Starting phenix.real_space_refine on Thu Jun 26 15:50:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqx_47117/06_2025/9dqx_47117.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqx_47117/06_2025/9dqx_47117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dqx_47117/06_2025/9dqx_47117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqx_47117/06_2025/9dqx_47117.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqx_47117/06_2025/9dqx_47117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqx_47117/06_2025/9dqx_47117.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 19564 2.51 5 N 5322 2.21 5 O 5822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30900 Number of models: 1 Model: "" Number of chains: 20 Chain: "J" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "K" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3174 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 27, 'TRANS': 376} Chain breaks: 1 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1188 Classifications: {'peptide': 154} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "D" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "G" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3300 Classifications: {'peptide': 437} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 409} Chain: "E" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 27, 'TRANS': 378} Chain: "H" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 27, 'TRANS': 378} Chain: "B" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3183 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 27, 'TRANS': 378} Chain: "F" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "I" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1193 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain breaks: 2 Chain: "C" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 19.16, per 1000 atoms: 0.62 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: 7.43 Conformation dependent library (CDL) restraints added in 4.1 seconds 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7372 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 96 sheets defined 12.0% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.80 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: 12.03 Time building geometry restraints manager: 8.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9991 1.35 - 1.47: 8022 1.47 - 1.60: 13431 1.60 - 1.73: 0 1.73 - 1.86: 248 Bond restraints: 31692 Sorted by residual: bond pdb=" C CYS J 328 " pdb=" N PRO J 329 " ideal model delta sigma weight residual 1.326 1.357 -0.031 1.44e-02 4.82e+03 4.72e+00 bond pdb=" CB CYS J 62 " pdb=" SG CYS J 62 " ideal model delta sigma weight residual 1.808 1.862 -0.054 3.30e-02 9.18e+02 2.63e+00 bond pdb=" N THR A 53 " pdb=" CA THR A 53 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.59e+00 bond pdb=" CB ASP F 62 " pdb=" CG ASP F 62 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.50e+00 bond pdb=" CB ASP C 62 " pdb=" CG ASP C 62 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.49e+00 ... (remaining 31687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 42000 2.44 - 4.88: 986 4.88 - 7.31: 122 7.31 - 9.75: 25 9.75 - 12.19: 8 Bond angle restraints: 43141 Sorted by residual: angle pdb=" N VAL A 148 " pdb=" CA VAL A 148 " pdb=" C VAL A 148 " ideal model delta sigma weight residual 112.90 106.58 6.32 9.60e-01 1.09e+00 4.33e+01 angle pdb=" C CYS G 94 " pdb=" N PHE G 95 " pdb=" CA PHE G 95 " ideal model delta sigma weight residual 120.28 125.97 -5.69 1.34e+00 5.57e-01 1.80e+01 angle pdb=" C GLU L 98 " pdb=" N ASN L 99 " pdb=" CA ASN L 99 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 angle pdb=" C TRP E 279 " pdb=" N PHE E 280 " pdb=" CA PHE E 280 " ideal model delta sigma weight residual 121.54 129.16 -7.62 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET I 8 " pdb=" CG MET I 8 " pdb=" SD MET I 8 " ideal model delta sigma weight residual 112.70 124.64 -11.94 3.00e+00 1.11e-01 1.58e+01 ... (remaining 43136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 17603 17.83 - 35.66: 1252 35.66 - 53.50: 248 53.50 - 71.33: 49 71.33 - 89.16: 17 Dihedral angle restraints: 19169 sinusoidal: 7654 harmonic: 11515 Sorted by residual: dihedral pdb=" CB CYS H 16 " pdb=" SG CYS H 16 " pdb=" SG CYS H 124 " pdb=" CB CYS H 124 " ideal model delta sinusoidal sigma weight residual 93.00 177.85 -84.85 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS H 152 " pdb=" SG CYS H 152 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual 93.00 175.77 -82.77 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual 93.00 169.53 -76.53 1 1.00e+01 1.00e-02 7.36e+01 ... (remaining 19166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3996 0.069 - 0.138: 768 0.138 - 0.207: 93 0.207 - 0.275: 14 0.275 - 0.344: 2 Chirality restraints: 4873 Sorted by residual: chirality pdb=" CB ILE F 18 " pdb=" CA ILE F 18 " pdb=" CG1 ILE F 18 " pdb=" CG2 ILE F 18 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CB ILE G 307 " pdb=" CA ILE G 307 " pdb=" CG1 ILE G 307 " pdb=" CG2 ILE G 307 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CB VAL K 268 " pdb=" CA VAL K 268 " pdb=" CG1 VAL K 268 " pdb=" CG2 VAL K 268 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 4870 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 409 " -0.019 2.00e-02 2.50e+03 2.21e-02 1.22e+01 pdb=" CG TRP A 409 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP A 409 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 409 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 409 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 409 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 409 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 409 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 409 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 409 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 279 " -0.017 2.00e-02 2.50e+03 1.98e-02 9.83e+00 pdb=" CG TRP B 279 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 279 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 279 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 279 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 279 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 279 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 137 " -0.277 9.50e-02 1.11e+02 1.24e-01 9.53e+00 pdb=" NE ARG B 137 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 137 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 137 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 137 " -0.009 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1990 2.74 - 3.28: 29856 3.28 - 3.82: 50293 3.82 - 4.36: 58306 4.36 - 4.90: 101694 Nonbonded interactions: 242139 Sorted by model distance: nonbonded pdb=" OG SER K 86 " pdb=" OG1 THR K 112 " model vdw 2.196 3.040 nonbonded pdb=" OG SER H 79 " pdb=" OE1 GLU H 81 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 309 " pdb=" OE1 GLN B 341 " model vdw 2.222 3.040 nonbonded pdb=" OD1 ASN K 405 " pdb=" OH TYR L 79 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 57 " pdb=" O SER B 240 " model vdw 2.228 3.040 ... (remaining 242134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = (chain 'B' and (resid 1 through 117 or resid 120 through 406 or resid 501 throug \ h 502)) selection = (chain 'E' and (resid 1 through 117 or resid 120 through 406 or resid 501 throug \ h 502)) selection = (chain 'H' and (resid 1 through 117 or resid 120 through 406 or resid 501 throug \ h 502)) selection = chain 'K' } ncs_group { reference = (chain 'C' and (resid 6 through 132 or resid 137 through 140 or resid 142 throug \ h 163)) selection = (chain 'F' and (resid 6 through 132 or resid 137 through 140 or resid 142 throug \ h 163)) selection = (chain 'I' and (resid 6 through 132 or resid 137 through 163)) selection = (chain 'L' and (resid 6 through 140 or resid 142 through 163)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 71.090 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31760 Z= 0.179 Angle : 0.879 12.188 43289 Z= 0.466 Chirality : 0.055 0.344 4873 Planarity : 0.007 0.124 5520 Dihedral : 12.538 89.162 11629 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3963 helix: 0.48 (0.23), residues: 426 sheet: -0.31 (0.16), residues: 1128 loop : -1.61 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 409 HIS 0.019 0.001 HIS B 73 PHE 0.044 0.002 PHE E 280 TYR 0.029 0.002 TYR C 27 ARG 0.015 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 1.81443 ( 36) hydrogen bonds : bond 0.12398 ( 1026) hydrogen bonds : angle 6.96231 ( 2733) SS BOND : bond 0.00441 ( 56) SS BOND : angle 2.14381 ( 112) covalent geometry : bond 0.00370 (31692) covalent geometry : angle 0.87224 (43141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1252 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8023 (t160) cc_final: 0.7812 (t0) REVERT: J 49 CYS cc_start: 0.7447 (p) cc_final: 0.7102 (p) REVERT: J 61 LYS cc_start: 0.7997 (tmmt) cc_final: 0.7536 (tmmt) REVERT: J 75 ASP cc_start: 0.8024 (t0) cc_final: 0.7823 (t0) REVERT: J 101 THR cc_start: 0.7271 (m) cc_final: 0.6990 (m) REVERT: J 143 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7608 (mmt90) REVERT: J 175 HIS cc_start: 0.8126 (t70) cc_final: 0.7713 (t70) REVERT: J 180 ARG cc_start: 0.8341 (ttt-90) cc_final: 0.8096 (ttt180) REVERT: J 186 ASN cc_start: 0.8487 (m-40) cc_final: 0.8196 (m-40) REVERT: J 227 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8087 (mtmm) REVERT: J 264 GLU cc_start: 0.8097 (tt0) cc_final: 0.7811 (tt0) REVERT: J 271 CYS cc_start: 0.6720 (m) cc_final: 0.6346 (m) REVERT: J 289 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7624 (mtt90) REVERT: J 318 LEU cc_start: 0.7676 (tp) cc_final: 0.7375 (tp) REVERT: J 395 ASP cc_start: 0.7263 (t0) cc_final: 0.6936 (t0) REVERT: J 406 SER cc_start: 0.8518 (t) cc_final: 0.7876 (p) REVERT: K 7 THR cc_start: 0.8536 (t) cc_final: 0.8277 (p) REVERT: K 25 CYS cc_start: 0.6021 (t) cc_final: 0.5387 (t) REVERT: K 36 ASP cc_start: 0.7270 (p0) cc_final: 0.7036 (p0) REVERT: K 37 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7584 (mm-30) REVERT: K 55 GLN cc_start: 0.8359 (tt0) cc_final: 0.8088 (tt0) REVERT: K 60 ASP cc_start: 0.7112 (t0) cc_final: 0.6833 (t0) REVERT: K 77 GLU cc_start: 0.8068 (pt0) cc_final: 0.7676 (pt0) REVERT: K 82 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8010 (mmmt) REVERT: K 152 CYS cc_start: 0.7124 (p) cc_final: 0.6629 (p) REVERT: K 156 ASP cc_start: 0.8155 (t0) cc_final: 0.7747 (t0) REVERT: K 158 LEU cc_start: 0.8688 (mp) cc_final: 0.8422 (mp) REVERT: K 159 LYS cc_start: 0.8786 (pttm) cc_final: 0.8491 (pttm) REVERT: K 181 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6652 (tm-30) REVERT: K 222 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8290 (mmtt) REVERT: K 324 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7656 (mt-10) REVERT: K 391 LYS cc_start: 0.8739 (tttm) cc_final: 0.8274 (tttm) REVERT: K 393 ARG cc_start: 0.8651 (ttt180) cc_final: 0.7383 (tpt170) REVERT: K 395 ASP cc_start: 0.8265 (m-30) cc_final: 0.7780 (m-30) REVERT: K 397 LEU cc_start: 0.8577 (mm) cc_final: 0.8335 (mm) REVERT: L 57 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7961 (mtmm) REVERT: L 79 TYR cc_start: 0.7313 (p90) cc_final: 0.7084 (p90) REVERT: D 37 GLU cc_start: 0.7272 (mp0) cc_final: 0.6979 (mp0) REVERT: D 99 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6387 (tm-30) REVERT: D 160 LYS cc_start: 0.8113 (tmmt) cc_final: 0.7723 (tmmt) REVERT: D 230 HIS cc_start: 0.7872 (t70) cc_final: 0.7632 (t70) REVERT: D 257 PHE cc_start: 0.8871 (m-80) cc_final: 0.8594 (m-80) REVERT: D 273 TYR cc_start: 0.8096 (p90) cc_final: 0.7678 (p90) REVERT: D 320 TYR cc_start: 0.7309 (p90) cc_final: 0.7097 (p90) REVERT: D 373 LYS cc_start: 0.7958 (mmtm) cc_final: 0.7754 (mmtm) REVERT: D 387 ILE cc_start: 0.8691 (mm) cc_final: 0.8015 (tp) REVERT: D 388 ILE cc_start: 0.8325 (tp) cc_final: 0.8055 (mm) REVERT: D 409 TRP cc_start: 0.7170 (m100) cc_final: 0.6866 (m100) REVERT: D 430 