 0.6788 (p) REVERT: K 159 LYS cc_start: 0.8759 (pttm) cc_final: 0.8482 (pttm) REVERT: K 181 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6670 (tm-30) REVERT: K 190 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7263 (ttpp) REVERT: K 195 LYS cc_start: 0.8406 (mppt) cc_final: 0.8124 (mppt) REVERT: K 222 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8301 (mmtt) REVERT: K 324 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7616 (mt-10) REVERT: K 391 LYS cc_start: 0.8827 (tttm) cc_final: 0.8337 (tttm) REVERT: K 395 ASP cc_start: 0.8150 (m-30) cc_final: 0.7719 (m-30) REVERT: L 19 MET cc_start: 0.6807 (mmp) cc_final: 0.6604 (mmp) REVERT: L 57 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7878 (mtmm) REVERT: L 80 THR cc_start: 0.8059 (t) cc_final: 0.7761 (m) REVERT: D 61 LYS cc_start: 0.7635 (pptt) cc_final: 0.7410 (ptmm) REVERT: D 76 TYR cc_start: 0.8055 (t80) cc_final: 0.7577 (t80) REVERT: D 99 GLU cc_start: 0.6742 (tm-30) cc_final: 0.6120 (tm-30) REVERT: D 160 LYS cc_start: 0.8101 (tmmt) cc_final: 0.7679 (tmmt) REVERT: D 174 ASP cc_start: 0.7871 (t0) cc_final: 0.7628 (t0) REVERT: D 230 HIS cc_start: 0.7918 (t70) cc_final: 0.7587 (t70) REVERT: D 249 ARG cc_start: 0.8533 (mmm160) cc_final: 0.8111 (mmm160) REVERT: D 257 PHE cc_start: 0.9062 (m-80) cc_final: 0.8833 (m-80) REVERT: D 320 TYR cc_start: 0.7652 (p90) cc_final: 0.7374 (p90) REVERT: D 321 LYS cc_start: 0.7783 (ptpp) cc_final: 0.7577 (pttm) REVERT: D 365 PHE cc_start: 0.8262 (p90) cc_final: 0.7961 (p90) REVERT: G 21 ARG cc_start: 0.8290 (mtp180) cc_final: 0.7933 (mtm180) REVERT: G 76 TYR cc_start: 0.8274 (t80) cc_final: 0.7525 (t80) REVERT: G 81 PHE cc_start: 0.7489 (m-10) cc_final: 0.7204 (m-10) REVERT: G 105 GLU cc_start: 0.7355 (tt0) cc_final: 0.6873 (tt0) REVERT: G 174 ASP cc_start: 0.8036 (m-30) cc_final: 0.7633 (m-30) REVERT: G 218 ASP cc_start: 0.8113 (t0) cc_final: 0.7594 (t0) REVERT: G 241 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7606 (mm-30) REVERT: G 246 ASN cc_start: 0.7618 (t0) cc_final: 0.7246 (t0) REVERT: G 341 GLU cc_start: 0.7518 (mp0) cc_final: 0.7122 (mp0) REVERT: G 402 VAL cc_start: 0.8184 (t) cc_final: 0.7928 (t) REVERT: G 404 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7910 (ttmm) REVERT: A 32 THR cc_start: 0.7109 (OUTLIER) cc_final: 0.6792 (m) REVERT: A 50 LYS cc_start: 0.8110 (tttp) cc_final: 0.7688 (ttpp) REVERT: A 202 ASP cc_start: 0.7507 (p0) cc_final: 0.7193 (p0) REVERT: A 263 VAL cc_start: 0.8137 (m) cc_final: 0.7894 (p) REVERT: A 320 TYR cc_start: 0.8050 (p90) cc_final: 0.7068 (p90) REVERT: A 323 ASN cc_start: 0.8497 (p0) cc_final: 0.8218 (p0) REVERT: A 373 LYS cc_start: 0.8406 (mptt) cc_final: 0.8084 (mptt) REVERT: A 388 ILE cc_start: 0.8244 (tp) cc_final: 0.8031 (tp) REVERT: E 13 LEU cc_start: 0.8306 (mt) cc_final: 0.8033 (mt) REVERT: E 36 ASP cc_start: 0.7697 (p0) cc_final: 0.7276 (p0) REVERT: E 51 PHE cc_start: 0.7860 (m-80) cc_final: 0.7467 (m-80) REVERT: E 67 MET cc_start: 0.7527 (tpp) cc_final: 0.7319 (tpp) REVERT: E 76 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8173 (mmtt) REVERT: E 129 LYS cc_start: 0.8512 (tppt) cc_final: 0.8130 (tppt) REVERT: E 131 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7591 (mmt180) REVERT: E 162 SER cc_start: 0.8924 (t) cc_final: 0.8692 (t) REVERT: E 168 MET cc_start: 0.7458 (tmm) cc_final: 0.7120 (tmm) REVERT: E 169 HIS cc_start: 0.7815 (m-70) cc_final: 0.7408 (m170) REVERT: E 229 TYR cc_start: 0.7596 (p90) cc_final: 0.7234 (p90) REVERT: E 254 LYS cc_start: 0.8226 (mttt) cc_final: 0.7780 (mttm) REVERT: E 278 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8147 (mtpp) REVERT: E 393 ARG cc_start: 0.5185 (tpt170) cc_final: 0.4420 (tpt170) REVERT: H 60 ASP cc_start: 0.7816 (t0) cc_final: 0.7334 (t0) REVERT: H 131 ARG cc_start: 0.8123 (mmt-90) cc_final: 0.7735 (mmt-90) REVERT: H 141 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7622 (mt) REVERT: H 179 TYR cc_start: 0.7706 (m-10) cc_final: 0.7319 (m-10) REVERT: H 347 ASP cc_start: 0.7582 (t0) cc_final: 0.6926 (t0) REVERT: H 393 ARG cc_start: 0.5763 (tpt170) cc_final: 0.4432 (ttt90) REVERT: B 4 ASP cc_start: 0.5569 (t70) cc_final: 0.5360 (t0) REVERT: B 76 LYS cc_start: 0.7961 (tppp) cc_final: 0.7542 (tppp) REVERT: B 159 LYS cc_start: 0.8338 (ptpt) cc_final: 0.8129 (ptpt) REVERT: B 224 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6993 (tmtt) REVERT: B 254 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7309 (mtpt) REVERT: B 265 VAL cc_start: 0.8937 (t) cc_final: 0.8490 (p) REVERT: B 276 VAL cc_start: 0.8639 (t) cc_final: 0.8321 (m) REVERT: B 281 LYS cc_start: 0.8234 (mttt) cc_final: 0.7827 (mttt) REVERT: B 347 ASP cc_start: 0.7898 (t0) cc_final: 0.7679 (t0) REVERT: B 354 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7571 (mt-10) REVERT: F 8 MET cc_start: 0.7425 (mmp) cc_final: 0.7215 (mmp) REVERT: F 19 MET cc_start: 0.6685 (mmp) cc_final: 0.5962 (mmp) REVERT: F 44 LYS cc_start: 0.7628 (pptt) cc_final: 0.7362 (pptt) REVERT: F 56 LYS cc_start: 0.8258 (ptpp) cc_final: 0.7810 (ptpp) REVERT: F 60 MET cc_start: 0.7886 (mmt) cc_final: 0.7641 (mmt) REVERT: F 101 ARG cc_start: 0.7260 (ttt180) cc_final: 0.6919 (ttt180) REVERT: I 25 ASN cc_start: 0.7028 (t0) cc_final: 0.6516 (t0) REVERT: I 42 GLU cc_start: 0.7885 (pm20) cc_final: 0.7681 (mp0) REVERT: I 44 LYS cc_start: 0.7816 (tptt) cc_final: 0.7537 (tptt) REVERT: I 101 ARG cc_start: 0.6868 (mmm-85) cc_final: 0.6328 (mmm-85) REVERT: I 111 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8310 (mtpp) REVERT: I 128 ILE cc_start: 0.8816 (mp) cc_final: 0.8579 (mt) REVERT: C 37 LYS cc_start: 0.8567 (tmmt) cc_final: 0.8145 (tmmt) REVERT: C 55 LEU cc_start: 0.8027 (mm) cc_final: 0.7437 (mm) REVERT: C 64 GLU cc_start: 0.7189 (tt0) cc_final: 0.6539 (tt0) outliers start: 101 outliers final: 66 residues processed: 1203 average time/residue: 0.1886 time to fit residues: 347.4639 Evaluate side-chains 1219 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1150 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 66 LEU 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 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 237 VAL 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 411 LEU Chi-restraints excluded: chain G residue 420 LEU 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 109 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain E residue 40 ASP 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 138 GLU 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 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 374 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 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 31 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 72 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 97 TYR Chi-restraints excluded: chain C residue 153 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 231 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 273 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 357 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 174 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 319 GLN D 327 HIS G 43 ASN G 52 HIS G 125 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 ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS F 96 GLN ** I 49 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** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121417 restraints weight = 56133.823| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.89 r_work: 0.3412 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31760 Z= 0.152 Angle : 0.637 16.857 43289 Z= 0.319 Chirality : 0.046 0.191 4873 Planarity : 0.005 0.060 5520 Dihedral : 5.475 81.170 4563 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 3.64 % Allowed : 15.37 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.13), residues: 3963 helix: 2.04 (0.25), residues: 412 sheet: -0.35 (0.15), residues: 1227 loop : -1.25 (0.13), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 303 TYR 0.028 0.001 TYR A 308 PHE 0.018 0.001 PHE H 238 TRP 0.020 0.001 TRP B 279 HIS 0.007 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00341 (31692) covalent geometry : angle 0.62913 (43141) SS BOND : bond 0.00468 ( 56) SS BOND : angle 1.85099 ( 112) hydrogen bonds : bond 0.03198 ( 1026) hydrogen bonds : angle 5.18277 ( 2733) link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 1.51065 ( 36) *********************** 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 1307 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1184 time to evaluate : 0.748 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: 0.7901 (t0) REVERT: J 24 TYR cc_start: 0.6824 (m-80) cc_final: 0.6404 (m-80) REVERT: J 50 LYS cc_start: 0.8288 (tttm) cc_final: 0.8046 (tttm) REVERT: J 61 LYS cc_start: 0.7823 (tmmt) cc_final: 0.7324 (ttpt) REVERT: J 99 GLU cc_start: 0.7195 (tt0) cc_final: 0.6499 (tt0) REVERT: J 123 LYS cc_start: 0.8199 (mttt) cc_final: 0.7946 (mttm) REVERT: J 130 LYS cc_start: 0.7853 (tttp) cc_final: 0.7607 (tppt) REVERT: J 176 LYS cc_start: 0.8554 (mttp) cc_final: 0.8215 (mttt) REVERT: J 191 GLU cc_start: 0.4493 (tt0) cc_final: 0.3809 (tt0) REVERT: J 289 ARG cc_start: 0.7884 (mtt90) cc_final: 0.7508 (mtt90) REVERT: J 318 LEU cc_start: 0.7654 (tp) cc_final: 0.7066 (tp) REVERT: J 319 GLN cc_start: 0.7323 (tp40) cc_final: 0.7025 (tp40) REVERT: K 4 ASP cc_start: 0.7476 (t0) cc_final: 0.7274 (t0) REVERT: K 6 PHE cc_start: 0.8080 (m-80) cc_final: 0.7744 (m-80) REVERT: K 7 THR cc_start: 0.8559 (t) cc_final: 0.8278 (p) REVERT: K 25 CYS cc_start: 0.5864 (t) cc_final: 0.5592 (t) REVERT: K 37 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7590 (mm-30) REVERT: K 60 ASP