CYS cc_start: 0.8143 (p) cc_final: 0.7937 (p) REVERT: D 433 MET cc_start: 0.8274 (ttm) cc_final: 0.8058 (ttm) REVERT: G 15 TYR cc_start: 0.7774 (t80) cc_final: 0.7342 (t80) REVERT: G 30 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7131 (mm-30) REVERT: G 67 GLU cc_start: 0.6787 (tp30) cc_final: 0.6580 (tp30) REVERT: G 76 TYR cc_start: 0.8190 (t80) cc_final: 0.7759 (t80) REVERT: G 105 GLU cc_start: 0.7300 (tt0) cc_final: 0.7051 (tt0) REVERT: G 139 ASN cc_start: 0.7366 (m110) cc_final: 0.7133 (m110) REVERT: G 174 ASP cc_start: 0.7980 (m-30) cc_final: 0.7758 (m-30) REVERT: G 218 ASP cc_start: 0.7937 (t0) cc_final: 0.7536 (t0) REVERT: G 241 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7646 (mm-30) REVERT: G 244 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8023 (mtmt) REVERT: G 264 GLU cc_start: 0.7528 (mp0) cc_final: 0.7094 (mp0) REVERT: G 311 ASP cc_start: 0.7355 (t0) cc_final: 0.7050 (t0) REVERT: G 324 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7688 (ptm-80) REVERT: G 341 GLU cc_start: 0.7400 (mp0) cc_final: 0.7085 (mp0) REVERT: A 52 HIS cc_start: 0.7886 (t-90) cc_final: 0.7638 (t-170) REVERT: A 136 VAL cc_start: 0.8340 (p) cc_final: 0.7997 (m) REVERT: A 203 ILE cc_start: 0.8570 (tt) cc_final: 0.8033 (pt) REVERT: A 234 THR cc_start: 0.8212 (m) cc_final: 0.7908 (t) REVERT: A 298 GLU cc_start: 0.6698 (tp30) cc_final: 0.6455 (tp30) REVERT: A 323 ASN cc_start: 0.8469 (p0) cc_final: 0.8203 (p0) REVERT: A 353 THR cc_start: 0.7362 (m) cc_final: 0.7118 (t) REVERT: A 386 HIS cc_start: 0.7776 (m-70) cc_final: 0.7516 (m-70) REVERT: A 388 ILE cc_start: 0.8254 (tp) cc_final: 0.7906 (tp) REVERT: A 430 CYS cc_start: 0.8374 (m) cc_final: 0.8106 (m) REVERT: A 434 LEU cc_start: 0.8694 (mm) cc_final: 0.8489 (mm) REVERT: E 27 SER cc_start: 0.8606 (t) cc_final: 0.8356 (t) REVERT: E 36 ASP cc_start: 0.7566 (p0) cc_final: 0.7257 (p0) REVERT: E 76 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8130 (mmtt) REVERT: E 109 ASP cc_start: 0.7537 (m-30) cc_final: 0.7116 (m-30) REVERT: E 129 LYS cc_start: 0.8393 (tppt) cc_final: 0.7892 (tppt) REVERT: E 131 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7420 (mmt-90) REVERT: E 139 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7225 (mt-10) REVERT: E 162 SER cc_start: 0.8867 (t) cc_final: 0.8627 (t) REVERT: E 195 LYS cc_start: 0.8320 (mttt) cc_final: 0.8110 (mttt) REVERT: E 250 SER cc_start: 0.8638 (m) cc_final: 0.8297 (t) REVERT: E 254 LYS cc_start: 0.8240 (mttt) cc_final: 0.7829 (mttm) REVERT: E 278 LYS cc_start: 0.8334 (mmtp) cc_final: 0.7770 (mmtp) REVERT: E 354 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7108 (mt-10) REVERT: E 391 LYS cc_start: 0.8313 (mptt) cc_final: 0.7915 (mptt) REVERT: E 393 ARG cc_start: 0.5124 (tpt170) cc_final: 0.4425 (tpt170) REVERT: H 60 ASP cc_start: 0.7830 (t0) cc_final: 0.7361 (t0) REVERT: H 77 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7808 (mm-30) REVERT: H 94 LEU cc_start: 0.8542 (mt) cc_final: 0.8319 (mt) REVERT: H 159 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8440 (ptpp) REVERT: H 161 THR cc_start: 0.7863 (p) cc_final: 0.7660 (p) REVERT: H 168 MET cc_start: 0.7448 (mtp) cc_final: 0.7075 (mtp) REVERT: H 179 TYR cc_start: 0.7585 (m-10) cc_final: 0.7341 (m-10) REVERT: H 393 ARG cc_start: 0.6112 (tpt170) cc_final: 0.5540 (tpt170) REVERT: H 405 ASN cc_start: 0.7452 (m-40) cc_final: 0.7150 (m-40) REVERT: B 76 LYS cc_start: 0.7961 (tppp) cc_final: 0.7472 (tppp) REVERT: B 80 MET cc_start: 0.7798 (ttt) cc_final: 0.7571 (ttt) REVERT: B 97 LYS cc_start: 0.7844 (tttp) cc_final: 0.7455 (tttp) REVERT: B 102 LEU cc_start: 0.8322 (tp) cc_final: 0.7996 (tt) REVERT: B 159 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8071 (ptpt) REVERT: B 265 VAL cc_start: 0.8830 (t) cc_final: 0.8355 (p) REVERT: B 281 LYS cc_start: 0.8158 (mttt) cc_final: 0.7832 (mttt) REVERT: B 391 LYS cc_start: 0.8742 (tttm) cc_final: 0.8293 (tttm) REVERT: B 393 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6270 (tpp80) REVERT: F 8 MET cc_start: 0.7384 (mmp) cc_final: 0.7153 (mmp) REVERT: F 19 MET cc_start: 0.7153 (mmp) cc_final: 0.6926 (mmm) REVERT: F 44 LYS cc_start: 0.7577 (pptt) cc_final: 0.7187 (pptt) REVERT: F 56 LYS cc_start: 0.8212 (ptpp) cc_final: 0.7961 (ptpp) REVERT: F 101 ARG cc_start: 0.7029 (ttt180) cc_final: 0.6722 (ttt180) REVERT: F 124 ARG cc_start: 0.6711 (ttp-110) cc_final: 0.6500 (ttp-110) REVERT: I 25 ASN cc_start: 0.6547 (t0) cc_final: 0.6273 (t0) REVERT: I 64 GLU cc_start: 0.7272 (mp0) cc_final: 0.6624 (mp0) REVERT: I 78 GLN cc_start: 0.8125 (mp-120) cc_final: 0.7892 (mp-120) REVERT: I 111 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8261 (mtpp) REVERT: C 37 LYS cc_start: 0.8490 (tmmt) cc_final: 0.8214 (tmmt) outliers start: 0 outliers final: 0 residues processed: 1252 average time/residue: 0.4600 time to fit residues: 877.1788 Evaluate side-chains 1170 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1170 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 9 ASN J 100 ASN K 50 GLN ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 HIS D 196 ASN D 228 ASN D 319 GLN D 327 HIS G 59 GLN G 175 HIS G 345 HIS A 43 ASN A 100 ASN A 246 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN H 174 HIS H 218 ASN H 256 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 153 HIS B 157 HIS ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 361 HIS ** I 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.119058 restraints weight = 56012.807| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.90 r_work: 0.3350 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 31760 Z= 0.262 Angle : 0.715 16.927 43289 Z= 0.369 Chirality : 0.049 0.266 4873 Planarity : 0.006 0.058 5520 Dihedral : 6.312 77.144 4563 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.21 % Favored : 93.69 % Rotamer: Outliers : 2.61 % Allowed : 11.49 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3963 helix: 1.60 (0.24), residues: 414 sheet: -0.45 (0.15), residues: 1197 loop : -1.46 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 279 HIS 0.014 0.001 HIS B 73 PHE 0.024 0.002 PHE K 134 TYR 0.030 0.002 TYR A 308 ARG 0.009 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00364 ( 12) link_NAG-ASN : angle 1.86915 ( 36) hydrogen bonds : bond 0.03829 ( 1026) hydrogen bonds : angle 5.71446 ( 2733) SS BOND : bond 0.00424 ( 56) SS BOND : angle 2.01975 ( 112) covalent geometry : bond 0.00563 (31692) covalent geometry : angle 0.70672 (43141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1223 time to evaluate : 3.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8430 (t0) cc_final: 0.7903 (t0) REVERT: J 49 CYS cc_start: 0.7608 (p) cc_final: 0.7370 (p) REVERT: J 50 LYS cc_start: 0.8291 (tttm) cc_final: 0.8015 (tttm) REVERT: J 61 LYS cc_start: 0.8021 (tmmt) cc_final: 0.7565 (ttpt) REVERT: J 130 LYS cc_start: 0.7922 (tttp) cc_final: 0.7642 (tppt) REVERT: J 180 ARG cc_start: 0.8560 (ttt-90) cc_final: 0.8356 (ttt-90) REVERT: J 191 GLU cc_start: 0.4682 (tt0) cc_final: 0.3857 (mt-10) REVERT: J 234 THR cc_start: 0.7953 (p) cc_final: 0.7711 (t) REVERT: J 271 CYS cc_start: 0.6618 (m) cc_final: 0.6313 (m) REVERT: J 289 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7590 (mtt90) REVERT: J 292 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7852 (mt-10) REVERT: J 318 LEU cc_start: 0.7655 (tp) cc_final: 0.7180 (tp) REVERT: K 4 ASP cc_start: 0.7587 (t0) cc_final: 0.7369 (t0) REVERT: K 7 THR cc_start: 0.8527 (t) cc_final: 0.8239 (p) REVERT: K 55 GLN cc_start: 0.8490 (tt0) cc_final: 0.8256 (tt0) REVERT: K 60 ASP cc_start: 0.7386 (t0) cc_final: 0.6786 (t0) REVERT: K 77 GLU cc_start: 0.8008 (pt0) cc_final: 0.7644 (pt0) REVERT: K 82 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8329 (mtpt) REVERT: K 127 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7390 (mm-30) REVERT: K 138 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7094 (mm-30) REVERT: K 152 CYS cc_start: 0.7273 (p) cc_final: 0.6882 (p) REVERT: K 156 ASP cc_start: 0.8180 (t0) cc_final: 0.7727 (t0) REVERT: K 158 LEU cc_start: 0.8696 (mp) cc_final: 0.8309 (mp) REVERT: K 159 LYS cc_start: 0.8769 (pttm) cc_final: 0.8456 (pttm) REVERT: K 176 TYR cc_start: 0.8046 (m-80) cc_final: 0.7771 (m-80) REVERT: K 181 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6583 (tm-30) REVERT: K 195 LYS cc_start: 0.8433 (mppt) cc_final: 0.8156 (mppt) REVERT: K 222 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8323 (mmtt) REVERT: K 324 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7651 (mt-10) REVERT: K 354 GLU cc_start: 0.7648 (mp0) cc_final: 0.7373 (mp0) REVERT: K 391 LYS cc_start: 0.8779 (tttm) cc_final: 0.8312 (tttm) REVERT: K 395 ASP cc_start: 0.8195 (m-30) cc_final: 0.7765 (m-30) REVERT: L 57 LYS cc_start: 0.8333 (mtmm) cc_final: 0.7992 (mtmm) REVERT: D 61 LYS cc_start: 0.7699 (pptt) cc_final: 0.7468 (ptmm) REVERT: D 76 TYR cc_start: 0.8223 (t80) cc_final: 0.7941 (t80) REVERT: D 99 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6203 (tm-30) REVERT: D 160 LYS cc_start: 0.8123 (tmmt) cc_final: 0.7737 (tmmt) REVERT: D 230 HIS cc_start: 0.7975 (t70) cc_final: 0.7714 (t70) REVERT: D 257 PHE cc_start: 0.9041 (m-80) cc_final: 0.8828 (m-80) REVERT: D 270 ASN cc_start: 0.7916 (m110) cc_final: 0.7620 (m110) REVERT: D 307 ILE cc_start: 0.7726 (mt) cc_final: 0.7432 (mp) REVERT: D 320 TYR cc_start: 0.7746 (p90) cc_final: 0.7427 (p90) REVERT: D 323 ASN cc_start: 0.8143 (p0) cc_final: 0.7884 (p0) REVERT: D 365 PHE cc_start: 0.8267 (p90) cc_final: 0.7953 (p90) REVERT: D 373 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7852 (mmtm) REVERT: D 390 GLU cc_start: 0.7568 (pm20) cc_final: 0.7291 (pm20) REVERT: D 430 CYS cc_start: 0.8230 (p) cc_final: 0.8008 (p) REVERT: G 174 ASP cc_start: 0.7988 (m-30) cc_final: 0.7609 (m-30) REVERT: G 218 ASP cc_start: 0.8237 (t0) cc_final: 0.7689 (t0) REVERT: G 241 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7571 (mm-30) REVERT: G 246 ASN cc_start: 0.7610 (t0) cc_final: 0.7293 (t0) REVERT: G 343 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8179 (m) REVERT: G 404 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7899 (ttmm) REVERT: A 50 LYS cc_start: 0.8109 (tttp) cc_final: 0.7744 (ttpp) REVERT: A 87 PHE cc_start: 0.7867 (t80) cc_final: 0.7493 (t80) REVERT: A 88 MET cc_start: 0.7742 (mtp) cc_final: 0.7519 (mtp) REVERT: A 202 ASP cc_start: 0.7528 (p0) cc_final: 0.7303 (p0) REVERT: A 263 VAL cc_start: 0.8169 (m) cc_final: 0.7944 (p) REVERT: A 298 GLU cc_start: 0.6931 (tp30) cc_final: 0.6666 (tp30) REVERT: A 321 LYS cc_start: 0.8361 (pptt) cc_final: 0.8120 (pptt) REVERT: A 323 ASN cc_start: 0.8668 (p0) cc_final: 0.8356 (p0) REVERT: A 373 LYS cc_start: 0.8435 (mptt) cc_final: 0.8161 (mptt) REVERT: A 430 CYS cc_start: 0.8475 (m) cc_final: 0.8244 (m) REVERT: E 34 VAL cc_start: 0.8946 (t) cc_final: 0.8495 (m) REVERT: E 36 ASP cc_start: 0.7642 (p0) cc_final: 0.7273 (p0) REVERT: E 76 LYS cc_start: 0.8489 (mmtt) cc_final: 0.8172 (mmtt) REVERT: E 129 LYS cc_start: 0.8564 (tppt) cc_final: 0.8178 (tppt) REVERT: E 131 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7649 (mmt180) REVERT: E 139 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7175 (mt-10) REVERT: E 168 MET cc_start: 0.7586 (tmm) cc_final: 0.7366 (tmm) REVERT: E 229 TYR cc_start: 0.7593 (p90) cc_final: 0.7205 (p90) REVERT: E 254 LYS cc_start: 0.8098 (mttt) cc_final: 0.7748 (mttt) REVERT: E 277 THR cc_start: 0.8444 (m) cc_final: 0.7923 (p) REVERT: E 393 ARG cc_start: 0.5466 (tpt170) cc_final: 0.4702 (tpt170) REVERT: E 394 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.7456 (ptm-80) REVERT: H 60 ASP cc_start: 0.7940 (t0) cc_final: 0.7425 (t0) REVERT: H 65 ARG cc_start: 0.8635 (ptm-80) cc_final: 0.7807 (ptm-80) REVERT: H 105 CYS cc_start: 0.6881 (m) cc_final: 0.6657 (m) REVERT: H 141 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7677 (mt) REVERT: H 179 TYR cc_start: 0.7769 (m-10) cc_final: 0.7422 (m-10) REVERT: H 224 LYS cc_start: 0.8141 (ptmm) cc_final: 0.7905 (ptmm) REVERT: H 347 ASP cc_start: 0.7575 (t0) cc_final: 0.6906 (t0) REVERT: H 393 ARG cc_start: 0.5899 (tpt170) cc_final: 0.5324 (tpt170) REVERT: H 394 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7756 (ttp-110) REVERT: B 76 LYS cc_start: 0.7961 (tppp) cc_final: 0.7504 (tppp) REVERT: B 97 LYS cc_start: 0.8119 (tttp) cc_final: 0.7851 (tttp) REVERT: B 159 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8114 (ptpt) REVERT: B 224 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7147 (tmtt) REVERT: B 254 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7395 (mtpt) REVERT: B 265 VAL cc_start: 0.9065 (t) cc_final: 0.8589 (p) REVERT: B 276 VAL cc_start: 0.8755 (t) cc_final: 0.8436 (m) REVERT: B 281 LYS cc_start: 0.8284 (mttt) cc_final: 0.7968 (mttt) REVERT: B 354 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 362 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8301 (mmm-85) REVERT: F 8 MET cc_start: 0.7486 (mmp) cc_final: 0.7231 (mmp) REVERT: F 19 MET cc_start: 0.6657 (mmp) cc_final: 0.5911 (mmp) REVERT: F 44 LYS cc_start: 0.7907 (pptt) cc_final: 0.7623 (pptt) REVERT: F 56 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7914 (ptpp) REVERT: F 60 MET cc_start: 0.7992 (mmt) cc_final: 0.7760 (mmt) REVERT: F 101 ARG cc_start: 0.7288 (ttt180) cc_final: 0.7087 (ttt180) REVERT: F 120 ASP cc_start: 0.8019 (p0) cc_final: 0.7640 (p0) REVERT: F 124 ARG cc_start: 0.6564 (ttp-110) cc_final: 0.5390 (ttp-110) REVERT: I 37 LYS cc_start: 0.8269 (ptmm) cc_final: 0.7159 (ptmm) REVERT: I 44 LYS cc_start: 0.7990 (tptt) cc_final: 0.7738 (tptt) REVERT: I 49 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7571 (tm-30) REVERT: I 64 GLU cc_start: 0.7198 (mp0) cc_final: 0.6594 (mp0) REVERT: I 101 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6489 (mmm-85) REVERT: I 111 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8405 (mtpp) REVERT: C 37 LYS cc_start: 0.8622 (tmmt) cc_final: 0.8309 (tmmt) REVERT: C 106 ARG cc_start: 0.8061 (ppt170) cc_final: 0.7804 (ppt170) outliers start: 88 outliers final: 57 residues processed: 1249 average time/residue: 0.4733 time to fit residues: 902.4026 Evaluate side-chains 1235 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 1175 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 207 SER Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain E residue 142 PHE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 27 optimal weight: 5.9990 chunk 375 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 314 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 390 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 277 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 93 GLN 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 196 ASN D 319 GLN D 327 HIS D 386 HIS D 408 ASN G 52 HIS G 139 ASN G 230 HIS G 345 HIS A 43 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN A 331 HIS H 46 GLN H 96 HIS ** B 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 96 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 47 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119771 restraints weight = 56177.810| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.91 r_work: 0.3368 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31760 Z= 0.171 Angle : 0.661 16.055 43289 Z= 0.335 Chirality : 0.047 0.218 4873 Planarity : 0.005 0.061 5520 Dihedral : 5.872 80.121 4563 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 3.64 % Allowed : 14.84 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 3963 helix: 1.87 (0.25), residues: 414 sheet: -0.41 (0.15), residues: 1218 loop : -1.36 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 279 HIS 0.011 0.001 HIS J 331 PHE 0.027 0.002 PHE E 51 TYR 0.027 0.002 TYR A 308 ARG 0.015 0.001 ARG F 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 12) link_NAG-ASN : angle 1.61783 ( 36) hydrogen bonds : bond 0.03422 ( 1026) hydrogen bonds : angle 5.47251 ( 2733) SS BOND : bond 0.00406 ( 56) SS BOND : angle 1.77194 ( 112) covalent geometry : bond 0.00382 (31692) covalent geometry : angle 0.65391 (43141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1195 time to evaluate : 3.307 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: 0.7867 (t0) REVERT: J 49 CYS cc_start: 0.7633 (p) cc_final: 0.7362 (p) REVERT: J 50 LYS cc_start: 0.8304 (tttm) cc_final: 0.8044 (tttm) REVERT: J 61 LYS cc_start: 0.7894 (tmmt) cc_final: 0.7456 (ttpt) REVERT: J 99 GLU cc_start: 0.7110 (tt0) cc_final: 0.6432 (tt0) REVERT: J 101 THR cc_start: 0.7907 (m) cc_final: 0.7628 (m) REVERT: J 130 LYS cc_start: 0.7848 (tttp) cc_final: 0.7579 (tppt) REVERT: J 191 GLU cc_start: 0.4634 (tt0) cc_final: 0.3859 (mt-10) REVERT: J 231 VAL cc_start: 0.8505 (t) cc_final: 0.8138 (m) REVERT: J 234 THR cc_start: 0.7950 (p) cc_final: 0.7699 (t) REVERT: J 289 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7588 (mtt90) REVERT: J 292 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7839 (mt-10) REVERT: J 318 LEU cc_start: 0.7650 (tp) cc_final: 0.7148 (tp) REVERT: K 7 THR cc_start: 0.8587 (t) cc_final: 0.8317 (p) REVERT: K 25 CYS cc_start: 0.5870 (t) cc_final: 0.5317 (t) REVERT: K 55 GLN cc_start: 0.8424 (tt0) cc_final: 0.8188 (tt0) REVERT: K 60 ASP cc_start: 0.7294 (t0) cc_final: 0.6690 (t0) REVERT: K 77 GLU cc_start: 0.8032 (pt0) cc_final: 0.7665 (pt0) REVERT: K 82 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8396 (mtpt) REVERT: K 127 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7422 (mm-30) REVERT: K 133 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8292 (mtmm) REVERT: K 138 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7008 (mm-30) REVERT: K 156 ASP cc_start: 0.8181 (t0) cc_final: 0.7764 (t0) REVERT: K 158 LEU cc_start: 0.8696 (mp) cc_final: 0.8204 (mp) REVERT: K 159 LYS cc_start: 0.8752 (pttm) cc_final: 0.8465 (pttm) REVERT: K 176 TYR cc_start: 0.8205 (m-80) cc_final: 0.7877 (m-80) REVERT: K 181 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6664 (tm-30) REVERT: K 190 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7420 (ttpp) REVERT: K 195 LYS cc_start: 0.8409 (mppt) cc_final: 0.8090 (mppt) REVERT: K 222 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8291 (mmtt) REVERT: K 324 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7663 (mt-10) REVERT: K 354 GLU cc_start: 0.7775 (mp0) cc_final: 0.7462 (mp0) REVERT: K 391 LYS cc_start: 0.8754 (tttm) cc_final: 0.8252 (tttm) REVERT: K 395 ASP cc_start: 0.8123 (m-30) cc_final: 0.7667 (m-30) REVERT: L 57 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7928 (mtmm) REVERT: L 80 THR cc_start: 0.8188 (t) cc_final: 0.7852 (m) REVERT: D 61 LYS cc_start: 0.7672 (pptt) cc_final: 0.7315 (ptmm) REVERT: D 76 TYR cc_start: 0.8182 (t80) cc_final: 0.7785 (t80) REVERT: D 99 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6124 (tm-30) REVERT: D 114 CYS cc_start: 0.7268 (m) cc_final: 0.6981 (m) REVERT: D 174 ASP cc_start: 0.7898 (t0) cc_final: 0.7677 (t0) REVERT: D 189 PHE cc_start: 0.8733 (p90) cc_final: 0.8318 (p90) REVERT: D 230 HIS cc_start: 0.8004 (t70) cc_final: 0.7766 (t70) REVERT: D 257 PHE cc_start: 0.9077 (m-80) cc_final: 0.8851 (m-80) REVERT: D 323 ASN cc_start: 0.8167 (p0) cc_final: 0.7916 (p0) REVERT: D 324 ARG cc_start: 0.6914 (mtm110) cc_final: 0.6689 (mtm180) REVERT: D 365 PHE cc_start: 0.8260 (p90) cc_final: 0.7971 (p90) REVERT: D 390 GLU cc_start: 0.7604 (pm20) cc_final: 0.7199 (pm20) REVERT: D 393 LYS cc_start: 0.7922 (mmtm) cc_final: 0.7653 (mmtm) REVERT: G 28 ASN cc_start: 0.8530 (p0) cc_final: 0.8302 (p0) REVERT: G 30 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6925 (mm-30) REVERT: G 76 TYR cc_start: 0.8309 (t80) cc_final: 0.7551 (t80) REVERT: G 105 GLU cc_start: 0.7369 (tt0) cc_final: 0.6962 (tt0) REVERT: G 174 ASP cc_start: 0.7931 (m-30) cc_final: 0.7016 (m-30) REVERT: G 186 ASN cc_start: 0.8502 (m-40) cc_final: 0.7690 (m-40) REVERT: G 218 ASP cc_start: 0.8153 (t0) cc_final: 0.7651 (t0) REVERT: G 241 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7583 (mm-30) REVERT: G 246 ASN cc_start: 0.7614 (t0) cc_final: 0.6929 (t0) REVERT: G 404 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7834 (ttmm) REVERT: A 50 LYS cc_start: 0.8207 (tttp) cc_final: 0.7800 (ttpt) REVERT: A 202 ASP cc_start: 0.7557 (p0) cc_final: 0.7181 (p0) REVERT: A 263 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7893 (p) REVERT: A 298 GLU cc_start: 0.6955 (tp30) cc_final: 0.6723 (tp30) REVERT: A 320 TYR cc_start: 0.8039 (p90) cc_final: 0.7175 (p90) REVERT: A 323 ASN cc_start: 0.8711 (p0) cc_final: 0.8366 (p0) REVERT: A 373 LYS cc_start: 0.8350 (mptt) cc_final: 0.8070 (mptt) REVERT: E 36 ASP cc_start: 0.7636 (p0) cc_final: 0.7308 (p0) REVERT: E 66 TYR cc_start: 0.7840 (p90) cc_final: 0.6988 (p90) REVERT: E 76 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8112 (mmtt) REVERT: E 129 LYS cc_start: 0.8575 (tppt) cc_final: 0.8124 (tppt) REVERT: E 131 ARG cc_start: 0.8063 (mmt90) cc_final: 0.7661 (mmt180) REVERT: E 139 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7161 (mt-10) REVERT: E 162 SER cc_start: 0.8901 (t) cc_final: 0.8659 (t) REVERT: E 168 MET cc_start: 0.7631 (tmm) cc_final: 0.7348 (tmm) REVERT: E 229 TYR cc_start: 0.7596 (p90) cc_final: 0.7187 (p90) REVERT: E 254 LYS cc_start: 0.8213 (mttt) cc_final: 0.7858 (mttt) REVERT: E 277 THR cc_start: 0.8416 (m) cc_final: 0.7872 (p) REVERT: E 278 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8239 (mtpp) REVERT: E 324 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 393 ARG cc_start: 0.5271 (tpt170) cc_final: 0.4604 (tpt170) REVERT: H 60 ASP cc_start: 0.7921 (t0) cc_final: 0.7408 (t0) REVERT: H 131 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7621 (mmt-90) REVERT: H 179 TYR cc_start: 0.7720 (m-10) cc_final: 0.7436 (m-10) REVERT: H 224 LYS cc_start: 0.8141 (ptmm) cc_final: 0.7894 (ptmm) REVERT: H 347 ASP cc_start: 0.7553 (t0) cc_final: 0.6925 (t0) REVERT: H 393 ARG cc_start: 0.5811 (tpt170) cc_final: 0.4875 (tpt170) REVERT: H 397 LEU cc_start: 0.8276 (mm) cc_final: 0.8025 (mm) REVERT: B 76 LYS cc_start: 0.7903 (tppp) cc_final: 0.7457 (tppp) REVERT: B 94 LEU cc_start: 0.8606 (mm) cc_final: 0.8404 (mp) REVERT: B 97 LYS cc_start: 0.8170 (tttp) cc_final: 0.7947 (tttp) REVERT: B 159 LYS cc_start: 0.8393 (ptpt) cc_final: 0.8152 (ptpt) REVERT: B 206 TYR cc_start: 0.7398 (t80) cc_final: 0.7176 (t80) REVERT: B 225 GLN cc_start: 0.5945 (tm-30) cc_final: 0.5658 (tm-30) REVERT: B 254 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7272 (mtpt) REVERT: B 265 VAL cc_start: 0.9083 (t) cc_final: 0.8598 (p) REVERT: B 276 VAL cc_start: 0.8740 (t) cc_final: 0.8403 (m) REVERT: B 281 LYS cc_start: 0.8308 (mttt) cc_final: 0.7933 (mttt) REVERT: B 354 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7579 (mt-10) REVERT: F 8 MET cc_start: 0.7370 (mmp) cc_final: 0.7138 (mmp) REVERT: F 14 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6895 (ptmm) REVERT: F 19 MET cc_start: 0.6857 (mmp) cc_final: 0.6100 (mmp) REVERT: F 44 LYS cc_start: 0.7949 (pptt) cc_final: 0.7702 (pptt) REVERT: F 56 LYS cc_start: 0.8276 (ptpp) cc_final: 0.7770 (ptpp) REVERT: F 60 MET cc_start: 0.7929 (mmt) cc_final: 0.7694 (mmt) REVERT: F 111 LYS cc_start: 0.8506 (mttt) cc_final: 0.8169 (mttt) REVERT: F 116 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8182 (mtp180) REVERT: I 44 LYS cc_start: 0.7971 (tptt) cc_final: 0.7726 (tptt) REVERT: I 60 MET cc_start: 0.7606 (mmp) cc_final: 0.7314 (mmp) REVERT: I 101 ARG cc_start: 0.6884 (mmm-85) cc_final: 0.6384 (mmm-85) REVERT: I 111 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8360 (mtpp) REVERT: I 128 ILE cc_start: 0.8854 (mp) cc_final: 0.8591 (mt) REVERT: C 37 LYS cc_start: 0.8555 (tmmt) cc_final: 0.8229 (tmmt) REVERT: C 55 LEU cc_start: 0.7966 (mm) cc_final: 0.7316 (mm) REVERT: C 64 GLU cc_start: 0.7089 (tt0) cc_final: 0.6546 (tt0) REVERT: C 106 ARG cc_start: 0.8072 (ppt170) cc_final: 0.7823 (ppt170) outliers start: 123 outliers final: 82 residues processed: 1235 average time/residue: 0.4721 time to fit residues: 890.9952 Evaluate side-chains 1261 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1177 time to evaluate : 3.