cc_start: 0.7239 (t0) cc_final: 0.6760 (t0) REVERT: K 77 GLU cc_start: 0.8078 (pt0) cc_final: 0.7685 (pt0) REVERT: K 82 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7956 (mmmt) REVERT: K 133 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8483 (mtmm) REVERT: K 156 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: K 159 LYS cc_start: 0.8804 (pttm) cc_final: 0.8546 (pttm) REVERT: K 181 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6705 (tm-30) REVERT: K 195 LYS cc_start: 0.8382 (mppt) cc_final: 0.8107 (mppt) REVERT: K 222 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8335 (mmtt) REVERT: K 324 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7653 (mt-10) REVERT: K 391 LYS cc_start: 0.8786 (tttm) cc_final: 0.8291 (tttm) REVERT: K 395 ASP cc_start: 0.8100 (m-30) cc_final: 0.7675 (m-30) REVERT: L 57 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7867 (mtmm) REVERT: L 80 THR cc_start: 0.8076 (t) cc_final: 0.7754 (m) REVERT: D 61 LYS cc_start: 0.7647 (pptt) cc_final: 0.7338 (ptmm) REVERT: D 76 TYR cc_start: 0.8099 (t80) cc_final: 0.7513 (t80) REVERT: D 99 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6168 (tm-30) REVERT: D 114 CYS cc_start: 0.7281 (m) cc_final: 0.6998 (m) REVERT: D 160 LYS cc_start: 0.8156 (tmmt) cc_final: 0.7755 (tmmt) REVERT: D 174 ASP cc_start: 0.7889 (t0) cc_final: 0.7675 (t0) REVERT: D 189 PHE cc_start: 0.8738 (p90) cc_final: 0.8423 (p90) REVERT: D 230 HIS cc_start: 0.7943 (t70) cc_final: 0.7586 (t70) REVERT: D 249 ARG cc_start: 0.8535 (mmm160) cc_final: 0.8103 (mmm160) REVERT: D 257 PHE cc_start: 0.9087 (m-80) cc_final: 0.8873 (m-80) REVERT: D 320 TYR cc_start: 0.7736 (p90) cc_final: 0.7408 (p90) REVERT: D 365 PHE cc_start: 0.8232 (p90) cc_final: 0.7917 (p90) REVERT: D 381 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7883 (mtmm) REVERT: D 430 CYS cc_start: 0.8248 (p) cc_final: 0.7997 (p) REVERT: G 28 ASN cc_start: 0.8556 (p0) cc_final: 0.8305 (p0) REVERT: G 30 GLU cc_start: 0.7436 (mm-30) cc_final: 0.6921 (mm-30) REVERT: G 80 VAL cc_start: 0.8841 (t) cc_final: 0.8511 (m) REVERT: G 174 ASP cc_start: 0.7947 (m-30) cc_final: 0.7066 (m-30) REVERT: G 186 ASN cc_start: 0.8480 (m-40) cc_final: 0.7687 (m-40) REVERT: G 202 ASP cc_start: 0.8327 (p0) cc_final: 0.7974 (p0) REVERT: G 218 ASP cc_start: 0.8159 (t0) cc_final: 0.7677 (t0) REVERT: G 241 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7619 (mm-30) REVERT: G 246 ASN cc_start: 0.7615 (t0) cc_final: 0.6944 (t0) REVERT: G 341 GLU cc_start: 0.7536 (mp0) cc_final: 0.7127 (mp0) REVERT: G 402 VAL cc_start: 0.8273 (t) cc_final: 0.8005 (t) REVERT: G 404 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7913 (ttmm) REVERT: A 50 LYS cc_start: 0.8291 (tttp) cc_final: 0.7920 (ttpp) REVERT: A 87 PHE cc_start: 0.7890 (t80) cc_final: 0.7362 (t80) REVERT: A 88 MET cc_start: 0.7714 (mtp) cc_final: 0.7381 (mtp) REVERT: A 202 ASP cc_start: 0.7446 (p0) cc_final: 0.7159 (p0) REVERT: A 263 VAL cc_start: 0.8135 (m) cc_final: 0.7901 (p) REVERT: A 320 TYR cc_start: 0.8068 (p90) cc_final: 0.7055 (p90) REVERT: A 323 ASN cc_start: 0.8574 (p0) cc_final: 0.8321 (p0) REVERT: A 373 LYS cc_start: 0.8413 (mptt) cc_final: 0.8104 (mptt) REVERT: E 36 ASP cc_start: 0.7642 (p0) cc_final: 0.7257 (p0) REVERT: E 51 PHE cc_start: 0.7912 (m-80) cc_final: 0.7685 (m-10) REVERT: E 67 MET cc_start: 0.7656 (tpp) cc_final: 0.7217 (tpp) REVERT: E 76 LYS cc_start: 0.8604 (mmtt) cc_final: 0.8221 (mmtt) REVERT: E 129 LYS cc_start: 0.8516 (tppt) cc_final: 0.8098 (tppt) REVERT: E 131 ARG cc_start: 0.8022 (mmt90) cc_final: 0.7623 (mmt180) REVERT: E 162 SER cc_start: 0.8909 (t) cc_final: 0.8688 (t) REVERT: E 168 MET cc_start: 0.7551 (tmm) cc_final: 0.7279 (tmm) REVERT: E 169 HIS cc_start: 0.7848 (m-70) cc_final: 0.7464 (m170) REVERT: E 195 LYS cc_start: 0.8272 (mttt) cc_final: 0.8055 (mttt) REVERT: E 229 TYR cc_start: 0.7601 (p90) cc_final: 0.7224 (p90) REVERT: E 254 LYS cc_start: 0.8265 (mttt) cc_final: 0.7936 (mttt) REVERT: E 277 THR cc_start: 0.8459 (m) cc_final: 0.7927 (p) REVERT: E 324 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7544 (mt-10) REVERT: E 339 TRP cc_start: 0.8368 (m-90) cc_final: 0.8158 (m-90) REVERT: E 393 ARG cc_start: 0.5159 (tpt170) cc_final: 0.4504 (tpt170) REVERT: H 51 PHE cc_start: 0.8303 (m-80) cc_final: 0.7957 (m-80) REVERT: H 60 ASP cc_start: 0.7889 (t0) cc_final: 0.7419 (t0) REVERT: H 67 MET cc_start: 0.7203 (mmm) cc_final: 0.6993 (mmm) REVERT: H 131 ARG cc_start: 0.8083 (mmt-90) cc_final: 0.7639 (mmt-90) REVERT: H 179 TYR cc_start: 0.7740 (m-10) cc_final: 0.7441 (m-10) REVERT: H 224 LYS cc_start: 0.8106 (ptmm) cc_final: 0.7866 (ptmm) REVERT: H 347 ASP cc_start: 0.7625 (t0) cc_final: 0.6989 (t0) REVERT: H 393 ARG cc_start: 0.5835 (tpt170) cc_final: 0.5313 (tpt170) REVERT: B 76 LYS cc_start: 0.7923 (tppp) cc_final: 0.7530 (tppp) REVERT: B 159 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8116 (ptpt) REVERT: B 168 MET cc_start: 0.7135 (mmm) cc_final: 0.6870 (mmm) REVERT: B 225 GLN cc_start: 0.5741 (tm-30) cc_final: 0.5469 (tm-30) REVERT: B 254 LYS cc_start: 0.7677 (mtpt) cc_final: 0.7379 (mtpt) REVERT: B 265 VAL cc_start: 0.9006 (t) cc_final: 0.8531 (p) REVERT: B 281 LYS cc_start: 0.8277 (mttt) cc_final: 0.7950 (mttt) REVERT: B 354 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7504 (mt-10) REVERT: F 8 MET cc_start: 0.7289 (mmp) cc_final: 0.7024 (mmp) REVERT: F 19 MET cc_start: 0.6649 (mmp) cc_final: 0.5966 (mmp) REVERT: F 56 LYS cc_start: 0.8268 (ptpp) cc_final: 0.7760 (ptpp) REVERT: F 101 ARG cc_start: 0.7086 (ttt180) cc_final: 0.6814 (ttt180) REVERT: I 14 LYS cc_start: 0.8080 (mmtp) cc_final: 0.7577 (mmtp) REVERT: I 44 LYS cc_start: 0.7830 (tptt) cc_final: 0.7600 (tptt) REVERT: I 60 MET cc_start: 0.7540 (mmp) cc_final: 0.7212 (mmp) REVERT: I 101 ARG cc_start: 0.6913 (mmm-85) cc_final: 0.6503 (mmm-85) REVERT: I 111 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8322 (mtpp) REVERT: I 128 ILE cc_start: 0.8847 (mp) cc_final: 0.8597 (mt) REVERT: C 37 LYS cc_start: 0.8575 (tmmt) cc_final: 0.8284 (tmmt) REVERT: C 50 LEU cc_start: 0.8337 (mp) cc_final: 0.8086 (mp) REVERT: C 55 LEU cc_start: 0.8064 (mm) cc_final: 0.7295 (mm) REVERT: C 64 GLU cc_start: 0.7236 (tt0) cc_final: 0.6702 (tt0) outliers start: 123 outliers final: 92 residues processed: 1221 average time/residue: 0.1956 time to fit residues: 367.5754 Evaluate side-chains 1262 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1168 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 62 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 207 SER 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 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 133 LYS Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 78 CYS 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 259 CYS Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 327 HIS 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 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 237 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 307 ILE 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 A residue 7 VAL 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 109 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 LYS 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 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 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 374 VAL 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 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 95 VAL 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 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 258 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 chunk 224 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 238 optimal weight: 0.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 174 HIS 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 319 GLN D 327 HIS G 52 HIS G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS E 50 GLN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS B 46 GLN B 96 HIS B 361 HIS F 96 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117906 restraints weight = 55931.497| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.87 r_work: 0.3343 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 31760 Z= 0.266 Angle : 0.701 17.738 43289 Z= 0.356 Chirality : 0.049 0.251 4873 Planarity : 0.005 0.059 5520 Dihedral : 5.646 79.395 4563 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.59 % Favored : 93.36 % Rotamer: Outliers : 4.27 % Allowed : 16.62 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.13), residues: 3963 helix: 2.07 (0.25), residues: 412 sheet: -0.49 (0.15), residues: 1216 loop : -1.33 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 20 TYR 0.029 0.002 TYR A 308 PHE 0.019 0.002 PHE H 238 TRP 0.019 0.002 TRP B 279 HIS 0.032 0.002 HIS D 327 Details of bonding type rmsd covalent geometry : bond 0.00583 (31692) covalent geometry : angle 0.69162 (43141) SS BOND : bond 0.00523 ( 56) SS BOND : angle 2.08541 ( 112) hydrogen bonds : bond 0.03614 ( 1026) hydrogen bonds : angle 5.38042 ( 2733) link_NAG-ASN : bond 0.00372 ( 12) link_NAG-ASN : angle 1.85401 ( 36) *********************** 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 1343 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1199 time to evaluate : 1.080 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: J 9 ASN cc_start: 0.8431 (t0) cc_final: 0.7885 (t0) REVERT: J 61 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7429 (ttpt) REVERT: J 101 THR cc_start: 0.7923 (m) cc_final: 0.7644 (m) REVERT: J 180 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.8316 (ttt-90) REVERT: J 191 GLU cc_start: 0.4949 (tt0) cc_final: 0.3996 (mt-10) REVERT: J 234 THR cc_start: 0.8032 (p) cc_final: 0.7787 (t) REVERT: J 289 ARG cc_start: 0.7927 (mtt90) cc_final: 0.7550 (mtt90) REVERT: J 318 LEU cc_start: 0.7676 (tp) cc_final: 0.7057 (tp) REVERT: J 319 GLN cc_start: 0.7382 (tp40) cc_final: 0.7123 (tp40) REVERT: K 6 PHE cc_start: 0.8198 (m-80) cc_final: 0.7915 (m-80) REVERT: K 7 THR cc_start: 0.8547 (t) cc_final: 0.8275 (p) REVERT: K 18 TYR cc_start: 0.7822 (t80) cc_final: 0.7044 (t80) REVERT: K 37 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7624 (mm-30) REVERT: K 60 ASP cc_start: 0.7279 (t0) cc_final: 0.6658 (t0) REVERT: K 77 GLU cc_start: 0.8067 (pt0) cc_final: 0.7642 (pt0) REVERT: K 127 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7286 (mm-30) REVERT: K 138 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6982 (mm-30) REVERT: K 152 CYS cc_start: 0.7266 (p) cc_final: 0.6947 (p) REVERT: K 156 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: K 159 LYS cc_start: 0.8812 (pttm) cc_final: 0.8539 (pttm) REVERT: K 181 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6799 (tm-30) REVERT: K 195 LYS cc_start: 0.8398 (mppt) cc_final: 0.8106 (mppt) REVERT: K 222 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8319 (mmtt) REVERT: K 324 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7646 (mt-10) REVERT: K 391 LYS cc_start: 0.8798 (tttm) cc_final: 0.8320 (tttm) REVERT: K 395 ASP cc_start: 0.8176 (m-30) cc_final: 0.7730 (m-30) REVERT: L 57 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7917 (mtmm) REVERT: L 80 THR cc_start: 0.8282 (t) cc_final: 0.7916 (m) REVERT: D 61 LYS cc_start: 0.7718 (pptt) cc_final: 0.7188 (ptmm) REVERT: D 99 GLU cc_start: 0.6761 (tm-30) cc_final: 0.6082 (tm-30) REVERT: D 230 HIS cc_start: 0.8074 (t70) cc_final: 0.7868 (t70) REVERT: D 249 ARG cc_start: 0.8557 (mmm160) cc_final: 0.8171 (mmm160) REVERT: D 257 PHE cc_start: 0.9058 (m-80) cc_final: 0.8832 (m-80) REVERT: D 270 ASN cc_start: 0.8000 (m110) cc_final: 0.7735 (m110) REVERT: D 320 TYR cc_start: 0.7875 (p90) cc_final: 0.7381 (p90) REVERT: D 373 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7895 (mmtm) REVERT: D 381 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7840 (mtmm) REVERT: D 393 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7683 (mmtm) REVERT: G 30 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6947 (mm-30) REVERT: G 80 VAL cc_start: 0.8836 (t) cc_final: 0.8557 (m) REVERT: G 81 PHE cc_start: 0.7543 (m-10) cc_final: 0.7172 (m-10) REVERT: G 105 GLU cc_start: 0.7271 (tt0) cc_final: 0.6921 (tt0) REVERT: G 174 ASP cc_start: 0.7939 (m-30) cc_final: 0.7444 (m-30) REVERT: G 202 ASP cc_start: 0.8353 (p0) cc_final: 0.7811 (p0) REVERT: G 218 ASP cc_start: 0.8269 (t0) cc_final: 0.7738 (t0) REVERT: G 241 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7559 (mm-30) REVERT: G 246 ASN cc_start: 0.7652 (t0) cc_final: 0.6974 (t0) REVERT: G 343 THR cc_start: 0.8562 (t) cc_final: 0.8213 (m) REVERT: G 402 VAL cc_start: 0.8282 (t) cc_final: 0.8045 (t) REVERT: G 404 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7908 (ttmm) REVERT: A 9 ASN cc_start: 0.7831 (p0) cc_final: 0.7380 (p0) REVERT: A 50 LYS cc_start: 0.8215 (tttp) cc_final: 0.7809 (ttpt) REVERT: A 188 ASP cc_start: 0.7931 (t0) cc_final: 0.7614 (t0) REVERT: A 202 ASP cc_start: 0.7524 (p0) cc_final: 0.7232 (p0) REVERT: A 323 ASN cc_start: 0.8722 (p0) cc_final: 0.8359 (p0) REVERT: A 373 LYS cc_start: 0.8364 (mptt) cc_final: 0.8057 (mptt) REVERT: E 34 VAL cc_start: 0.9029 (t) cc_final: 0.8599 (m) REVERT: E 36 ASP cc_start: 0.7605 (p0) cc_final: 0.7259 (p0) REVERT: E 67 MET cc_start: 0.7795 (tpp) cc_final: 0.7391 (tpp) REVERT: E 76 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8196 (mmtt) REVERT: E 129 LYS cc_start: 0.8626 (tppt) cc_final: 0.8348 (tppt) REVERT: E 131 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7800 (mmt-90) REVERT: E 162 SER cc_start: 0.8882 (t) cc_final: 0.8659 (t) REVERT: E 168 MET cc_start: 0.7619 (tmm) cc_final: 0.7336 (tmm) REVERT: E 254 LYS cc_start: 0.8213 (mttt) cc_final: 0.7890 (mttt) REVERT: E 277 THR cc_start: 0.8502 (m) cc_final: 0.7956 (p) REVERT: E 324 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7673 (mt-10) REVERT: E 393 ARG cc_start: 0.5478 (tpt170) cc_final: 0.4775 (tpt170) REVERT: H 60 ASP cc_start: 0.7977 (t0) cc_final: 0.7490 (t0) REVERT: H 168 MET cc_start: 0.7280 (tpp) cc_final: 0.6528 (mmm) REVERT: H 179 TYR cc_start: 0.7727 (m-10) cc_final: 0.7511 (m-10) REVERT: H 224 LYS cc_start: 0.8208 (ptmm) cc_final: 0.7950 (ptmm) REVERT: H 342 GLU cc_start: 0.7052 (pm20) cc_final: 0.6796 (pm20) REVERT: H 347 ASP cc_start: 0.7556 (t0) cc_final: 0.6909 (t0) REVERT: H 393 ARG cc_start: 0.5835 (tpt170) cc_final: 0.5269 (tpt170) REVERT: B 20 ARG cc_start: 0.7105 (mmp80) cc_final: 0.6659 (mmp80) REVERT: B 76 LYS cc_start: 0.7976 (tppp) cc_final: 0.7534 (tppp) REVERT: B 97 LYS cc_start: 0.8062 (tttp) cc_final: 0.7819 (tttp) REVERT: B 121 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7494 (mp0) REVERT: B 159 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8012 (ptpt) REVERT: B 225 GLN cc_start: 0.6123 (tm-30) cc_final: 0.5701 (tm-30) REVERT: B 254 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7425 (mtpt) REVERT: B 265 VAL cc_start: 0.9177 (t) cc_final: 0.8737 (p) REVERT: B 276 VAL cc_start: 0.8717 (t) cc_final: 0.8417 (m) REVERT: B 281 LYS cc_start: 0.8361 (mttt) cc_final: 0.8050 (mttt) REVERT: B 354 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7555 (mt-10) REVERT: F 8 MET cc_start: 0.7444 (mmp) cc_final: 0.7183 (mmp) REVERT: F 56 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7802 (ptpp) REVERT: F 97 TYR cc_start: 0.5534 (m-80) cc_final: 0.5086 (m-80) REVERT: F 101 ARG cc_start: 0.7334 (ttt180) cc_final: 0.7006 (ttt180) REVERT: F 111 LYS cc_start: 0.8595 (mttt) cc_final: 0.8254 (mttt) REVERT: F 120 ASP cc_start: 0.7994 (p0) cc_final: 0.7421 (p0) REVERT: F 124 ARG cc_start: 0.6488 (ttp-110) cc_final: 0.5237 (ttp-110) REVERT: I 44 LYS cc_start: 0.8139 (tptt) cc_final: 0.7886 (tptt) REVERT: I 88 TYR cc_start: 0.7296 (m-80) cc_final: 0.7035 (m-80) REVERT: I 101 ARG cc_start: 0.7094 (mmm-85) cc_final: 0.6638 (mmm-85) REVERT: I 102 PHE cc_start: 0.8176 (m-80) cc_final: 0.7890 (m-80) REVERT: I 111 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8438 (mtpp) REVERT: C 37 LYS cc_start: 0.8630 (tmmt) cc_final: 0.8368 (tmmt) REVERT: C 50 LEU cc_start: 0.8291 (mp) cc_final: 0.8064 (mp) REVERT: C 55 LEU cc_start: 0.8153 (mm) cc_final: 0.7210 (mm) REVERT: C 64 GLU cc_start: 0.7075 (tt0) cc_final: 0.6516 (tt0) outliers start: 144 outliers final: 112 residues processed: 1243 average time/residue: 0.1997 time to fit residues: 382.0396 Evaluate side-chains 1271 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1158 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 66 LEU 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 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 396 CYS Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 68 VAL 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 65 SER 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 347 THR 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 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 195 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE 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 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 109 GLU Chi-restraints excluded: chain A residue 148 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 316 LEU Chi-restraints excluded: chain A residue 319 GLN 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 40 ASP Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 230 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 138 GLU 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 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 374 VAL 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 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 143 VAL 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 I residue 95 VAL Chi-restraints excluded: chain I residue 143 VAL Chi-restraints excluded: chain C residue 8 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 97 TYR Chi-restraints excluded: chain C residue 99 ASN 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 25 optimal weight: 0.0370 chunk 329 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 343 optimal weight: 6.9990 chunk 324 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 274 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 361 optimal weight: 5.9990 chunk 360 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 overall best weight: 1.3862 ------------------------------------------------------------------------------- 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 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN G 52 HIS G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 332 ASN H 96 HIS B 96 HIS ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.143323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126355 restraints weight = 55861.051| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.87 r_work: 0.3390 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31760 Z= 0.131 Angle : 0.661 16.634 43289 Z= 0.331 Chirality : 0.046 0.244 4873 Planarity : 0.005 0.052 5520 Dihedral : 5.390 81.884 4563 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.40 % Favored : 94.55 % Rotamer: Outliers : 3.88 % Allowed : 19.14 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.13), residues: 3963 helix: 2.25 (0.24), residues: 406 sheet: -0.26 (0.16), residues: 1125 loop : -1.25 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 