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 78 CYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 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 151 LYS 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 104 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 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 69 LYS Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 327 HIS 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 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 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 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 48 optimal weight: 1.9990 chunk 289 optimal weight: 0.5980 chunk 77 optimal weight: 0.0370 chunk 316 optimal weight: 0.0770 chunk 21 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 271 optimal weight: 8.9990 chunk 290 optimal weight: 10.0000 overall best weight: 1.3420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 196 ASN D 319 GLN D 327 HIS G 52 HIS ** G 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN H 96 HIS B 96 HIS F 47 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120811 restraints weight = 56415.609| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.91 r_work: 0.3380 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31760 Z= 0.127 Angle : 0.635 16.133 43289 Z= 0.319 Chirality : 0.046 0.190 4873 Planarity : 0.005 0.057 5520 Dihedral : 5.511 82.771 4563 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.63 % Favored : 94.35 % Rotamer: Outliers : 3.67 % Allowed : 16.26 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3963 helix: 2.02 (0.25), residues: 412 sheet: -0.26 (0.15), residues: 1173 loop : -1.31 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 279 HIS 0.016 0.001 HIS J 331 PHE 0.023 0.001 PHE E 51 TYR 0.032 0.001 TYR D 320 ARG 0.007 0.001 ARG E 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00276 ( 12) link_NAG-ASN : angle 1.44563 ( 36) hydrogen bonds : bond 0.03144 ( 1026) hydrogen bonds : angle 5.24486 ( 2733) SS BOND : bond 0.00507 ( 56) SS BOND : angle 1.86311 ( 112) covalent geometry : bond 0.00290 (31692) covalent geometry : angle 0.62762 (43141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1197 time to evaluate : 3.179 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: J 9 ASN cc_start: 0.8377 (t0) cc_final: 0.7880 (t0) REVERT: J 49 CYS cc_start: 0.7760 (p) cc_final: 0.7490 (p) REVERT: J 50 LYS cc_start: 0.8298 (tttm) cc_final: 0.8023 (tttm) REVERT: J 61 LYS cc_start: 0.7832 (tmmt) cc_final: 0.7323 (ttpt) REVERT: J 99 GLU cc_start: 0.7124 (tt0) cc_final: 0.6471 (tt0) REVERT: J 101 THR cc_start: 0.7880 (m) cc_final: 0.7597 (m) REVERT: J 130 LYS cc_start: 0.7836 (tttp) cc_final: 0.7582 (tppt) REVERT: J 191 GLU cc_start: 0.4597 (tt0) cc_final: 0.3585 (mt-10) REVERT: J 289 ARG cc_start: 0.7948 (mtt90) cc_final: 0.7550 (mtt90) REVERT: J 292 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7829 (mt-10) REVERT: J 318 LEU cc_start: 0.7637 (tp) cc_final: 0.7074 (tp) REVERT: K 6 PHE cc_start: 0.8105 (m-80) cc_final: 0.7760 (m-80) REVERT: K 7 THR cc_start: 0.8564 (t) cc_final: 0.8305 (p) REVERT: K 18 TYR cc_start: 0.7725 (t80) cc_final: 0.7034 (t80) REVERT: K 55 GLN cc_start: 0.8386 (tt0) cc_final: 0.8141 (tt0) REVERT: K 60 ASP cc_start: 0.7294 (t0) cc_final: 0.6775 (t0) REVERT: K 77 GLU cc_start: 0.8036 (pt0) cc_final: 0.7660 (pt0) REVERT: K 82 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8279 (mtpt) REVERT: K 109 ASP cc_start: 0.7650 (m-30) cc_final: 0.7434 (t0) REVERT: K 138 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7002 (mm-30) REVERT: K 152 CYS cc_start: 0.7262 (p) cc_final: 0.6993 (p) REVERT: K 159 LYS cc_start: 0.8774 (pttm) cc_final: 0.8499 (pttm) REVERT: K 176 TYR cc_start: 0.8235 (m-80) cc_final: 0.7949 (m-80) REVERT: K 181 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6708 (tm-30) REVERT: K 190 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7530 (ttpp) REVERT: K 195 LYS cc_start: 0.8384 (mppt) cc_final: 0.8111 (mppt) REVERT: K 222 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8338 (mmtt) REVERT: K 324 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7659 (mt-10) REVERT: K 354 GLU cc_start: 0.7701 (mp0) cc_final: 0.7319 (mp0) REVERT: K 391 LYS cc_start: 0.8657 (tttm) cc_final: 0.8104 (tttm) REVERT: K 395 ASP cc_start: 0.8128 (m-30) cc_final: 0.7683 (m-30) REVERT: L 57 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7864 (mtmm) REVERT: L 80 THR cc_start: 0.8105 (t) cc_final: 0.7821 (m) REVERT: D 61 LYS cc_start: 0.7639 (pptt) cc_final: 0.7256 (ptmm) REVERT: D 76 TYR cc_start: 0.8121 (t80) cc_final: 0.7615 (t80) REVERT: D 99 GLU cc_start: 0.6829 (tm-30) cc_final: 0.6179 (tm-30) REVERT: D 114 CYS cc_start: 0.7286 (m) cc_final: 0.7001 (m) REVERT: D 160 LYS cc_start: 0.8200 (tmmt) cc_final: 0.7794 (tmmt) REVERT: D 230 HIS cc_start: 0.7979 (t70) cc_final: 0.7673 (t70) REVERT: D 257 PHE cc_start: 0.9056 (m-80) cc_final: 0.8848 (m-80) REVERT: D 320 TYR cc_start: 0.7519 (p90) cc_final: 0.7036 (p90) REVERT: D 323 ASN cc_start: 0.8082 (p0) cc_final: 0.7739 (p0) REVERT: D 347 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7753 (p) REVERT: D 365 PHE cc_start: 0.8224 (p90) cc_final: 0.7905 (p90) REVERT: D 390 GLU cc_start: 0.7566 (pm20) cc_final: 0.7216 (pm20) REVERT: D 430 CYS cc_start: 0.8238 (p) cc_final: 0.7971 (p) REVERT: G 21 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7889 (mtm180) REVERT: G 30 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6964 (mm-30) REVERT: G 76 TYR cc_start: 0.8313 (t80) cc_final: 0.7551 (t80) REVERT: G 103 LEU cc_start: 0.7756 (tp) cc_final: 0.7489 (tp) REVERT: G 105 GLU cc_start: 0.7363 (tt0) cc_final: 0.6947 (tt0) REVERT: G 174 ASP cc_start: 0.7944 (m-30) cc_final: 0.6975 (m-30) REVERT: G 186 ASN cc_start: 0.8475 (m-40) cc_final: 0.7632 (m-40) REVERT: G 218 ASP cc_start: 0.8160 (t0) cc_final: 0.7739 (t0) REVERT: G 241 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7652 (mm-30) REVERT: G 246 ASN cc_start: 0.7629 (t0) cc_final: 0.6944 (t0) REVERT: G 404 LYS cc_start: 0.8172 (ttmm) cc_final: 0.7927 (ttmm) REVERT: A 9 ASN cc_start: 0.7549 (p0) cc_final: 0.7227 (p0) REVERT: A 32 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6904 (m) REVERT: A 50 LYS cc_start: 0.8183 (tttp) cc_final: 0.7800 (ttpp) REVERT: A 202 ASP cc_start: 0.7431 (p0) cc_final: 0.7129 (p0) REVERT: A 263 VAL cc_start: 0.8101 (m) cc_final: 0.7882 (p) REVERT: A 320 TYR cc_start: 0.8087 (p90) cc_final: 0.7305 (p90) REVERT: A 323 ASN cc_start: 0.8648 (p0) cc_final: 0.8289 (p0) REVERT: A 373 LYS cc_start: 0.8351 (mptt) cc_final: 0.8033 (mptt) REVERT: E 36 ASP cc_start: 0.7648 (p0) cc_final: 0.7294 (p0) REVERT: E 76 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8161 (mmtt) REVERT: E 129 LYS cc_start: 0.8586 (tppt) cc_final: 0.8143 (tppt) REVERT: E 131 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7675 (mmt180) REVERT: E 132 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.8090 (ttm-80) REVERT: E 162 SER cc_start: 0.8868 (t) cc_final: 0.8639 (t) REVERT: E 168 MET cc_start: 0.7617 (tmm) cc_final: 0.7287 (tmm) REVERT: E 169 HIS cc_start: 0.7758 (m170) cc_final: 0.7179 (m170) REVERT: E 195 LYS cc_start: 0.8250 (mttt) cc_final: 0.8046 (mttt) REVERT: E 229 TYR cc_start: 0.7622 (p90) cc_final: 0.7200 (p90) REVERT: E 254 LYS cc_start: 0.8213 (mttt) cc_final: 0.7871 (mttt) REVERT: E 277 THR cc_start: 0.8439 (m) cc_final: 0.7899 (p) REVERT: E 324 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7433 (mt-10) REVERT: E 393 ARG cc_start: 0.5198 (tpt170) cc_final: 0.4567 (tpt170) REVERT: H 60 ASP cc_start: 0.7926 (t0) cc_final: 0.7427 (t0) REVERT: H 67 MET cc_start: 0.7249 (mmm) cc_final: 0.7034 (mmm) REVERT: H 80 MET cc_start: 0.8681 (tpp) cc_final: 0.8438 (tpp) REVERT: H 131 ARG cc_start: 0.8163 (mmt-90) cc_final: 0.7621 (mmt-90) REVERT: H 179 TYR cc_start: 0.7698 (m-10) cc_final: 0.7439 (m-10) REVERT: H 224 LYS cc_start: 0.8128 (ptmm) cc_final: 0.7893 (ptmm) REVERT: H 347 ASP cc_start: 0.7561 (t0) cc_final: 0.6952 (t0) REVERT: H 393 ARG cc_start: 0.5802 (tpt170) cc_final: 0.4868 (tpt170) REVERT: H 397 LEU cc_start: 0.8271 (mm) cc_final: 0.8006 (mm) REVERT: B 76 LYS cc_start: 0.7906 (tppp) cc_final: 0.7478 (tppp) REVERT: B 206 TYR cc_start: 0.7318 (t80) cc_final: 0.7040 (t80) REVERT: B 225 GLN cc_start: 0.6003 (tm-30) cc_final: 0.5589 (tm-30) REVERT: B 254 LYS cc_start: 0.7725 (mtpt) cc_final: 0.7378 (mtpt) REVERT: B 265 VAL cc_start: 0.9065 (t) cc_final: 0.8572 (p) REVERT: B 281 LYS cc_start: 0.8306 (mttt) cc_final: 0.7939 (mttt) REVERT: B 354 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7557 (mt-10) REVERT: F 8 MET cc_start: 0.7355 (mmp) cc_final: 0.7066 (mmp) REVERT: F 19 MET cc_start: 0.6961 (mmp) cc_final: 0.6330 (mmp) REVERT: F 56 LYS cc_start: 0.8295 (ptpp) cc_final: 0.7774 (ptpp) REVERT: F 60 MET cc_start: 0.7861 (mmt) cc_final: 0.7648 (mmt) REVERT: F 96 GLN cc_start: 0.6591 (OUTLIER) cc_final: 0.6007 (mm110) REVERT: F 111 LYS cc_start: 0.8432 (mttt) cc_final: 0.8094 (mttt) REVERT: I 14 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7647 (mmtp) REVERT: I 44 LYS cc_start: 0.7931 (tptt) cc_final: 0.7681 (tptt) REVERT: I 101 ARG cc_start: 0.6838 (mmm-85) cc_final: 0.6534 (mmm-85) REVERT: I 111 LYS cc_start: 0.8589 (mtpp) cc_final: 0.8358 (mtpp) REVERT: I 144 VAL cc_start: 0.8727 (p) cc_final: 0.8430 (m) REVERT: C 37 LYS cc_start: 0.8606 (tmmt) cc_final: 0.8312 (tmmt) REVERT: C 55 LEU cc_start: 0.8112 (mm) cc_final: 0.7358 (mm) REVERT: C 64 GLU cc_start: 0.7120 (tt0) cc_final: 0.6606 (tt0) REVERT: C 106 ARG cc_start: 0.8031 (ppt170) cc_final: 0.7771 (ppt170) outliers start: 124 outliers final: 87 residues processed: 1233 average time/residue: 0.4675 time to fit residues: 881.0089 Evaluate side-chains 1274 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1184 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 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 345 HIS 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 266 CYS Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 144 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 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 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 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 196 ASN 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 316 LEU Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 366 ILE 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 E residue 40 ASP 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 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 B residue 96 HIS Chi-restraints excluded: chain B residue 135 VAL 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 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 96 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 354 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 377 optimal weight: 10.0000 chunk 380 optimal weight: 0.0970 chunk 103 optimal weight: 1.9990 chunk 352 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 211 optimal weight: 0.0470 overall best weight: 1.