214 TYR 0.027 0.001 TYR A 308 PHE 0.028 0.001 PHE C 16 TRP 0.022 0.001 TRP C 90 HIS 0.008 0.001 HIS H 96 Details of bonding type rmsd covalent geometry : bond 0.00302 (31692) covalent geometry : angle 0.65402 (43141) SS BOND : bond 0.00406 ( 56) SS BOND : angle 1.91116 ( 112) hydrogen bonds : bond 0.03089 ( 1026) hydrogen bonds : angle 5.18160 ( 2733) link_NAG-ASN : bond 0.00286 ( 12) link_NAG-ASN : angle 1.42461 ( 36) *********************** 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 1293 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1162 time to evaluate : 1.115 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: 0.8388 (t0) cc_final: 0.7921 (t0) REVERT: J 61 LYS cc_start: 0.7827 (ttmt) cc_final: 0.7407 (ttpp) REVERT: J 101 THR cc_start: 0.7904 (m) cc_final: 0.7596 (m) REVERT: J 130 LYS cc_start: 0.7806 (tttp) cc_final: 0.7540 (tttp) REVERT: J 134 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7948 (ttm-80) REVERT: J 180 ARG cc_start: 0.8552 (ttt-90) cc_final: 0.8178 (ttt-90) REVERT: J 191 GLU cc_start: 0.4740 (tt0) cc_final: 0.3920 (mt-10) REVERT: J 234 THR cc_start: 0.7960 (p) cc_final: 0.7735 (t) REVERT: J 289 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7520 (mtt90) REVERT: K 6 PHE cc_start: 0.8118 (m-80) cc_final: 0.7888 (m-80) REVERT: K 7 THR cc_start: 0.8511 (t) cc_final: 0.8238 (p) REVERT: K 18 TYR cc_start: 0.7633 (t80) cc_final: 0.6920 (t80) REVERT: K 37 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7580 (mm-30) REVERT: K 60 ASP cc_start: 0.7257 (t0) cc_final: 0.6717 (t0) REVERT: K 77 GLU cc_start: 0.8036 (pt0) cc_final: 0.7634 (pt0) REVERT: K 138 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6954 (mm-30) REVERT: K 152 CYS cc_start: 0.7236 (p) cc_final: 0.6901 (p) REVERT: K 156 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: K 159 LYS cc_start: 0.8790 (pttm) cc_final: 0.8519 (pttm) REVERT: K 181 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6749 (tm-30) REVERT: K 195 LYS cc_start: 0.8413 (mppt) cc_final: 0.8104 (mppt) REVERT: K 222 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8311 (mmtt) REVERT: K 324 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7622 (mt-10) REVERT: K 391 LYS cc_start: 0.8647 (tttm) cc_final: 0.8090 (tttm) REVERT: K 395 ASP cc_start: 0.8085 (m-30) cc_final: 0.7652 (m-30) REVERT: L 80 THR cc_start: 0.8180 (t) cc_final: 0.7878 (m) REVERT: D 46 TYR cc_start: 0.8323 (p90) cc_final: 0.8094 (p90) REVERT: D 61 LYS cc_start: 0.7650 (pptt) cc_final: 0.7131 (ptmm) REVERT: D 99 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6119 (tm-30) REVERT: D 230 HIS cc_start: 0.7979 (t70) cc_final: 0.7697 (t70) REVERT: D 249 ARG cc_start: 0.8558 (mmm160) cc_final: 0.8138 (mmm160) REVERT: D 270 ASN cc_start: 0.7912 (m110) cc_final: 0.7672 (m110) REVERT: D 308 TYR cc_start: 0.7858 (p90) cc_final: 0.7460 (p90) REVERT: D 381 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7788 (mtmm) REVERT: G 21 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7893 (mtm180) REVERT: G 30 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6918 (mm-30) REVERT: G 105 GLU cc_start: 0.7241 (tt0) cc_final: 0.6901 (tt0) REVERT: G 174 ASP cc_start: 0.7939 (m-30) cc_final: 0.7420 (m-30) REVERT: G 202 ASP cc_start: 0.8305 (p0) cc_final: 0.7879 (p0) REVERT: G 218 ASP cc_start: 0.8165 (t0) cc_final: 0.7659 (t0) REVERT: G 241 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7578 (mm-30) REVERT: G 246 ASN cc_start: 0.7636 (t0) cc_final: 0.6943 (t0) REVERT: G 402 VAL cc_start: 0.8273 (t) cc_final: 0.7973 (t) REVERT: G 404 LYS cc_start: 0.8190 (ttmm) cc_final: 0.7928 (ttmm) REVERT: A 9 ASN cc_start: 0.7497 (p0) cc_final: 0.7149 (p0) REVERT: A 88 MET cc_start: 0.7851 (mtp) cc_final: 0.7517 (mtp) REVERT: A 107 TYR cc_start: 0.7592 (p90) cc_final: 0.7359 (p90) REVERT: A 202 ASP cc_start: 0.7485 (p0) cc_final: 0.7221 (p0) REVERT: A 249 ARG cc_start: 0.8752 (mmp80) cc_final: 0.8503 (mmp80) REVERT: A 323 ASN cc_start: 0.8646 (p0) cc_final: 0.8297 (p0) REVERT: A 373 LYS cc_start: 0.8312 (mptt) cc_final: 0.8016 (mptt) REVERT: E 36 ASP cc_start: 0.7581 (p0) cc_final: 0.7255 (p0) REVERT: E 67 MET cc_start: 0.7714 (tpp) cc_final: 0.7501 (tpp) REVERT: E 76 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8242 (mmtt) REVERT: E 129 LYS cc_start: 0.8593 (tppt) cc_final: 0.8131 (tppt) REVERT: E 131 ARG cc_start: 0.8087 (mmt90) cc_final: 0.7668 (mmt-90) REVERT: E 162 SER cc_start: 0.8866 (t) cc_final: 0.8657 (t) REVERT: E 168 MET cc_start: 0.7625 (tmm) cc_final: 0.7323 (tmm) REVERT: E 254 LYS cc_start: 0.8267 (mttt) cc_final: 0.7954 (mttt) REVERT: E 277 THR cc_start: 0.8485 (m) cc_final: 0.7962 (p) REVERT: E 278 LYS cc_start: 0.8601 (mmtp) cc_final: 0.8239 (mtpp) REVERT: E 393 ARG cc_start: 0.5115 (tpt170) cc_final: 0.4572 (tpt170) REVERT: H 60 ASP cc_start: 0.7932 (t0) cc_final: 0.7450 (t0) REVERT: H 67 MET cc_start: 0.7233 (mmm) cc_final: 0.6986 (mmm) REVERT: H 131 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.7698 (mmt-90) REVERT: H 179 TYR cc_start: 0.7697 (m-10) cc_final: 0.7463 (m-10) REVERT: H 224 LYS cc_start: 0.8179 (ptmm) cc_final: 0.7925 (ptmm) REVERT: H 347 ASP cc_start: 0.7562 (t0) cc_final: 0.6923 (t0) REVERT: H 393 ARG cc_start: 0.5683 (tpt170) cc_final: 0.4976 (tpt170) REVERT: B 63 LYS cc_start: 0.8256 (mttm) cc_final: 0.7859 (mttm) REVERT: B 76 LYS cc_start: 0.7934 (tppp) cc_final: 0.7499 (tppp) REVERT: B 121 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7497 (mp0) REVERT: B 225 GLN cc_start: 0.6303 (tm-30) cc_final: 0.5840 (tm-30) REVERT: B 265 VAL cc_start: 0.9142 (t) cc_final: 0.8685 (p) REVERT: B 276 VAL cc_start: 0.8704 (t) cc_final: 0.8379 (m) REVERT: B 281 LYS cc_start: 0.8300 (mttt) cc_final: 0.7981 (mttt) REVERT: B 354 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7517 (mt-10) REVERT: F 8 MET cc_start: 0.7348 (mmp) cc_final: 0.7076 (mmp) REVERT: F 56 LYS cc_start: 0.8277 (ptpp) cc_final: 0.7793 (ptpp) REVERT: F 76 THR cc_start: 0.7713 (p) cc_final: 0.7241 (p) REVERT: F 97 TYR cc_start: 0.5605 (m-80) cc_final: 0.5261 (m-80) REVERT: F 101 ARG cc_start: 0.7181 (ttt180) cc_final: 0.6877 (ttt180) REVERT: F 111 LYS cc_start: 0.8447 (mttt) cc_final: 0.8135 (mttt) REVERT: F 143 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8332 (p) REVERT: I 14 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7457 (mmtp) REVERT: I 44 LYS cc_start: 0.7954 (tptt) cc_final: 0.7748 (tptt) REVERT: I 101 ARG cc_start: 0.7053 (mmm-85) cc_final: 0.6702 (mmm-85) REVERT: I 111 LYS cc_start: 0.8583 (mtpp) cc_final: 0.8354 (mtpp) REVERT: C 37 LYS cc_start: 0.8531 (tmmt) cc_final: 0.8258 (tmmt) REVERT: C 64 GLU cc_start: 0.7047 (tt0) cc_final: 0.6606 (tt0) outliers start: 131 outliers final: 100 residues processed: 1200 average time/residue: 0.2017 time to fit residues: 371.5101 Evaluate side-chains 1240 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1138 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 195 MET 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 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 156 ASP 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 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 68 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 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 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 69 LYS 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 298 GLU Chi-restraints excluded: chain G residue 307 ILE 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 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 109 GLU Chi-restraints excluded: chain A residue 148 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 217 THR Chi-restraints excluded: chain A residue 253 GLU 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 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 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 161 THR 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 H residue 374 VAL Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 24 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 I residue 23 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain C residue 8 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 137 THR 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 287 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 166 optimal weight: 0.3980 chunk 188 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 chunk 246 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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 ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN G 52 HIS G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN H 96 HIS B 46 GLN B 96 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118554 restraints weight = 55994.237| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.84 r_work: 0.3366 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31760 Z= 0.218 Angle : 0.696 18.176 43289 Z= 0.350 Chirality : 0.048 0.225 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.514 79.362 4563 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 4.21 % Allowed : 19.73 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.13), residues: 3963 helix: 2.25 (0.25), residues: 405 sheet: -0.33 (0.15), residues: 1184 loop : -1.34 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 20 TYR 0.030 0.002 TYR A 308 PHE 0.030 0.002 PHE C 16 TRP 0.019 0.002 TRP C 146 HIS 0.011 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00486 (31692) covalent geometry : angle 0.68562 (43141) SS BOND : bond 0.00547 ( 56) SS BOND : angle 2.32209 ( 112) hydrogen bonds : bond 0.03369 ( 1026) hydrogen bonds : angle 5.24811 ( 2733) link_NAG-ASN : bond 0.00297 ( 12) link_NAG-ASN : angle 1.70895 ( 36) *********************** 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 1295 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1153 time to evaluate : 1.160 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: J 9 ASN cc_start: 0.8405 (t0) cc_final: 0.7899 (t0) REVERT: J 101 THR cc_start: 0.7930 (m) cc_final: 0.7638 (m) REVERT: J 134 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7800 (ttm-80) REVERT: J 191 GLU cc_start: 0.5034 (tt0) cc_final: 0.4116 (mt-10) REVERT: J 234 THR cc_start: 0.7993 (p) cc_final: 0.7749 (t) REVERT: J 282 ILE cc_start: 0.8593 (mt) cc_final: 0.8168 (tp) REVERT: J 289 ARG cc_start: 0.8002 (mtt90) cc_final: 0.7604 (mtt90) REVERT: K 6 PHE cc_start: 0.8226 (m-80) cc_final: 0.7953 (m-80) REVERT: K 7 THR cc_start: 0.8525 (t) cc_final: 0.8268 (p) REVERT: K 37 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7611 (mm-30) REVERT: K 55 GLN cc_start: 0.8192 (tt0) cc_final: 0.7944 (tt0) REVERT: K 60 ASP cc_start: 0.7256 (t0) cc_final: 0.6640 (t0) REVERT: K 77 GLU cc_start: 0.8014 (pt0) cc_final: 0.7582 (pt0) REVERT: K 127 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7277 (mm-30) REVERT: K 138 GLU cc_start: 0.7359 (mm-30) cc_final: 0.7003 (mm-30) REVERT: K 152 CYS cc_start: 0.7222 (p) cc_final: 0.6917 (p) REVERT: K 156 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8023 (m-30) REVERT: K 159 LYS cc_start: 0.8790 (pttm) cc_final: 0.8521 (pttm) REVERT: K 181 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6839 (tm-30) REVERT: K 195 LYS cc_start: 0.8390 (mppt) cc_final: 0.8073 (mppt) REVERT: K 222 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8323 (mmtt) REVERT: K 287 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8558 (pp) REVERT: K 324 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7635 (mt-10) REVERT: K 391 LYS cc_start: 0.8746 (tttm) cc_final: 0.8265 (tttm) REVERT: K 395 ASP cc_start: 0.8108 (m-30) cc_final: 0.7666 (m-30) REVERT: L 80 THR cc_start: 0.8293 (t) cc_final: 0.7916 (m) REVERT: D 61 LYS cc_start: 0.7738 (pptt) cc_final: 0.7497 (ptmm) REVERT: D 99 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6108 (tm-30) REVERT: D 249 ARG cc_start: 0.8570 (mmm160) cc_final: 0.8168 (mmm160) REVERT: D 257 PHE cc_start: 0.9075 (m-80) cc_final: 0.8849 (m-80) REVERT: D 270 ASN cc_start: 0.8004 (m110) cc_final: 0.7753 (m110) REVERT: D 308 TYR cc_start: 0.7888 (p90) cc_final: 0.7548 (p90) REVERT: D 373 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7873 (mmtm) REVERT: D 381 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7799 (mtmm) REVERT: G 30 GLU cc_start: 0.7365 (mm-30) cc_final: 0.6920 (mm-30) REVERT: G 76 TYR cc_start: 0.8236 (t80) cc_final: 0.7366 (t80) REVERT: G 103 LEU cc_start: 0.7749 (tp) cc_final: 0.7522 (tp) REVERT: G 105 GLU cc_start: 0.7185 (tt0) cc_final: 0.6703 (tt0) REVERT: G 174 ASP cc_start: 0.7928 (m-30) cc_final: 0.7414 (m-30) REVERT: G 202 ASP cc_start: 0.8301 (p0) cc_final: 0.7873 (p0) REVERT: G 218 ASP cc_start: 0.8255 (t0) cc_final: 0.7740 (t0) REVERT: G 241 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7576 (mm-30) REVERT: G 246 ASN cc_start: 0.7665 (t0) cc_final: 0.6961 (t0) REVERT: G 346 VAL cc_start: 0.7967 (t) cc_final: 0.7548 (m) REVERT: G 402 VAL cc_start: 0.8294 (t) cc_final: 0.8019 (t) REVERT: G 404 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7928 (ttmm) REVERT: A 9 ASN cc_start: 0.7839 (p0) cc_final: 0.7518 (p0) REVERT: A 117 ASP cc_start: 0.7145 (t0) cc_final: 0.6639 (t0) REVERT: A 202 ASP cc_start: 0.7485 (p0) cc_final: 0.7238 (p0) REVERT: A 249 ARG cc_start: 0.8776 (mmp80) cc_final: 0.8526 (mmp80) REVERT: A 320 TYR cc_start: 0.7976 (p90) cc_final: 0.7110 (p90) REVERT: A 323 ASN cc_start: 0.8751 (p0) cc_final: 0.8407 (p0) REVERT: A 373 LYS cc_start: 0.8389 (mptt) cc_final: 0.8110 (mptt) REVERT: A 388 ILE cc_start: 0.8158 (tp) cc_final: 0.7928 (tp) REVERT: E 36 ASP cc_start: 0.7597 (p0) cc_final: 0.7268 (p0) REVERT: E 67 MET cc_start: 0.7800 (tpp) cc_final: 0.7539 (tpp) REVERT: E 76 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8263 (mmtt) REVERT: E 105 CYS cc_start: 0.7385 (m) cc_final: 0.6985 (m) REVERT: E 129 LYS cc_start: 0.8626 (tppt) cc_final: 0.8358 (tppt) REVERT: E 131 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7852 (mmt-90) REVERT: E 162 SER cc_start: 0.8864 (t) cc_final: 0.8647 (t) REVERT: E 168 MET cc_start: 0.7600 (tmm) cc_final: 0.7330 (tmm) REVERT: E 169 HIS cc_start: 0.7864 (m170) cc_final: 0.7519 (m170) REVERT: E 254 LYS cc_start: 0.8229 (mttt) cc_final: 0.7927 (mttt) REVERT: E 277 THR cc_start: 0.8530 (m) cc_final: 0.8002 (p) REVERT: E 278 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8251 (mtpp) REVERT: E 299 LYS cc_start: 0.8390 (mttt) cc_final: 0.7934 (mtpp) REVERT: E 321 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8386 (p) REVERT: E 393 ARG cc_start: 0.5301 (tpt170) cc_final: 0.4636 (tpt170) REVERT: H 60 ASP cc_start: 0.7954 (t0) cc_final: 0.7478 (t0) REVERT: H 168 MET cc_start: 0.7316 (tpp) cc_final: 0.6575 (mpp) REVERT: H 224 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7951 (ptmm) REVERT: H 347 ASP cc_start: 0.7533 (t0) cc_final: 0.6922 (t0) REVERT: H 393 ARG cc_start: 0.5837 (tpt170) cc_final: 0.5149 (tpt170) REVERT: B 63 LYS cc_start: 0.8253 (mttm) cc_final: 0.7886 (mttm) REVERT: B 67 MET cc_start: 0.7075 (mmm) cc_final: 0.6474 (mmm) REVERT: B 76 LYS cc_start: 0.7960 (tppp) cc_final: 0.7532 (tppp) REVERT: B 225 GLN cc_start: 0.6637 (tm-30) cc_final: 0.6163 (tm-30) REVERT: B 265 VAL cc_start: 0.9207 (t) cc_final: 0.8772 (p) REVERT: B 276 VAL cc_start: 0.8705 (t) cc_final: 0.8395 (m) REVERT: B 281 LYS cc_start: 0.8355 (mttt) cc_final: 0.8051 (mttt) REVERT: B 354 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7533 (mt-10) REVERT: B 393 ARG cc_start: 0.7358 (tpt170) cc_final: 0.7056 (tpt170) REVERT: F 56 LYS cc_start: 0.8325 (ptpp) cc_final: 0.7843 (ptpp) REVERT: F 88 TYR cc_start: 0.5758 (m-80) cc_final: 0.5344 (m-10) REVERT: F 97 TYR cc_start: 0.5716 (m-80) cc_final: 0.5299 (m-80) REVERT: F 101 ARG cc_start: 0.7278 (ttt180) cc_final: 0.7031 (ttt180) REVERT: F 111 LYS cc_start: 0.8559 (mttt) cc_final: 0.8226 (mttt) REVERT: I 14 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7468 (mmtp) REVERT: I 111 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8372 (mtpp) REVERT: C 37 LYS cc_start: 0.8542 (tmmt) cc_final: 0.8311 (tmmt) REVERT: C 64 GLU cc_start: 0.7155 (tt0) cc_final: 0.6208 (tt0) outliers start: 142 outliers final: 113 residues processed: 1199 average time/residue: 0.2008 time to fit residues: 369.7334 Evaluate side-chains 1251 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1135 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 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 207 SER 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 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 156 ASP 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 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 68 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 78 CYS Chi-restraints excluded: chain D residue 139 ASN 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 259 CYS Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE 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 307 ILE 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 A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 67 GLU 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 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 317 THR Chi-restraints excluded: chain A residue 319 GLN 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 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 138 GLU 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 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 H residue 374 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 149 LEU 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 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 24 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 149 LYS Chi-restraints excluded: chain I residue 23 GLN 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 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 166 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 D 230 HIS G 52 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN H 96 HIS ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119290 restraints weight = 55984.984| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.85 r_work: 0.3380 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31760 Z= 0.186 Angle : 0.702 17.834 43289 Z= 0.352 Chirality : 0.047 0.218 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.495 79.696 4563 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 4.41 % Allowed : 20.62 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 3963 helix: 2.23 (0.25), residues: 405 sheet: -0.36 (0.15), residues: 1144 loop : -1.30 (0.13), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 124 TYR 0.029 0.002 TYR A 308 PHE 0.028 0.002 PHE E 51 TRP 0.025 0.001 TRP B 279 HIS 0.010 0.001 HIS K 353 Details of bonding type rmsd covalent geometry : bond 0.00419 (31692) covalent geometry : angle 0.69106 (43141) SS BOND : bond 0.00500 ( 56) SS BOND : angle 2.38781 ( 112) hydrogen bonds : bond 0.03261 ( 1026) hydrogen bonds : angle 5.21904 ( 2733) link_NAG-ASN : bond 0.00248 ( 12) link_NAG-ASN : angle 1.58487 ( 36) *********************** 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 1307 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1158 time to evaluate : 0.883 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: J 9 ASN cc_start: 0.8381 (t0) cc_final: 0.7855 (t0) REVERT: J 101 THR cc_start: 0.7859 (m) cc_final: 0.7584 (m) REVERT: J 134 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7764 (ttm-80) REVERT: J 180 ARG cc_start: 0.8554 (ttt-90) cc_final: 0.8347 (ttt-90) REVERT: J 191 GLU cc_start: 0.4977 (tt0) cc_final: 0.4008 (mt-10) REVERT: J 227 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8106 (ptmm) REVERT: J 234 THR cc_start: 0.7989 (p) cc_final: 0.7752 (t) REVERT: J 282 ILE cc_start: 0.8575 (mt) cc_final: 0.8145 (tp) REVERT: J 289 ARG cc_start: 0.8014 (mtt90) cc_final: 0.7594 (mtt90) REVERT: K 6 PHE cc_start: 0.8216 (m-80) cc_final: 0.7922 (m-80) REVERT: K 7 THR cc_start: 0.8507 (t) cc_final: 0.8234 (p) REVERT: K 37 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7577 (mm-30) REVERT: K 55 GLN cc_start: 0.8212 (tt0) cc_final: 0.7955 (tt0) REVERT: K 60 ASP cc_start: 0.7259 (t0) cc_final: 0.6614 (t0) REVERT: K 77 GLU cc_start: 0.7993 (pt0) cc_final: 0.7590 (pt0) REVERT: K 127 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7347 (mm-30) REVERT: K 138 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7036 (mm-30) REVERT: K 152 CYS cc_start: 0.7191 (p) cc_final: 0.6885 (p) REVERT: K 156 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: K 159 LYS cc_start: 0.8801 (pttm) cc_final: 0.8540 (pttm) REVERT: K 181 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6867 (tm-30) REVERT: K 195 LYS cc_start: 0.8401 (mppt) cc_final: 0.8090 (mppt) REVERT: K 222 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8290 (mmtt) REVERT: K 287 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8542 (pp) REVERT: K 324 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7597 (mt-10) REVERT: K 391 LYS cc_start: 0.8748 (tttm) cc_final: 0.8274 (tttm) REVERT: K 395 ASP cc_start: 0.8043 (m-30) cc_final: 0.7635 (m-30) REVERT: L 80 THR cc_start: 0.8310 (t) cc_final: 0.7961 (m) REVERT: D 61 LYS cc_start: 0.7735 (pptt) cc_final: 0.7039 (ptmm) REVERT: D 99 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6087 (tm-30) REVERT: D 249 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8140 (mmm160) REVERT: D 270 ASN cc_start: 0.7976 (m110) cc_final: 0.7714 (m110) REVERT: D 308 TYR cc_start: 0.7864 (p90) cc_final: 0.7475 (p90) REVERT: D 373 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7885 (mmtm) REVERT: D 381 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7768 (mtmm) REVERT: G 30 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6951 (mm-30) REVERT: G 103 LEU cc_start: 0.7719 (tp) cc_final: 0.7476 (tp) REVERT: G 105 GLU cc_start: 0.7184 (tt0) cc_final: 0.6757 (tt0) REVERT: G 174 ASP cc_start: 0.7951 (m-30) cc_final: 0.7384 (m-30) REVERT: G 218 ASP cc_start: 0.8262 (t0) cc_final: 0.7738 (t0) REVERT: G 241 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7527 (mm-30) REVERT: G 246 ASN cc_start: 0.7596 (t0) cc_final: 0.6923 (t0) REVERT: G 346 VAL cc_start: 0.7785 (t) cc_final: 0.7402 (m) REVERT: G 402 VAL cc_start: 0.8300 (t) cc_final: 0.8015 (t) REVERT: G 404 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7895 (ttmm) REVERT: A 9 ASN cc_start: 0.7831 (p0) cc_final: 0.7507 (p0) REVERT: A 20 GLU cc_start: 0.7394 (tt0) cc_final: 0.7161 (tt0) REVERT: A 107 TYR cc_start: 0.7770 (p90) cc_final: 0.7392 (p90) REVERT: A 117 ASP cc_start: 0.7119 (t0) cc_final: 0.6656 (t0) REVERT: A 202 ASP cc_start: 0.7497 (p0) cc_final: 0.7249 (p0) REVERT: A 249 ARG cc_start: 0.8774 (mmp80) cc_final: 0.8503 (mmp80) REVERT: A 320 TYR cc_start: 0.7998 (p90) cc_final: 0.7171 (p90) REVERT: E 36 ASP cc_start: 0.7529 (p0) cc_final: 0.7240 (p0) REVERT: E 67 MET cc_start: 0.7757 (tpp) cc_final: 0.7521 (tpp) REVERT: E 76 LYS cc_start: 0.8455 (mmtt) cc_final: 0.8254 (mmtt) REVERT: E 105 CYS cc_start: 0.7445 (m) cc_final: 0.7076 (m) REVERT: E 129 LYS cc_start: 0.8654 (tppt) cc_final: 0.8404 (tppt) REVERT: E 131 ARG cc_start: 0.8073 (mmt90) cc_final: 0.7837 (mmt-90) REVERT: E 162 SER cc_start: 0.8859 (t) cc_final: 0.8645 (t) REVERT: E 168 MET cc_start: 0.7554 (tmm) cc_final: 0.7300 (tmm) REVERT: E 169 HIS cc_start: 0.7849 (m170) cc_final: 0.7563 (m170) REVERT: E 254 LYS cc_start: 0.8162 (mttt) cc_final: 0.7864 (mttt) REVERT: E 277 THR cc_start: 0.8483 (m) cc_final: 0.7947 (p) REVERT: E 393 ARG cc_start: 0.5216 (tpt170) cc_final: 0.4706 (tpt170) REVERT: H 25 CYS cc_start: 0.5793 (t) cc_final: 0.5506 (t) REVERT: H 60 ASP cc_start: 0.7980 (t0) cc_final: 0.7469 (t0) REVERT: H 87 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7901 (p) REVERT: H 168 MET cc_start: 0.7318 (tpp) cc_final: 0.6974 (tpp) REVERT: H 179 TYR cc_start: 0.7683 (m-10) cc_final: 0.7448 (m-10) REVERT: H 224 LYS cc_start: 0.8247 (ptmm) cc_final: 0.7921 (ptmm) REVERT: H 239 ASN cc_start: 0.8316 (p0) cc_final: 0.8096 (p0) REVERT: H 347 ASP cc_start: 0.7501 (t0) cc_final: 0.6879 (t0) REVERT: H 393 ARG cc_start: 0.5778 (tpt170) cc_final: 0.5079 (tpt170) REVERT: B 63 LYS cc_start: 0.8295 (mttm) cc_final: 0.7866 (mttm) REVERT: B 67 MET cc_start: 0.7074 (mmm) cc_final: 0.6351 (mmm) REVERT: B 76 LYS cc_start: 0.7980 (tppp) cc_final: 0.7549 (tppp) REVERT: B 225 GLN cc_start: 0.6648 (tm-30) cc_final: 0.6127 (tm-30) REVERT: B 265 VAL cc_start: 0.9201 (t) cc_final: 0.8767 (p) REVERT: B 281 LYS cc_start: 0.8328 (mttt) cc_final: 0.8021 (mttt) REVERT: B 354 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7576 (mt-10) REVERT: F 56 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7827 (ptpp) REVERT: F 88 TYR cc_start: 0.5619 (m-80) cc_final: 0.5164 (m-10) REVERT: F 97 TYR cc_start: 0.5808 (m-80) cc_final: 0.5295 (m-80) REVERT: F 101 ARG cc_start: 0.7383 (ttt180) cc_final: 0.7030 (ttt180) REVERT: F 111 LYS cc_start: 0.8562 (mttt) cc_final: 0.8225 (mttt) REVERT: F 116 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7997 (mtp180) REVERT: I 14 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7395 (mmtp) REVERT: I 44 LYS cc_start: 0.8002 (tptt) cc_final: 0.7653 (tptt) REVERT: I 111 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8406 (mtpp) REVERT: C 37 LYS cc_start: 0.8548 (tmmt) cc_final: 0.8299 (tmmt) REVERT: C 55 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.6863 (mm) REVERT: C 64 GLU cc_start: 0.7089 (tt0) cc_final: 0.6144 (tt0) outliers start: 149 outliers final: 118 residues processed: 1211 average time/residue: 0.1900 time to fit residues: 356.3147 Evaluate side-chains 1269 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1147 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 207 SER 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 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 156 ASP 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 K residue 397 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 78 CYS 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 259 CYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 390 GLU 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 297 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU 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 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 251 LEU 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 317 THR 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 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 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 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 138 GLU 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 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 374 VAL 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 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 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 73 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 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 12 SER 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 55 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 48 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 362 optimal weight: 10.0000 chunk 348 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 351 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 245 optimal weight: 20.0000 chunk 384 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS D 196 ASN D 230 HIS G 52 HIS ** 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 E 50 GLN H 55 GLN H 96 HIS ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** 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 = 0.3733 r_free = 0.3733 target = 0.135590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118902 restraints weight = 55888.222| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.84 r_work: 0.3387 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 31760 Z= 0.192 Angle : 0.712 17.886 43289 Z= 0.357 Chirality : 0.048 0.300 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.524 79.275 4563 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.46 % Rotamer: Outliers : 4.38 % Allowed : 20.68 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 3963 helix: 2.22 (0.25), residues: 405 sheet: -0.30 (0.15), residues: 1126 loop : -1.32 (0.12), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 124 TYR 0.030 0.002 TYR A 308 PHE 0.027 0.002 PHE E 51 TRP 0.031 0.002 TRP B 279 HIS 0.015 0.001 HIS D 230 Details of bonding type rmsd covalent geometry : bond 0.00434 (31692) covalent geometry : angle 0.70293 (43141) SS BOND : bond 0.00523 ( 56) SS BOND : angle 2.24964 ( 112) hydrogen bonds : bond 0.03271 ( 1026) hydrogen bonds : angle 5.22448 ( 2733) link_NAG-ASN : bond 0.00253 ( 12) link_NAG-ASN : angle 1.58890 ( 36) *********************** 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 1301 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1153 time to evaluate : 1.158 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: J 9 ASN cc_start: 0.8368 (t0) cc_final: 0.7871 (t0) REVERT: J 101 THR cc_start: 0.7886 (m) cc_final: 0.7599 (m) REVERT: J 134 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7739 (ttm-80) REVERT: J 180 ARG cc_start: 0.8604 (ttt-90) cc_final: 0.8340 (ttt-90) REVERT: J 191 GLU cc_start: 0.5070 (tt0) cc_final: 0.3936 (mt-10) REVERT: J 227 LYS cc_start: 0.8412 (mtmm) cc_final: 0.8128 (ptmm) REVERT: J 234 THR cc_start: 0.7990 (p) cc_final: 0.7734 (t) REVERT: J 282 ILE cc_start: 0.8550 (mt) cc_final: 0.8121 (tp) REVERT: J 289 ARG cc_start: 0.7860 (mtt90) cc_final: 0.7503 (mtt90) REVERT: K 6 PHE cc_start: 0.8209 (m-80) cc_final: 0.7911 (m-80) REVERT: K 7 THR cc_start: 0.8530 (t) cc_final: 0.8262 (p) REVERT: K 37 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7548 (mm-30) REVERT: K 55 GLN cc_start: 0.8189 (tt0) cc_final: 0.7931 (tt0) REVERT: K 60 ASP cc_start: 0.7246 (t0) cc_final: 0.6603 (t0) REVERT: K 77 GLU cc_start: 0.8055 (pt0) cc_final: 0.7652 (pt0) REVERT: K 127 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7375 (mm-30) REVERT: K 138 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6993 (mm-30) REVERT: K 152 CYS cc_start: 0.7178 (p) cc_final: 0.6854 (p) REVERT: K 156 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7999 (m-30) REVERT: K 159 LYS cc_start: 0.8795 (pttm) cc_final: 0.8521 (pttm) REVERT: K 181 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6861 (tm-30) REVERT: K 195 LYS cc_start: 0.8440 (mppt) cc_final: 0.8121 (mppt) REVERT: K 222 LYS cc_start: 0.8570 (mmtt) cc_final: 0.8235 (mmtt) REVERT: K 287 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8542 (pp) REVERT: K 324 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7622 (mt-10) REVERT: K 391 LYS cc_start: 0.8738 (tttm) cc_final: 0.8265 (tttm) REVERT: K 395 ASP cc_start: 0.8020 (m-30) cc_final: 0.7610 (m-30) REVERT: L 80 THR cc_start: 0.8303 (t) cc_final: 0.7960 (m) REVERT: L 122 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7198 (mtm-85) REVERT: D 61 LYS cc_start: 0.7792 (pptt) cc_final: 0.7098 (ptmm) REVERT: D 99 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6099 (tm-30) REVERT: D 174 ASP cc_start: 0.7887 (t0) cc_final: 0.7645 (t0) REVERT: D 249 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8148 (mmm160) REVERT: D 270 ASN cc_start: 0.8002 (m110) cc_final: 0.7757 (m110) REVERT: D 308 TYR cc_start: 0.7907 (p90) cc_final: 0.7559 (p90) REVERT: D 373 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7894 (mmtm) REVERT: D 381 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7827 (mtmm) REVERT: G 30 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6914 (mm-30) REVERT: G 103 LEU cc_start: 0.7756 (tp) cc_final: 0.7551 (tp) REVERT: G 105 GLU cc_start: 0.7220 (tt0) cc_final: 0.6800 (tt0) REVERT: G 174 ASP cc_start: 0.7947 (m-30) cc_final: 0.7401 (m-30) REVERT: G 218 ASP cc_start: 0.8177 (t0) cc_final: 0.7684 (t0) REVERT: G 241 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7581 (mm-30) REVERT: G 246 ASN cc_start: 0.7683 (t0) cc_final: 0.6984 (t0) REVERT: G 346 VAL cc_start: 0.7791 (t) cc_final: 0.7441 (m) REVERT: G 402 VAL cc_start: 0.8246 (t) cc_final: 0.7963 (t) REVERT: G 404 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7852 (ttmm) REVERT: A 9 ASN cc_start: 0.7840 (p0) cc_final: 0.7517 (p0) REVERT: A 20 GLU cc_start: 0.7375 (tt0) cc_final: 0.7135 (tt0) REVERT: A 107 TYR cc_start: 0.7804 (p90) cc_final: 0.7402 (p90) REVERT: A 117 ASP cc_start: 0.7096 (t0) cc_final: 0.6588 (t0) REVERT: A 186 ASN cc_start: 0.8880 (m-40) cc_final: 0.8659 (m110) REVERT: A 202 ASP cc_start: 0.7453 (p0) cc_final: 0.7209 (p0) REVERT: A 249 ARG cc_start: 0.8772 (mmp80) cc_final: 0.8507 (mmp80) REVERT: A 320 TYR cc_start: 0.7895 (p90) cc_final: 0.7101 (p90) REVERT: A 373 LYS cc_start: 0.8375 (mptt) cc_final: 0.8085 (mptt) REVERT: E 36 ASP cc_start: 0.7551 (p0) cc_final: 0.7262 (p0) REVERT: E 67 MET cc_start: 0.7777 (tpp) cc_final: 0.7556 (tpp) REVERT: E 105 CYS cc_start: 0.7401 (m) cc_final: 0.7072 (m) REVERT: E 129 LYS cc_start: 0.8686 (tppt) cc_final: 0.8481 (tppt) REVERT: E 131 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7754 (mmt180) REVERT: E 162 SER cc_start: 0.8845 (t) cc_final: 0.8627 (t) REVERT: E 168 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: E 169 HIS cc_start: 0.7847 (m170) cc_final: 0.7584 (m170) REVERT: E 200 GLU cc_start: 0.7268 (tt0) cc_final: 0.6814 (tt0) REVERT: E 254 LYS cc_start: 0.8209 (mttt) cc_final: 0.7936 (mttt) REVERT: E 277 THR cc_start: 0.8505 (m) cc_final: 0.8030 (p) REVERT: E 278 LYS cc_start: 0.8645 (mmtp) cc_final: 0.8338 (mtpp) REVERT: E 393 ARG cc_start: 0.5313 (tpt170) cc_final: 0.4680 (tpt170) REVERT: H 60 ASP cc_start: 0.7981 (t0) cc_final: 0.7473 (t0) REVERT: H 168 MET cc_start: 0.7309 (tpp) cc_final: 0.6585 (mpp) REVERT: H 179 TYR cc_start: 0.7686 (m-10) cc_final: 0.7483 (m-10) REVERT: H 224 LYS cc_start: 0.8253 (ptmm) cc_final: 0.7966 (ptmm) REVERT: H 239 ASN cc_start: 0.8340 (p0) cc_final: 0.8096 (p0) REVERT: H 347 ASP cc_start: 0.7492 (t0) cc_final: 0.6865 (t0) REVERT: H 393 ARG cc_start: 0.5826 (tpt170) cc_final: 0.5139 (tpt170) REVERT: B 63 LYS cc_start: 0.8267 (mttm) cc_final: 0.7877 (mttm) REVERT: B 67 MET cc_start: 0.7021 (mmm) cc_final: 0.6179 (mmm) REVERT: B 76 LYS cc_start: 0.7992 (tppp) cc_final: 0.7558 (tppp) REVERT: B 225 GLN cc_start: 0.6642 (tm-30) cc_final: 0.6076 (tm-30) REVERT: B 265 VAL cc_start: 0.9195 (t) cc_final: 0.8758 (p) REVERT: B 281 LYS cc_start: 0.8364 (mttt) cc_final: 0.8050 (mttt) REVERT: B 354 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7533 (mt-10) REVERT: F 56 LYS cc_start: 0.8352 (ptpp) cc_final: 0.7851 (ptpp) REVERT: F 97 TYR cc_start: 0.5680 (m-80) cc_final: 0.5171 (m-80) REVERT: F 101 ARG cc_start: 0.7185 (ttt180) cc_final: 0.6847 (ttt180) REVERT: F 111 LYS cc_start: 0.8523 (mttt) cc_final: 0.8214 (mttt) REVERT: F 116 ARG cc_start: 0.8177 (mtp180) cc_final: 0.7949 (mtp180) REVERT: F 143 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8361 (p) REVERT: I 14 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7518 (mmtp) REVERT: I 44 LYS cc_start: 0.8082 (tptt) cc_final: 0.7691 (tptt) REVERT: I 111 LYS cc_start: 0.8625 (mtpp) cc_final: 0.8424 (mtpp) REVERT: I 143 VAL cc_start: 0.8466 (p) cc_final: 0.8201 (m) REVERT: C 55 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.6808 (mm) REVERT: C 64 GLU cc_start: 0.7122 (tt0) cc_final: 0.6209 (tt0) outliers start: 148 outliers final: 121 residues processed: 1208 average time/residue: 0.1970 time to fit residues: 367.0152 Evaluate side-chains 1271 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1145 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 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 207 SER 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 405 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 156 ASP 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 K residue 397 LEU Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain D residue 78 CYS 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 230 HIS 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 347 THR Chi-restraints excluded: chain D residue 390 GLU 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 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 307 ILE Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU 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 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 302 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 LEU 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 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 217 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 324 GLU 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 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 374 VAL 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 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 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 73 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 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 55 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 321 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 390 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 D 230 HIS G 52 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN H 96 HIS B 96 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.136157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119487 restraints weight = 55905.328| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.85 r_work: 0.3392 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31760 Z= 0.166 Angle : 0.721 17.811 43289 Z= 0.359 Chirality : 0.048 0.266 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.478 79.844 4563 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 3.97 % Allowed : 21.56 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.13), residues: 3963 helix: 2.21 (0.25), residues: 405 sheet: -0.27 (0.16), residues: 1117 loop : -1.30 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 124 TYR 0.029 0.002 TYR A 308 PHE 0.026 0.002 PHE E 51 TRP 0.034 0.001 TRP B 279 HIS 0.030 0.001 HIS D 230 Details of bonding type rmsd covalent geometry : bond 0.00381 (31692) covalent geometry : angle 0.71239 (43141) SS BOND : bond 0.00514 ( 56) SS BOND : angle 2.16754 ( 112) hydrogen bonds : bond 0.03183 ( 1026) hydrogen bonds : angle 5.18678 ( 2733) link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 1.49077 ( 36) ********************** 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 1289 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1155 time to evaluate : 1.194 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: J 9 ASN