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 332 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 D 319 GLN D 327 HIS G 52 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN E 50 GLN ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126721 restraints weight = 55698.937| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.86 r_work: 0.3399 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31760 Z= 0.135 Angle : 0.633 16.794 43289 Z= 0.317 Chirality : 0.046 0.274 4873 Planarity : 0.005 0.051 5520 Dihedral : 5.368 83.153 4563 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 4.18 % Allowed : 18.22 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.13), residues: 3963 helix: 2.07 (0.25), residues: 412 sheet: -0.20 (0.16), residues: 1087 loop : -1.26 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 279 HIS 0.013 0.001 HIS D 327 PHE 0.022 0.001 PHE E 51 TYR 0.027 0.001 TYR A 308 ARG 0.011 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.46404 ( 36) hydrogen bonds : bond 0.03111 ( 1026) hydrogen bonds : angle 5.17521 ( 2733) SS BOND : bond 0.00386 ( 56) SS BOND : angle 1.87323 ( 112) covalent geometry : bond 0.00305 (31692) covalent geometry : angle 0.62572 (43141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1185 time to evaluate : 3.617 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: 0.8365 (t0) cc_final: 0.7890 (t0) REVERT: J 49 CYS cc_start: 0.7728 (p) cc_final: 0.7444 (p) REVERT: J 50 LYS cc_start: 0.8312 (tttm) cc_final: 0.8042 (tttm) REVERT: J 61 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7330 (ttpt) REVERT: J 99 GLU cc_start: 0.7233 (tt0) cc_final: 0.6622 (tt0) REVERT: J 101 THR cc_start: 0.7884 (m) cc_final: 0.7605 (m) REVERT: J 130 LYS cc_start: 0.7834 (tttp) cc_final: 0.7578 (tttp) REVERT: J 191 GLU cc_start: 0.4842 (tt0) cc_final: 0.3837 (mt-10) REVERT: J 217 THR cc_start: 0.7321 (OUTLIER) cc_final: 0.7118 (m) REVERT: J 289 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7527 (mtt90) REVERT: J 318 LEU cc_start: 0.7650 (tp) cc_final: 0.7070 (tp) REVERT: K 6 PHE cc_start: 0.8036 (m-80) cc_final: 0.7742 (m-80) REVERT: K 18 TYR cc_start: 0.7657 (t80) cc_final: 0.7055 (t80) REVERT: K 55 GLN cc_start: 0.8310 (tt0) cc_final: 0.8069 (tt0) REVERT: K 60 ASP cc_start: 0.7257 (t0) cc_final: 0.6741 (t0) REVERT: K 77 GLU cc_start: 0.8059 (pt0) cc_final: 0.7713 (pt0) REVERT: K 82 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8352 (mtpt) REVERT: K 109 ASP cc_start: 0.7667 (m-30) cc_final: 0.7449 (t0) REVERT: K 138 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6881 (mm-30) REVERT: K 152 CYS cc_start: 0.7217 (p) cc_final: 0.6903 (p) REVERT: K 159 LYS cc_start: 0.8772 (pttm) cc_final: 0.8517 (pttm) REVERT: K 176 TYR cc_start: 0.8243 (m-80) cc_final: 0.7973 (m-80) REVERT: K 181 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6720 (tm-30) REVERT: K 190 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7582 (ttpp) REVERT: K 195 LYS cc_start: 0.8394 (mppt) cc_final: 0.8074 (mppt) REVERT: K 222 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8309 (mmtt) REVERT: K 324 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7679 (mt-10) REVERT: K 354 GLU cc_start: 0.7611 (mp0) cc_final: 0.7168 (mp0) REVERT: K 391 LYS cc_start: 0.8736 (tttm) cc_final: 0.8252 (tttm) REVERT: K 395 ASP cc_start: 0.8042 (m-30) cc_final: 0.7625 (m-30) REVERT: L 57 LYS cc_start: 0.8188 (mtmm) cc_final: 0.7822 (mtmm) REVERT: L 80 THR cc_start: 0.8076 (t) cc_final: 0.7774 (m) REVERT: D 61 LYS cc_start: 0.7615 (pptt) cc_final: 0.7057 (ptmm) REVERT: D 99 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6131 (tm-30) REVERT: D 114 CYS cc_start: 0.7252 (m) cc_final: 0.6992 (m) REVERT: D 160 LYS cc_start: 0.8179 (tmmt) cc_final: 0.7850 (tmmt) REVERT: D 189 PHE cc_start: 0.8717 (p90) cc_final: 0.8403 (p90) REVERT: D 230 HIS cc_start: 0.7911 (t70) cc_final: 0.7636 (t70) REVERT: D 270 ASN cc_start: 0.7920 (m110) cc_final: 0.7674 (m110) REVERT: D 320 TYR cc_start: 0.7510 (p90) cc_final: 0.6944 (p90) REVERT: D 323 ASN cc_start: 0.8075 (p0) cc_final: 0.7821 (p0) REVERT: D 347 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7787 (p) REVERT: D 365 PHE cc_start: 0.8230 (p90) cc_final: 0.7950 (p90) REVERT: D 381 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7790 (mtmm) REVERT: D 390 GLU cc_start: 0.7358 (pm20) cc_final: 0.6817 (pm20) REVERT: D 430 CYS cc_start: 0.8217 (p) cc_final: 0.7919 (p) REVERT: G 21 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7889 (mtm180) REVERT: G 30 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6924 (mm-30) REVERT: G 76 TYR cc_start: 0.8338 (t80) cc_final: 0.7551 (t80) REVERT: G 103 LEU cc_start: 0.7792 (tp) cc_final: 0.7530 (tp) REVERT: G 105 GLU cc_start: 0.7355 (tt0) cc_final: 0.6898 (tt0) REVERT: G 174 ASP cc_start: 0.7946 (m-30) cc_final: 0.7186 (m-30) REVERT: G 218 ASP cc_start: 0.8183 (t0) cc_final: 0.7760 (t0) REVERT: G 241 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7637 (mm-30) REVERT: G 246 ASN cc_start: 0.7699 (t0) cc_final: 0.7033 (t0) REVERT: G 404 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7888 (ttmm) REVERT: A 9 ASN cc_start: 0.7583 (p0) cc_final: 0.7227 (p0) REVERT: A 50 LYS cc_start: 0.8150 (tttp) cc_final: 0.7802 (ttpp) REVERT: A 188 ASP cc_start: 0.7666 (t0) cc_final: 0.7407 (t0) REVERT: A 202 ASP cc_start: 0.7396 (p0) cc_final: 0.7102 (p0) REVERT: A 263 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7926 (p) REVERT: A 311 ASP cc_start: 0.7726 (m-30) cc_final: 0.7458 (m-30) REVERT: A 320 TYR cc_start: 0.8081 (p90) cc_final: 0.7273 (p90) REVERT: A 323 ASN cc_start: 0.8669 (p0) cc_final: 0.8347 (p0) REVERT: A 373 LYS cc_start: 0.8348 (mptt) cc_final: 0.8041 (mptt) REVERT: E 36 ASP cc_start: 0.7650 (p0) cc_final: 0.7255 (p0) REVERT: E 50 GLN cc_start: 0.7805 (mm110) cc_final: 0.7538 (mm-40) REVERT: E 76 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8228 (mmtt) REVERT: E 129 LYS cc_start: 0.8593 (tppt) cc_final: 0.8105 (tppt) REVERT: E 131 ARG cc_start: 0.8088 (mmt90) cc_final: 0.7631 (mmt180) REVERT: E 132 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8071 (ttm-80) REVERT: E 162 SER cc_start: 0.8866 (t) cc_final: 0.8659 (t) REVERT: E 168 MET cc_start: 0.7643 (tmm) cc_final: 0.7385 (tmm) REVERT: E 169 HIS cc_start: 0.7833 (m170) cc_final: 0.7320 (m170) REVERT: E 229 TYR cc_start: 0.7650 (p90) cc_final: 0.7205 (p90) REVERT: E 254 LYS cc_start: 0.8304 (mttt) cc_final: 0.7985 (mttt) REVERT: E 277 THR cc_start: 0.8491 (m) cc_final: 0.7989 (p) REVERT: E 393 ARG cc_start: 0.5202 (tpt170) cc_final: 0.4480 (tpt170) REVERT: H 60 ASP cc_start: 0.7930 (t0) cc_final: 0.7445 (t0) REVERT: H 80 MET cc_start: 0.8645 (tpp) cc_final: 0.8405 (tpp) REVERT: H 131 ARG cc_start: 0.8104 (mmt-90) cc_final: 0.7577 (mmt-90) REVERT: H 179 TYR cc_start: 0.7719 (m-10) cc_final: 0.7466 (m-10) REVERT: H 224 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7909 (ptmm) REVERT: H 342 GLU cc_start: 0.7083 (pm20) cc_final: 0.6866 (pm20) REVERT: H 347 ASP cc_start: 0.7560 (t0) cc_final: 0.6919 (t0) REVERT: H 393 ARG cc_start: 0.5839 (tpt170) cc_final: 0.4884 (tpt170) REVERT: H 397 LEU cc_start: 0.8312 (mm) cc_final: 0.8064 (mm) REVERT: B 76 LYS cc_start: 0.7929 (tppp) cc_final: 0.7511 (tppp) REVERT: B 206 TYR cc_start: 0.7424 (t80) cc_final: 0.7116 (t80) REVERT: B 225 GLN cc_start: 0.6170 (tm-30) cc_final: 0.5731 (tm-30) REVERT: B 254 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7509 (mtpt) REVERT: B 265 VAL cc_start: 0.9070 (t) cc_final: 0.8600 (p) REVERT: B 272 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7763 (t70) REVERT: B 281 LYS cc_start: 0.8302 (mttt) cc_final: 0.7994 (mttt) REVERT: B 354 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7529 (mt-10) REVERT: F 8 MET cc_start: 0.7173 (mmp) cc_final: 0.6922 (mmp) REVERT: F 56 LYS cc_start: 0.8266 (ptpp) cc_final: 0.7787 (ptpp) REVERT: F 60 MET cc_start: 0.7930 (mmt) cc_final: 0.7724 (mmt) REVERT: F 97 TYR cc_start: 0.5476 (m-80) cc_final: 0.5010 (m-80) REVERT: F 143 VAL cc_start: 0.8547 (t) cc_final: 0.8299 (p) REVERT: I 44 LYS cc_start: 0.7940 (tptt) cc_final: 0.7721 (tptt) REVERT: I 101 ARG cc_start: 0.6968 (mmm-85) cc_final: 0.6639 (mmm-85) REVERT: I 111 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8335 (mtpp) REVERT: C 55 LEU cc_start: 0.7976 (mm) cc_final: 0.7104 (mm) REVERT: C 64 GLU cc_start: 0.6969 (tt0) cc_final: 0.6523 (tt0) REVERT: C 106 ARG cc_start: 0.8048 (ppt170) cc_final: 0.7784 (ppt170) outliers start: 141 outliers final: 103 residues processed: 1232 average time/residue: 0.4670 time to fit residues: 881.3633 Evaluate side-chains 1275 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1168 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 217 THR 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 345 HIS 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 213 THR 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 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 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 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 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 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 217 THR Chi-restraints excluded: chain A residue 263 VAL 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 321 LYS Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 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 272 HIS 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 47 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 149 LYS Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 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 53 VAL Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 91 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 272 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 276 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 339 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS G 52 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS B 332 ASN F 96 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.137046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120255 restraints weight = 56113.695| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.87 r_work: 0.3379 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31760 Z= 0.154 Angle : 0.648 17.199 43289 Z= 0.324 Chirality : 0.046 0.248 4873 Planarity : 0.005 0.050 5520 Dihedral : 5.331 82.579 4563 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 4.24 % Allowed : 19.14 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.13), residues: 3963 helix: 2.23 (0.24), residues: 406 sheet: -0.21 (0.16), residues: 1083 loop : -1.24 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 279 HIS 0.012 0.001 HIS J 331 PHE 0.021 0.001 PHE E 51 TYR 0.028 0.001 TYR A 308 ARG 0.009 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 12) link_NAG-ASN : angle 1.50000 ( 36) hydrogen bonds : bond 0.03127 ( 1026) hydrogen bonds : angle 5.11675 ( 2733) SS BOND : bond 0.00484 ( 56) SS BOND : angle 2.05257 ( 112) covalent geometry : bond 0.00349 (31692) covalent geometry : angle 0.63925 (43141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1321 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1178 time to evaluate : 3.521 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: J 9 ASN cc_start: 0.8378 (t0) cc_final: 0.7866 (t0) REVERT: J 49 CYS cc_start: 0.7708 (p) cc_final: 0.7452 (p) REVERT: J 50 LYS cc_start: 0.8328 (tttm) cc_final: 0.8062 (tttm) REVERT: J 61 LYS cc_start: 0.7844 (ttmt) cc_final: 0.7394 (ttpp) REVERT: J 101 THR cc_start: 0.7865 (m) cc_final: 0.7568 (m) REVERT: J 130 LYS cc_start: 0.7848 (tttp) cc_final: 0.7572 (tttp) REVERT: J 176 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8214 (mttt) REVERT: J 180 ARG cc_start: 0.8627 (ttt-90) cc_final: 0.8285 (ttt-90) REVERT: J 191 GLU cc_start: 0.5005 (tt0) cc_final: 0.3963 (mt-10) REVERT: J 234 THR cc_start: 0.7944 (p) cc_final: 0.7726 (t) REVERT: J 289 ARG cc_start: 0.7964 (mtt90) cc_final: 0.7573 (mtt90) REVERT: J 318 LEU cc_start: 0.7654 (tp) cc_final: 0.7061 (tp) REVERT: K 6 PHE cc_start: 0.8001 (m-80) cc_final: 0.7767 (m-80) REVERT: K 18 TYR cc_start: 0.7708 (t80) cc_final: 0.7029 (t80) REVERT: K 55 GLN cc_start: 0.8298 (tt0) cc_final: 0.8097 (tt0) REVERT: K 60 ASP cc_start: 0.7269 (t0) cc_final: 0.6737 (t0) REVERT: K 77 GLU cc_start: 0.8047 (pt0) cc_final: 0.7664 (pt0) REVERT: K 82 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8387 (mttm) REVERT: K 109 ASP cc_start: 0.7649 (m-30) cc_final: 0.7429 (t0) REVERT: K 138 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6927 (mm-30) REVERT: K 152 CYS cc_start: 0.7251 (p) cc_final: 0.6895 (p) REVERT: K 159 LYS cc_start: 0.8793 (pttm) cc_final: 0.8528 (pttm) REVERT: K 176 TYR cc_start: 0.8290 (m-80) cc_final: 0.8006 (m-80) REVERT: K 181 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6752 (tm-30) REVERT: K 