cc_start: 0.8345 (t0) cc_final: 0.7865 (t0) REVERT: J 101 THR cc_start: 0.7830 (m) cc_final: 0.7568 (m) REVERT: J 134 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7713 (ttm-80) REVERT: J 180 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8372 (ttt-90) REVERT: J 191 GLU cc_start: 0.5015 (tt0) cc_final: 0.3896 (mt-10) REVERT: J 227 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8114 (ptmm) REVERT: J 234 THR cc_start: 0.7969 (p) cc_final: 0.7714 (t) REVERT: J 282 ILE cc_start: 0.8547 (mt) cc_final: 0.8123 (tp) REVERT: J 289 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7483 (mtt90) REVERT: K 7 THR cc_start: 0.8529 (t) cc_final: 0.8261 (p) REVERT: K 37 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7552 (mm-30) REVERT: K 55 GLN cc_start: 0.8180 (tt0) cc_final: 0.7923 (tt0) REVERT: K 60 ASP cc_start: 0.7211 (t0) cc_final: 0.6579 (t0) REVERT: K 77 GLU cc_start: 0.8018 (pt0) cc_final: 0.7634 (pt0) REVERT: K 127 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7345 (mm-30) REVERT: K 138 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6987 (mm-30) REVERT: K 152 CYS cc_start: 0.7225 (p) cc_final: 0.6907 (p) REVERT: K 156 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: K 159 LYS cc_start: 0.8785 (pttm) cc_final: 0.8510 (pttm) REVERT: K 181 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6850 (tm-30) REVERT: K 195 LYS cc_start: 0.8428 (mppt) cc_final: 0.8111 (mppt) REVERT: K 222 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8185 (mmtt) REVERT: K 324 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7608 (mt-10) REVERT: K 391 LYS cc_start: 0.8652 (tttm) cc_final: 0.8116 (tttm) REVERT: K 395 ASP cc_start: 0.7999 (m-30) cc_final: 0.7611 (m-30) REVERT: L 80 THR cc_start: 0.8309 (t) cc_final: 0.7941 (m) REVERT: D 46 TYR cc_start: 0.8305 (p90) cc_final: 0.8089 (p90) REVERT: D 61 LYS cc_start: 0.7767 (pptt) cc_final: 0.7065 (ptmm) REVERT: D 99 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6108 (tm-30) REVERT: D 174 ASP cc_start: 0.7907 (t0) cc_final: 0.7637 (t0) REVERT: D 270 ASN cc_start: 0.7888 (m110) cc_final: 0.7670 (m110) REVERT: D 308 TYR cc_start: 0.7883 (p90) cc_final: 0.7542 (p90) REVERT: D 365 PHE cc_start: 0.8182 (p90) cc_final: 0.7964 (p90) REVERT: D 373 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7901 (mmtm) REVERT: D 381 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7834 (mtmm) REVERT: G 30 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6929 (mm-30) REVERT: G 103 LEU cc_start: 0.7755 (tp) cc_final: 0.7551 (tp) REVERT: G 105 GLU cc_start: 0.7211 (tt0) cc_final: 0.6786 (tt0) REVERT: G 174 ASP cc_start: 0.7944 (m-30) cc_final: 0.7387 (m-30) REVERT: G 218 ASP cc_start: 0.8210 (t0) cc_final: 0.7693 (t0) REVERT: G 241 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7505 (mm-30) REVERT: G 246 ASN cc_start: 0.7683 (t0) cc_final: 0.6989 (t0) REVERT: G 346 VAL cc_start: 0.7775 (t) cc_final: 0.7462 (m) REVERT: G 402 VAL cc_start: 0.8244 (t) cc_final: 0.7964 (t) REVERT: G 404 LYS cc_start: 0.8187 (ttmm) cc_final: 0.7922 (ttmm) REVERT: A 9 ASN cc_start: 0.7726 (p0) cc_final: 0.7379 (p0) REVERT: A 20 GLU cc_start: 0.7362 (tt0) cc_final: 0.7118 (tt0) REVERT: A 107 TYR cc_start: 0.7800 (p90) cc_final: 0.7361 (p90) REVERT: A 117 ASP cc_start: 0.7064 (t0) cc_final: 0.6557 (t0) REVERT: A 186 ASN cc_start: 0.8881 (m-40) cc_final: 0.8650 (m110) REVERT: A 202 ASP cc_start: 0.7425 (p0) cc_final: 0.7192 (p0) REVERT: A 249 ARG cc_start: 0.8767 (mmp80) cc_final: 0.8496 (mmp80) REVERT: A 320 TYR cc_start: 0.7857 (p90) cc_final: 0.7084 (p90) REVERT: E 36 ASP cc_start: 0.7529 (p0) cc_final: 0.7254 (p0) REVERT: E 50 GLN cc_start: 0.7758 (mm110) cc_final: 0.7526 (mm-40) REVERT: E 67 MET cc_start: 0.7783 (tpp) cc_final: 0.7538 (tpp) REVERT: E 105 CYS cc_start: 0.7384 (m) cc_final: 0.7089 (m) REVERT: E 129 LYS cc_start: 0.8667 (tppt) cc_final: 0.8242 (tppt) REVERT: E 131 ARG cc_start: 0.8051 (mmt90) cc_final: 0.7693 (mmt-90) REVERT: E 162 SER cc_start: 0.8853 (t) cc_final: 0.8639 (t) REVERT: E 168 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7274 (tmm) REVERT: E 169 HIS cc_start: 0.7813 (m170) cc_final: 0.7556 (m170) REVERT: E 195 LYS cc_start: 0.8337 (mttt) cc_final: 0.7922 (mttt) REVERT: E 200 GLU cc_start: 0.7271 (tt0) cc_final: 0.6812 (tt0) REVERT: E 254 LYS cc_start: 0.8206 (mttt) cc_final: 0.7928 (mttt) REVERT: E 277 THR cc_start: 0.8492 (m) cc_final: 0.7992 (p) REVERT: E 278 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8301 (mtpp) REVERT: E 299 LYS cc_start: 0.8403 (mttt) cc_final: 0.8068 (mtpp) REVERT: E 393 ARG cc_start: 0.5229 (tpt170) cc_final: 0.4602 (tpt170) REVERT: H 60 ASP cc_start: 0.7955 (t0) cc_final: 0.7445 (t0) REVERT: H 168 MET cc_start: 0.7338 (tpp) cc_final: 0.6997 (tpp) REVERT: H 179 TYR cc_start: 0.7667 (m-10) cc_final: 0.7427 (m-10) REVERT: H 224 LYS cc_start: 0.8248 (ptmm) cc_final: 0.7940 (ptmm) REVERT: H 239 ASN cc_start: 0.8358 (p0) cc_final: 0.8104 (p0) REVERT: H 347 ASP cc_start: 0.7472 (t0) cc_final: 0.6859 (t0) REVERT: H 393 ARG cc_start: 0.5795 (tpt170) cc_final: 0.5111 (tpt170) REVERT: B 63 LYS cc_start: 0.8266 (mttm) cc_final: 0.7909 (mttm) REVERT: B 67 MET cc_start: 0.6987 (mmm) cc_final: 0.6112 (mmm) REVERT: B 76 LYS cc_start: 0.7995 (tppp) cc_final: 0.7553 (tppp) REVERT: B 225 GLN cc_start: 0.6646 (tm-30) cc_final: 0.6030 (tm-30) REVERT: B 265 VAL cc_start: 0.9172 (t) cc_final: 0.8724 (p) REVERT: B 281 LYS cc_start: 0.8342 (mttt) cc_final: 0.8038 (mttt) REVERT: B 354 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7528 (mt-10) REVERT: F 56 LYS cc_start: 0.8312 (ptpp) cc_final: 0.7898 (ptpp) REVERT: F 97 TYR cc_start: 0.5608 (m-80) cc_final: 0.5154 (m-80) REVERT: F 101 ARG cc_start: 0.7112 (ttt180) cc_final: 0.6764 (ttt180) REVERT: F 111 LYS cc_start: 0.8493 (mttt) cc_final: 0.8178 (mttt) REVERT: F 116 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7927 (mtp180) REVERT: I 44 LYS cc_start: 0.7993 (tptt) cc_final: 0.7668 (tptt) REVERT: I 111 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8384 (mtpp) REVERT: I 143 VAL cc_start: 0.8438 (p) cc_final: 0.8191 (m) REVERT: C 55 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7610 (mm) REVERT: C 101 ARG cc_start: 0.6914 (tpm170) cc_final: 0.6697 (tpm170) outliers start: 134 outliers final: 120 residues processed: 1207 average time/residue: 0.1930 time to fit residues: 359.6220 Evaluate side-chains 1280 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1157 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 207 SER 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 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 80 MET Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 156 ASP 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 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain D residue 78 CYS 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 259 CYS Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 390 GLU Chi-restraints excluded: chain G residue 69 LYS 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 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 307 ILE Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU 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 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 302 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 354 LEU 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 37 GLU 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 324 GLU 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 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 374 VAL 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 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 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 24 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 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 55 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 259 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 317 optimal weight: 0.2980 chunk 147 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 350 optimal weight: 5.9990 chunk 361 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 360 optimal weight: 2.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN ** 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 52 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 HIS B 96 HIS ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** 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 = 0.3731 r_free = 0.3731 target = 0.135481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118838 restraints weight = 55986.199| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.84 r_work: 0.3378 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 31760 Z= 0.194 Angle : 0.730 18.101 43289 Z= 0.365 Chirality : 0.048 0.222 4873 Planarity : 0.005 0.054 5520 Dihedral : 5.523 79.250 4563 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 3.94 % Allowed : 21.80 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.13), residues: 3963 helix: 2.20 (0.25), residues: 399 sheet: -0.41 (0.15), residues: 1172 loop : -1.29 (0.13), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 124 TYR 0.030 0.002 TYR A 308 PHE 0.025 0.002 PHE E 51 TRP 0.039 0.002 TRP B 279 HIS 0.016 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00439 (31692) covalent geometry : angle 0.72138 (43141) SS BOND : bond 0.00544 ( 56) SS BOND : angle 2.22300 ( 112) hydrogen bonds : bond 0.03268 ( 1026) hydrogen bonds : angle 5.20130 ( 2733) link_NAG-ASN : bond 0.00248 ( 12) link_NAG-ASN : angle 1.56461 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8493.78 seconds wall clock time: 145 minutes 59.02 seconds (8759.02 seconds total)