222 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8323 (mmtt) REVERT: K 324 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7674 (mt-10) REVERT: K 354 GLU cc_start: 0.7645 (mp0) cc_final: 0.7192 (mp0) REVERT: K 391 LYS cc_start: 0.8745 (tttm) cc_final: 0.8249 (tttm) REVERT: K 395 ASP cc_start: 0.8113 (m-30) cc_final: 0.7660 (m-30) REVERT: L 80 THR cc_start: 0.8146 (t) cc_final: 0.7831 (m) REVERT: D 61 LYS cc_start: 0.7682 (pptt) cc_final: 0.7026 (ptmm) REVERT: D 76 TYR cc_start: 0.8243 (t80) cc_final: 0.7793 (t80) REVERT: D 99 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6108 (tm-30) REVERT: D 114 CYS cc_start: 0.7279 (m) cc_final: 0.7038 (m) REVERT: D 160 LYS cc_start: 0.8182 (tmmt) cc_final: 0.7862 (tmmt) REVERT: D 189 PHE cc_start: 0.8720 (p90) cc_final: 0.8375 (p90) REVERT: D 230 HIS cc_start: 0.7981 (t70) cc_final: 0.7692 (t70) REVERT: D 270 ASN cc_start: 0.7941 (m110) cc_final: 0.7690 (m110) REVERT: D 320 TYR cc_start: 0.7632 (p90) cc_final: 0.7058 (p90) REVERT: D 365 PHE cc_start: 0.8213 (p90) cc_final: 0.7929 (p90) REVERT: D 381 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7868 (mtmm) REVERT: D 390 GLU cc_start: 0.7474 (pm20) cc_final: 0.6880 (pm20) REVERT: G 30 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6938 (mm-30) REVERT: G 76 TYR cc_start: 0.8388 (t80) cc_final: 0.7805 (t80) REVERT: G 81 PHE cc_start: 0.7313 (m-10) cc_final: 0.6987 (m-10) REVERT: G 103 LEU cc_start: 0.7794 (tp) cc_final: 0.7549 (tp) REVERT: G 174 ASP cc_start: 0.7905 (m-30) cc_final: 0.7351 (m-30) REVERT: G 218 ASP cc_start: 0.8186 (t0) cc_final: 0.7753 (t0) REVERT: G 241 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7629 (mm-30) REVERT: G 246 ASN cc_start: 0.7666 (t0) cc_final: 0.6975 (t0) REVERT: G 404 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7936 (ttmm) REVERT: A 9 ASN cc_start: 0.7529 (p0) cc_final: 0.7133 (p0) REVERT: A 107 TYR cc_start: 0.7698 (p90) cc_final: 0.7388 (p90) REVERT: A 188 ASP cc_start: 0.7658 (t0) cc_final: 0.7440 (t0) REVERT: A 202 ASP cc_start: 0.7389 (p0) cc_final: 0.7118 (p0) REVERT: A 311 ASP cc_start: 0.7721 (m-30) cc_final: 0.7461 (m-30) REVERT: A 320 TYR cc_start: 0.8105 (p90) cc_final: 0.7222 (p90) REVERT: A 323 ASN cc_start: 0.8653 (p0) cc_final: 0.8320 (p0) REVERT: A 373 LYS cc_start: 0.8372 (mptt) cc_final: 0.8065 (mptt) REVERT: E 36 ASP cc_start: 0.7601 (p0) cc_final: 0.7264 (p0) REVERT: E 76 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8209 (mmtt) REVERT: E 129 LYS cc_start: 0.8596 (tppt) cc_final: 0.8274 (tppt) REVERT: E 131 ARG cc_start: 0.8060 (mmt90) cc_final: 0.7695 (mmt180) REVERT: E 132 ARG cc_start: 0.8217 (ttm-80) cc_final: 0.7999 (ttm-80) REVERT: E 162 SER cc_start: 0.8863 (t) cc_final: 0.8656 (t) REVERT: E 168 MET cc_start: 0.7600 (tmm) cc_final: 0.7273 (tmm) REVERT: E 169 HIS cc_start: 0.7907 (m170) cc_final: 0.7480 (m170) REVERT: E 254 LYS cc_start: 0.8272 (mttt) cc_final: 0.7965 (mttt) REVERT: E 277 THR cc_start: 0.8465 (m) cc_final: 0.7950 (p) REVERT: E 278 LYS cc_start: 0.8581 (mmtp) cc_final: 0.8228 (mtpp) REVERT: E 393 ARG cc_start: 0.5190 (tpt170) cc_final: 0.4464 (tpt170) REVERT: H 51 PHE cc_start: 0.8253 (m-80) cc_final: 0.7843 (m-80) REVERT: H 60 ASP cc_start: 0.7921 (t0) cc_final: 0.7439 (t0) REVERT: H 67 MET cc_start: 0.7246 (mmm) cc_final: 0.6996 (mmm) REVERT: H 131 ARG cc_start: 0.8100 (mmt-90) cc_final: 0.7567 (mmt-90) REVERT: H 168 MET cc_start: 0.7199 (mpp) cc_final: 0.6542 (mmm) REVERT: H 179 TYR cc_start: 0.7734 (m-10) cc_final: 0.7506 (m-10) REVERT: H 224 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7932 (ptmm) REVERT: H 259 PHE cc_start: 0.8285 (m-80) cc_final: 0.7885 (m-80) REVERT: H 347 ASP cc_start: 0.7540 (t0) cc_final: 0.6922 (t0) REVERT: H 393 ARG cc_start: 0.5756 (tpt170) cc_final: 0.5185 (tpt170) REVERT: B 76 LYS cc_start: 0.7918 (tppp) cc_final: 0.7485 (tppp) REVERT: B 129 LYS cc_start: 0.8781 (tptt) cc_final: 0.8567 (tptt) REVERT: B 206 TYR cc_start: 0.7466 (t80) cc_final: 0.7128 (t80) REVERT: B 225 GLN cc_start: 0.6679 (tm-30) cc_final: 0.6163 (tm-30) REVERT: B 265 VAL cc_start: 0.9127 (t) cc_final: 0.8668 (p) REVERT: B 272 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7763 (t70) REVERT: B 281 LYS cc_start: 0.8307 (mttt) cc_final: 0.8001 (mttt) REVERT: B 354 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7497 (mt-10) REVERT: F 8 MET cc_start: 0.7233 (mmp) cc_final: 0.6977 (mmp) REVERT: F 56 LYS cc_start: 0.8262 (ptpp) cc_final: 0.7792 (ptpp) REVERT: F 60 MET cc_start: 0.7934 (mmt) cc_final: 0.7718 (mmt) REVERT: F 97 TYR cc_start: 0.5641 (OUTLIER) cc_final: 0.5242 (m-80) REVERT: F 111 LYS cc_start: 0.8464 (mttt) cc_final: 0.8135 (mttt) REVERT: F 143 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8408 (p) REVERT: I 14 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7483 (mmtp) REVERT: I 44 LYS cc_start: 0.7922 (tptt) cc_final: 0.7699 (tptt) REVERT: I 101 ARG cc_start: 0.7120 (mmm-85) cc_final: 0.6779 (mmm-85) REVERT: I 111 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8316 (mtpp) REVERT: C 37 LYS cc_start: 0.8584 (tmmt) cc_final: 0.8363 (tmmt) REVERT: C 55 LEU cc_start: 0.7993 (mm) cc_final: 0.6881 (mm) REVERT: C 106 ARG cc_start: 0.8084 (ppt170) cc_final: 0.7826 (ppt170) outliers start: 143 outliers final: 119 residues processed: 1230 average time/residue: 0.4649 time to fit residues: 872.5806 Evaluate side-chains 1290 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1168 time to evaluate : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 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 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 345 HIS 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 151 LYS Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 266 CYS 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 44 LYS Chi-restraints excluded: chain L residue 62 ASP Chi-restraints excluded: chain L residue 83 LYS Chi-restraints excluded: chain L residue 141 LEU 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 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 354 LEU 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 217 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 381 LYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain E residue 37 GLU Chi-restraints excluded: chain E residue 40 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 288 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 151 LYS Chi-restraints excluded: chain H residue 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 B residue 45 ILE 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 177 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain F residue 16 PHE Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 97 TYR 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 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 30 VAL 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 97 TYR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 68 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 chunk 245 optimal weight: 20.0000 chunk 202 optimal weight: 6.9990 chunk 222 optimal weight: 0.0980 chunk 330 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 278 optimal weight: 9.9990 chunk 384 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 ASN J 331 HIS K 50 GLN K 272 HIS ** K 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS D 196 ASN D 327 HIS ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 345 HIS A 43 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116011 restraints weight = 55869.382| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.82 r_work: 0.3337 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 31760 Z= 0.331 Angle : 0.759 18.824 43289 Z= 0.388 Chirality : 0.051 0.301 4873 Planarity : 0.006 0.064 5520 Dihedral : 5.849 76.832 4563 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 4.86 % Allowed : 19.58 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3963 helix: 1.96 (0.25), residues: 412 sheet: -0.55 (0.15), residues: 1201 loop : -1.52 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 279 HIS 0.021 0.002 HIS B 96 PHE 0.029 0.002 PHE C 16 TYR 0.029 0.002 TYR A 308 ARG 0.016 0.001 ARG F 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 12) link_NAG-ASN : angle 2.02122 ( 36) hydrogen bonds : bond 0.03841 ( 1026) hydrogen bonds : angle 5.48636 ( 2733) SS BOND : bond 0.00603 ( 56) SS BOND : angle 2.48737 ( 112) covalent geometry : bond 0.00721 (31692) covalent geometry : angle 0.74787 (43141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1196 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8430 (t0) cc_final: 0.7842 (t0) REVERT: J 61 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7340 (ttpt) REVERT: J 63 CYS cc_start: 0.5968 (OUTLIER) cc_final: 0.4977 (m) REVERT: J 99 GLU cc_start: 0.7310 (tt0) cc_final: 0.6600 (tt0) REVERT: J 101 THR cc_start: 0.7894 (m) cc_final: 0.7617 (m) REVERT: J 191 GLU cc_start: 0.4928 (tt0) cc_final: 0.4084 (mt-10) REVERT: J 217 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7153 (p) REVERT: J 282 ILE cc_start: 0.8638 (mt) cc_final: 0.8217 (tp) REVERT: J 289 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7594 (mtt90) REVERT: K 18 TYR cc_start: 0.7870 (t80) cc_final: 0.7171 (t80) REVERT: K 60 ASP cc_start: 0.7342 (t0) cc_final: 0.6685 (t0) REVERT: K 77 GLU cc_start: 0.8081 (pt0) cc_final: 0.7680 (pt0) REVERT: K 82 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8459 (mtpt) REVERT: K 109 ASP cc_start: 0.7763 (m-30) cc_final: 0.7511 (t0) REVERT: K 127 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7469 (mm-30) REVERT: K 138 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7115 (mm-30) REVERT: K 159 LYS cc_start: 0.8792 (pttm) cc_final: 0.8543 (pttm) REVERT: K 176 TYR cc_start: 0.8296 (m-80) cc_final: 0.7932 (m-80) REVERT: K 181 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6790 (tm-30) REVERT: K 195 LYS cc_start: 0.8434 (mppt) cc_final: 0.8107 (mppt) REVERT: K 222 LYS cc_start: 0.8561 (mmtt) cc_final: 0.8320 (mmtt) REVERT: K 354 GLU cc_start: 0.7723 (mp0) cc_final: 0.7200 (mp0) REVERT: K 391 LYS cc_start: 0.8798 (tttm) cc_final: 0.8328 (tttm) REVERT: K 395 ASP cc_start: 0.8055 (m-30) cc_final: 0.7636 (m-30) REVERT: L 80 THR cc_start: 0.8324 (t) cc_final: 0.7922 (m) REVERT: D 61 LYS cc_start: 0.7903 (pptt) cc_final: 0.7259 (ptmm) REVERT: D 99 GLU cc_start: 0.6727 (tm-30) cc_final: 0.6058 (tm-30) REVERT: D 114 CYS cc_start: 0.7299 (m) cc_final: 0.7081 (m) REVERT: D 174 ASP cc_start: 0.7877 (t0) cc_final: 0.7651 (t0) REVERT: D 270 ASN cc_start: 0.8040 (m110) cc_final: 0.7772 (m110) REVERT: D 308 TYR cc_start: 0.7892 (p90) cc_final: 0.7589 (p90) REVERT: D 321 LYS cc_start: 0.8222 (ptpp) cc_final: 0.8015 (ptpp) REVERT: D 364 ASN cc_start: 0.8191 (m-40) cc_final: 0.7922 (m-40) REVERT: D 381 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7715 (mtmm) REVERT: D 390 GLU cc_start: 0.7595 (pm20) cc_final: 0.7065 (pm20) REVERT: G 76 TYR cc_start: 0.8429 (t80) cc_final: 0.7530 (t80) REVERT: G 78 CYS cc_start: 0.6408 (p) cc_final: 0.6157 (p) REVERT: G 174 ASP cc_start: 0.7908 (m-30) cc_final: 0.7350 (m-30) REVERT: G 218 ASP cc_start: 0.8223 (t0) cc_final: 0.7716 (t0) REVERT: G 241 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7543 (mm-30) REVERT: G 246 ASN cc_start: 0.7650 (t0) cc_final: 0.6967 (t0) REVERT: G 343 THR cc_start: 0.8595 (t) cc_final: 0.8236 (m) REVERT: G 346 VAL cc_start: 0.7873 (t) cc_final: 0.7468 (m) REVERT: G 404 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7895 (ttmm) REVERT: A 9 ASN cc_start: 0.8118 (p0) cc_final: 0.7817 (p0) REVERT: A 188 ASP cc_start: 0.7796 (t0) cc_final: 0.7550 (t0) REVERT: A 202 ASP cc_start: 0.7491 (p0) cc_final: 0.7258 (p0) REVERT: A 311 ASP cc_start: 0.7974 (m-30) cc_final: 0.7650 (m-30) REVERT: A 319 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: A 373 LYS cc_start: 0.8451 (mptt) cc_final: 0.8176 (mptt) REVERT: E 36 ASP cc_start: 0.7577 (p0) cc_final: 0.7258 (p0) REVERT: E 105 CYS cc_start: 0.7443 (m) cc_final: 0.7066 (m) REVERT: E 131 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7869 (mmt-90) REVERT: E 162 SER cc_start: 0.8817 (t) cc_final: 0.8593 (t) REVERT: E 168 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: E 200 GLU cc_start: 0.7325 (tt0) cc_final: 0.6792 (tt0) REVERT: E 254 LYS cc_start: 0.8169 (mttt) cc_final: 0.7896 (mttt) REVERT: E 277 THR cc_start: 0.8500 (m) cc_final: 0.7998 (p) REVERT: E 278 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8299 (mtpp) REVERT: E 393 ARG cc_start: 0.5377 (tpt170) cc_final: 0.4742 (tpt170) REVERT: H 60 ASP cc_start: 0.7975 (t0) cc_final: 0.7438 (t0) REVERT: H 61 VAL cc_start: 0.8692 (t) cc_final: 0.8302 (t) REVERT: H 80 MET cc_start: 0.8787 (tpp) cc_final: 0.8036 (tpp) REVERT: H 131 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7608 (mmt-90) REVERT: H 141 LEU cc_start: 0.8365 (mt) cc_final: 0.8025 (mt) REVERT: H 168 MET cc_start: 0.7244 (mpp) cc_final: 0.6516 (mmm) REVERT: H 224 LYS cc_start: 0.8281 (ptmm) cc_final: 0.7980 (ptmm) REVERT: H 347 ASP cc_start: 0.7504 (t0) cc_final: 0.6872 (t0) REVERT: H 393 ARG cc_start: 0.5927 (tpt170) cc_final: 0.5304 (tpt170) REVERT: B 67 MET cc_start: 0.7191 (mmm) cc_final: 0.6637 (mmm) REVERT: B 76 LYS cc_start: 0.7900 (tppp) cc_final: 0.7500 (tppp) REVERT: B 129 LYS cc_start: 0.8828 (tptt) cc_final: 0.8583 (tptt) REVERT: B 206 TYR cc_start: 0.7663 (t80) cc_final: 0.7273 (t80) REVERT: B 225 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6117 (tm-30) REVERT: B 239 ASN cc_start: 0.7594 (p0) cc_final: 0.7304 (t0) REVERT: B 281 LYS cc_start: 0.8381 (mttt) cc_final: 0.8086 (mttt) REVERT: B 354 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7557 (mt-10) REVERT: F 8 MET cc_start: 0.7376 (mmp) cc_final: 0.7136 (mmp) REVERT: F 56 LYS cc_start: 0.8386 (ptpp) cc_final: 0.7934 (ptpp) REVERT: F 76 THR cc_start: 0.7759 (p) cc_final: 0.7494 (p) REVERT: F 97 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.5550 (m-80) REVERT: F 111 LYS cc_start: 0.8704 (mttt) cc_final: 0.8431 (mttt) REVERT: F 116 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7957 (mtp180) REVERT: I 14 LYS cc_start: 0.8033 (mmtp) cc_final: 0.7433 (mmtp) REVERT: I 36 MET cc_start: 0.8016 (mtm) cc_final: 0.7773 (mtm) REVERT: I 111 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8472 (mtpp) REVERT: C 11 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8021 (tp30) REVERT: C 55 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 106 ARG cc_start: 0.8322 (ppt170) cc_final: 0.8086 (ppt170) outliers start: 164 outliers final: 120 residues processed: 1255 average time/residue: 0.4622 time to fit residues: 884.8739 Evaluate side-chains 1298 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1170 time to evaluate : 3.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 217 THR Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 292 GLU Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 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 151 LYS Chi-restraints excluded: chain K residue 213 THR 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 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 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 195 MET Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 425 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 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 319 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain 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 168 MET Chi-restraints excluded: chain E residue 217 MET 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 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 288 THR Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 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 31 VAL Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 116 ARG 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 C residue 8 MET Chi-restraints excluded: chain C residue 11 GLU 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 90 TRP Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 319 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 366 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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 230 HIS D 327 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 ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN B 96 HIS B 332 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117597 restraints weight = 55957.981| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.84 r_work: 0.3354 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31760 Z= 0.216 Angle : 0.730 17.801 43289 Z= 0.366 Chirality : 0.049 0.263 4873 Planarity : 0.005 0.061 5520 Dihedral : 5.701 78.211 4563 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.26 % Favored : 93.69 % Rotamer: Outliers : 4.71 % Allowed : 21.39 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3963 helix: 2.06 (0.25), residues: 406 sheet: -0.63 (0.15), residues: 1205 loop : -1.43 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 279 HIS 0.015 0.001 HIS B 349 PHE 0.032 0.002 PHE C 16 TYR 0.034 0.002 TYR H 206 ARG 0.010 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 12) link_NAG-ASN : angle 1.70857 ( 36) hydrogen bonds : bond 0.03426 ( 1026) hydrogen bonds : angle 5.40634 ( 2733) SS BOND : bond 0.00497 ( 56) SS BOND : angle 2.34810 ( 112) covalent geometry : bond 0.00481 (31692) covalent geometry : angle 0.72007 (43141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1179 time to evaluate : 3.559 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: 0.8404 (t0) cc_final: 0.7837 (t0) REVERT: J 61 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7425 (ttpt) REVERT: J 99 GLU cc_start: 0.7286 (tt0) cc_final: 0.6567 (tt0) REVERT: J 101 THR cc_start: 0.7928 (m) cc_final: 0.7633 (m) REVERT: J 130 LYS cc_start: 0.7805 (tttp) cc_final: 0.7571 (tttp) REVERT: J 180 ARG cc_start: 0.8632 (ttt-90) cc_final: 0.8414 (ttt-90) REVERT: J 191 GLU cc_start: 0.4791 (tt0) cc_final: 0.3816 (mt-10) REVERT: J 234 THR cc_start: 0.8014 (p) cc_final: 0.7775 (t) REVERT: J 282 ILE cc_start: 0.8619 (mt) cc_final: 0.8196 (tp) REVERT: J 289 ARG cc_start: 0.8026 (mtt90) cc_final: 0.7622 (mtt90) REVERT: K 18 TYR cc_start: 0.7807 (t80) cc_final: 0.7043 (t80) REVERT: K 60 ASP cc_start: 0.7301 (t0) cc_final: 0.6662 (t0) REVERT: K 77 GLU cc_start: 0.8002 (pt0) cc_final: 0.7636 (pt0) REVERT: K 82 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8382 (mtpt) REVERT: K 109 ASP cc_start: 0.7734 (m-30) cc_final: 0.7462 (t0) REVERT: K 127 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7464 (mt-10) REVERT: K 138 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7057 (mm-30) REVERT: K 159 LYS cc_start: 0.8782 (pttm) cc_final: 0.8518 (pttm) REVERT: K 176 TYR cc_start: 0.8282 (m-80) cc_final: 0.7938 (m-80) REVERT: K 181 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6841 (tm-30) REVERT: K 195 LYS cc_start: 0.8400 (mppt) cc_final: 0.8071 (mppt) REVERT: K 222 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8257 (mmtt) REVERT: K 354 GLU cc_start: 0.7730 (mp0) cc_final: 0.7187 (mp0) REVERT: K 395 ASP cc_start: 0.8033 (m-30) cc_final: 0.7780 (m-30) REVERT: D 37 GLU cc_start: 0.7419 (mp0) cc_final: 0.7182 (mp0) REVERT: D 61 LYS cc_start: 0.7850 (pptt) cc_final: 0.7139 (ptmm) REVERT: D 114 CYS cc_start: 0.7287 (m) cc_final: 0.7082 (m) REVERT: D 174 ASP cc_start: 0.7896 (t0) cc_final: 0.7662 (t0) REVERT: D 270 ASN cc_start: 0.8056 (m110) cc_final: 0.7808 (m110) REVERT: D 319 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7240 (mm-40) REVERT: D 321 LYS cc_start: 0.8162 (ptpp) cc_final: 0.7952 (pttm) REVERT: D 364 ASN cc_start: 0.8227 (m-40) cc_final: 0.7983 (m-40) REVERT: D 381 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7855 (mtmm) REVERT: D 390 GLU cc_start: 0.7454 (pm20) cc_final: 0.6912 (pm20) REVERT: G 30 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6977 (mm-30) REVERT: G 76 TYR cc_start: 0.8410 (t80) cc_final: 0.7667 (t80) REVERT: G 174 ASP cc_start: 0.7878 (m-30) cc_final: 0.7329 (m-30) REVERT: G 218 ASP cc_start: 0.8211 (t0) cc_final: 0.7666 (t0) REVERT: G 237 VAL cc_start: 0.8626 (p) cc_final: 0.8401 (m) REVERT: G 241 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7593 (mm-30) REVERT: G 246 ASN cc_start: 0.7669 (t0) cc_final: 0.6980 (t0) REVERT: G 346 VAL cc_start: 0.7805 (t) cc_final: 0.7416 (m) REVERT: G 404 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7887 (ttmm) REVERT: A 9 ASN cc_start: 0.7963 (p0) cc_final: 0.7669 (p0) REVERT: A 20 GLU cc_start: 0.7475 (tt0) cc_final: 0.7214 (tt0) REVERT: A 117 ASP cc_start: 0.7080 (t0) cc_final: 0.6630 (t0) REVERT: A 188 ASP cc_start: 0.7796 (t0) cc_final: 0.7549 (t0) REVERT: A 202 ASP cc_start: 0.7387 (p0) cc_final: 0.7182 (p0) REVERT: A 311 ASP cc_start: 0.7941 (m-30) cc_final: 0.7589 (m-30) REVERT: A 320 TYR cc_start: 0.8026 (p90) cc_final: 0.7115 (p90) REVERT: A 373 LYS cc_start: 0.8429 (mptt) cc_final: 0.8148 (mptt) REVERT: E 36 ASP cc_start: 0.7566 (p0) cc_final: 0.7284 (p0) REVERT: E 50 GLN cc_start: 0.7833 (mm110) cc_final: 0.7632 (mm-40) REVERT: E 105 CYS cc_start: 0.7417 (m) cc_final: 0.7078 (m) REVERT: E 131 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7787 (mmt-90) REVERT: E 162 SER cc_start: 0.8851 (t) cc_final: 0.8623 (t) REVERT: E 168 MET cc_start: 0.7601 (tmm) cc_final: 0.7274 (tmm) REVERT: E 169 HIS cc_start: 0.7901 (m170) cc_final: 0.7555 (m170) REVERT: E 176 TYR cc_start: 0.6631 (m-80) cc_final: 0.6252 (m-10) REVERT: E 200 GLU cc_start: 0.7328 (tt0) cc_final: 0.6833 (tt0) REVERT: E 254 LYS cc_start: 0.8184 (mttt) cc_final: 0.7914 (mttt) REVERT: E 277 THR cc_start: 0.8476 (m) cc_final: 0.8004 (p) REVERT: E 278 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8238 (mtpp) REVERT: E 299 LYS cc_start: 0.8383 (mttt) cc_final: 0.8016 (mtpp) REVERT: E 321 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8557 (p) REVERT: E 393 ARG cc_start: 0.5268 (tpt170) cc_final: 0.4784 (tpt170) REVERT: H 60 ASP cc_start: 0.7964 (t0) cc_final: 0.7448 (t0) REVERT: H 61 VAL cc_start: 0.8679 (t) cc_final: 0.8316 (t) REVERT: H 80 MET cc_start: 0.8770 (tpp) cc_final: 0.7834 (tpp) REVERT: H 131 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7570 (mmt-90) REVERT: H 141 LEU cc_start: 0.8325 (mt) cc_final: 0.8047 (mt) REVERT: H 224 LYS cc_start: 0.8290 (ptmm) cc_final: 0.7977 (ptmm) REVERT: H 347 ASP cc_start: 0.7493 (t0) cc_final: 0.6864 (t0) REVERT: H 393 ARG cc_start: 0.5844 (tpt170) cc_final: 0.5256 (tpt170) REVERT: B 67 MET cc_start: 0.7143 (mmm) cc_final: 0.6537 (mmm) REVERT: B 76 LYS cc_start: 0.7915 (tppp) cc_final: 0.7520 (tppp) REVERT: B 77 GLU cc_start: 0.7794 (tt0) cc_final: 0.7475 (tt0) REVERT: B 129 LYS cc_start: 0.8815 (tptt) cc_final: 0.8579 (tptt) REVERT: B 206 TYR cc_start: 0.7540 (t80) cc_final: 0.7169 (t80) REVERT: B 225 GLN cc_start: 0.6343 (tm-30) cc_final: 0.5807 (tm-30) REVERT: B 265 VAL cc_start: 0.9192 (t) cc_final: 0.8818 (p) REVERT: B 272 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: B 281 LYS cc_start: 0.8344 (mttt) cc_final: 0.8035 (mttt) REVERT: B 354 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7549 (mt-10) REVERT: F 56 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7936 (ptpp) REVERT: F 97 TYR cc_start: 0.5779 (OUTLIER) cc_final: 0.5324 (m-80) REVERT: F 111 LYS cc_start: 0.8655 (mttt) cc_final: 0.8346 (mttt) REVERT: F 116 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7898 (mtp85) REVERT: I 14 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7540 (mmtp) REVERT: I 36 MET cc_start: 0.8092 (mtm) cc_final: 0.7828 (mtm) REVERT: I 111 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8393 (mtpp) REVERT: C 106 ARG cc_start: 0.8284 (ppt170) cc_final: 0.8059 (ppt170) outliers start: 159 outliers final: 134 residues processed: 1240 average time/residue: 0.4779 time to fit residues: 902.7124 Evaluate side-chains 1298 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1160 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 345 HIS Chi-restraints excluded: chain J residue 351 SER Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 7 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 213 THR Chi-restraints excluded: chain K residue 268 VAL 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 83 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 296 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 73 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 123 LYS Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain 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 179 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 357 SER 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 29 ILE 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 230 LYS 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 321 VAL 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 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 188 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 334 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 353 HIS K 361 HIS D 230 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 345 HIS A 43 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117360 restraints weight = 55675.604| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.83 r_work: 0.3356 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31760 Z= 0.229 Angle : 0.741 18.192 43289 Z= 0.373 Chirality : 0.049 0.228 4873 Planarity : 0.005 0.062 5520 Dihedral : 5.752 78.382 4563 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.09 % Favored : 92.86 % Rotamer: Outliers : 4.83 % Allowed : 21.50 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 3963 helix: 2.03 (0.25), residues: 405 sheet: -0.65 (0.15), residues: 1213 loop : -1.47 (0.12), residues: 2345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 279 HIS 0.019 0.001 HIS B 349 PHE 0.028 0.002 PHE E 51 TYR 0.030 0.002 TYR A 308 ARG 0.012 0.001 ARG B 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00289 ( 12) link_NAG-ASN : angle 1.75147 ( 36) hydrogen bonds : bond 0.03476 ( 1026) hydrogen bonds : angle 5.40965 ( 2733) SS BOND : bond 0.00553 ( 56) SS BOND : angle 2.38974 ( 112) covalent geometry : bond 0.00509 (31692) covalent geometry : angle 0.73080 (43141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1166 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 ASN cc_start: 0.8386 (t0) cc_final: 0.7838 (t0) REVERT: J 63 CYS cc_start: 0.5745 (OUTLIER) cc_final: 0.4557 (m) REVERT: J 99 GLU cc_start: 0.7330 (tt0) cc_final: 0.6814 (tt0) REVERT: J 101 THR cc_start: 0.7922 (m) cc_final: 0.7627 (m) REVERT: J 180 ARG cc_start: 0.8608 (ttt-90) cc_final: 0.8281 (ttt-90) REVERT: J 191 GLU cc_start: 0.4542 (tt0) cc_final: 0.3893 (mt-10) REVERT: J 234 THR cc_start: 0.8013 (p) cc_final: 0.7767 (t) REVERT: J 282 ILE cc_start: 0.8579 (mt) cc_final: 0.8166 (tp) REVERT: J 289 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7617 (mtt90) REVERT: J 319 GLN cc_start: 0.7260 (tp-100) cc_final: 0.6999 (tp40) REVERT: K 18 TYR cc_start: 0.7809 (t80) cc_final: 0.7050 (t80) REVERT: K 60 ASP cc_start: 0.7319 (t0) cc_final: 0.6685 (t0) REVERT: K 77 GLU cc_start: 0.8008 (pt0) cc_final: 0.7638 (pt0) REVERT: K 82 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8384 (mtpt) REVERT: K 109 ASP cc_start: 0.7740 (m-30) cc_final: 0.7470 (t0) REVERT: K 127 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7456 (mt-10) REVERT: K 138 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7139 (mm-30) REVERT: K 159 LYS cc_start: 0.8740 (pttm) cc_final: 0.8484 (pttm) REVERT: K 176 TYR cc_start: 0.8278 (m-80) cc_final: 0.7912 (m-80) REVERT: K 181 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6832 (tm-30) REVERT: K 195 LYS cc_start: 0.8417 (mppt) cc_final: 0.8086 (mppt) REVERT: K 222 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8199 (mmtt) REVERT: K 354 GLU cc_start: 0.7769 (mp0) cc_final: 0.7256 (mp0) REVERT: K 395 ASP cc_start: 0.8022 (m-30) cc_final: 0.7792 (m-30) REVERT: D 37 GLU cc_start: 0.7468 (mp0) cc_final: 0.7204 (mp0) REVERT: D 61 LYS cc_start: 0.7858 (pptt) cc_final: 0.7139 (ptmm) REVERT: D 114 CYS cc_start: 0.7338 (m) cc_final: 0.7126 (m) REVERT: D 321 LYS cc_start: 0.8234 (ptpp) cc_final: 0.7912 (mtmm) REVERT: D 364 ASN cc_start: 0.8225 (m-40) cc_final: 0.7990 (m-40) REVERT: D 381 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7849 (mtmm) REVERT: D 390 GLU cc_start: 0.7470 (pm20) cc_final: 0.6908 (pm20) REVERT: G 30 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6951 (mm-30) REVERT: G 76 TYR cc_start: 0.8412 (t80) cc_final: 0.7654 (t80) REVERT: G 174 ASP cc_start: 0.7887 (m-30) cc_final: 0.7340 (m-30) REVERT: G 218 ASP cc_start: 0.8209 (t0) cc_final: 0.7682 (t0) REVERT: G 237 VAL cc_start: 0.8606 (p) cc_final: 0.8397 (m) REVERT: G 241 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7540 (mm-30) REVERT: G 246 ASN cc_start: 0.7667 (t0) cc_final: 0.6982 (t0) REVERT: G 346 VAL cc_start: 0.7827 (t) cc_final: 0.7444 (m) REVERT: G 404 LYS cc_start: 0.8118 (ttmm) cc_final: 0.7864 (ttmm) REVERT: A 9 ASN cc_start: 0.7991 (p0) cc_final: 0.7679 (p0) REVERT: A 20 GLU cc_start: 0.7481 (tt0) cc_final: 0.7220 (tt0) REVERT: A 117 ASP cc_start: 0.7079 (t0) cc_final: 0.6628 (t0) REVERT: A 188 ASP cc_start: 0.7801 (t0) cc_final: 0.7555 (t0) REVERT: A 202 ASP cc_start: 0.7386 (p0) cc_final: 0.7168 (p0) REVERT: A 311 ASP cc_start: 0.7950 (m-30) cc_final: 0.7603 (m-30) REVERT: A 319 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7604 (tp40) REVERT: A 320 TYR cc_start: 0.8012 (p90) cc_final: 0.6712 (p90) REVERT: A 379 GLU cc_start: 0.6382 (tm-30) cc_final: 0.6123 (tt0) REVERT: E 36 ASP cc_start: 0.7560 (p0) cc_final: 0.7281 (p0) REVERT: E 105 CYS cc_start: 0.7424 (m) cc_final: 0.7125 (m) REVERT: E 131 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7766 (mmt180) REVERT: E 162 SER cc_start: 0.8885 (t) cc_final: 0.8657 (t) REVERT: E 168 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7264 (tmm) REVERT: E 169 HIS cc_start: 0.7888 (m170) cc_final: 0.7486 (m170) REVERT: E 176 TYR cc_start: 0.6631 (m-80) cc_final: 0.6254 (m-10) REVERT: E 200 GLU cc_start: 0.7356 (tt0) cc_final: 0.6849 (tt0) REVERT: E 254 LYS cc_start: 0.8166 (mttt) cc_final: 0.7902 (mttt) REVERT: E 277 THR cc_start: 0.8514 (m) cc_final: 0.8008 (p) REVERT: E 278 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8279 (mtpp) REVERT: E 281 LYS cc_start: 0.7902 (mptt) cc_final: 0.7681 (mptt) REVERT: E 299 LYS cc_start: 0.8413 (mttt) cc_final: 0.8044 (mtpp) REVERT: E 321 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8576 (p) REVERT: E 393 ARG cc_start: 0.5334 (tpt170) cc_final: 0.4741 (tpt170) REVERT: H 25 CYS cc_start: 0.5822 (t) cc_final: 0.5522 (t) REVERT: H 60 ASP cc_start: 0.7960 (t0) cc_final: 0.7476 (t0) REVERT: H 61 VAL cc_start: 0.8665 (t) cc_final: 0.8289 (t) REVERT: H 80 MET cc_start: 0.8789 (tpp) cc_final: 0.8442 (tpp) REVERT: H 131 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7547 (mmt-90) REVERT: H 141 LEU cc_start: 0.8302 (mt) cc_final: 0.8025 (mt) REVERT: H 224 LYS cc_start: 0.8285 (ptmm) cc_final: 0.7960 (ptmm) REVERT: H 347 ASP cc_start: 0.7491 (t0) cc_final: 0.6870 (t0) REVERT: H 393 ARG cc_start: 0.5825 (tpt170) cc_final: 0.5212 (tpt170) REVERT: B 67 MET cc_start: 0.7130 (mmm) cc_final: 0.6443 (mmm) REVERT: B 76 LYS cc_start: 0.7926 (tppp) cc_final: 0.7528 (tppp) REVERT: B 77 GLU cc_start: 0.7767 (tt0) cc_final: 0.7434 (tt0) REVERT: B 97 LYS cc_start: 0.7995 (tttp) cc_final: 0.7599 (tttp) REVERT: B 129 LYS cc_start: 0.8819 (tptt) cc_final: 0.8607 (tptt) REVERT: B 206 TYR cc_start: 0.7557 (t80) cc_final: 0.7154 (t80) REVERT: B 225 GLN cc_start: 0.6377 (tm-30) cc_final: 0.5749 (tm-30) REVERT: B 272 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7504 (t-90) REVERT: B 281 LYS cc_start: 0.8345 (mttt) cc_final: 0.8054 (mttt) REVERT: B 354 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7546 (mt-10) REVERT: F 19 MET cc_start: 0.6764 (mmp) cc_final: 0.6469 (mmp) REVERT: F 56 LYS cc_start: 0.8371 (ptpp) cc_final: 0.7954 (ptpp) REVERT: F 88 TYR cc_start: 0.5806 (m-80) cc_final: 0.5404 (m-80) REVERT: F 97 TYR cc_start: 0.5801 (m-80) cc_final: 0.5152 (m-80) REVERT: F 111 LYS cc_start: 0.8658 (mttt) cc_final: 0.8361 (mttt) REVERT: F 116 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7803 (mtp180) REVERT: I 25 ASN cc_start: 0.7265 (t0) cc_final: 0.6728 (t0) REVERT: I 36 MET cc_start: 0.8105 (mtm) cc_final: 0.7838 (mtm) REVERT: I 111 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8396 (mtpp) REVERT: C 55 LEU cc_start: 0.7946 (mm) cc_final: 0.7597 (mt) REVERT: C 106 ARG cc_start: 0.8230 (ppt170) cc_final: 0.8009 (ppt170) outliers start: 163 outliers final: 141 residues processed: 1232 average time/residue: 0.4647 time to fit residues: 875.5804 Evaluate side-chains 1308 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1161 time to evaluate : 3.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain J residue 303 VAL Chi-restraints excluded: chain J residue 323 ASN Chi-restraints excluded: chain J residue 351 SER Chi-restraints excluded: chain J residue 367 VAL Chi-restraints excluded: chain J residue 370 CYS 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 213 THR Chi-restraints excluded: chain K residue 266 CYS 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 83 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 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 259 CYS Chi-restraints excluded: chain D residue 262 GLU 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 403 SER 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 307 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 372 LYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 431 SER 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 179 ILE Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 357 SER 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 29 ILE 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 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 321 VAL 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 159 LYS Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 255 LEU Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 116 ARG Chi-restraints excluded: chain F residue 122 ARG Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain C residue 11 GLU 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 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 156 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 192 optimal weight: 7.9990 chunk 355 optimal weight: 0.6980 chunk 135 optimal weight: 0.0060 chunk 354 optimal weight: 0.3980 chunk 364 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 369 optimal weight: 4.9990 chunk 363 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 199 optimal weight: 0.0020 overall best weight: 0.4004 ------------------------------------------------------------------------------- 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 230 HIS D 270 ASN D 327 HIS G 52 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 139 ASN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.144528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127688 restraints weight = 56015.815| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.91 r_work: 0.3396 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31760 Z= 0.123 Angle : 0.711 16.773 43289 Z= 0.354 Chirality : 0.047 0.287 4873 Planarity : 0.005 0.053 5520 Dihedral : 5.385 83.305 4563 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 3.70 % Allowed : 22.81 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3963 helix: 2.11 (0.25), residues: 398 sheet: -0.42 (0.16), residues: 1130 loop : -1.30 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 279 HIS 0.013 0.001 HIS D 230 PHE 0.022 0.001 PHE D 257 TYR 0.034 0.001 TYR A 308 ARG 0.011 0.001 ARG E 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 12) link_NAG-ASN : angle 1.23122 ( 36) hydrogen bonds : bond 0.03021 ( 1026) hydrogen bonds : angle 5.14406 ( 2733) SS BOND : bond 0.00502 ( 56) SS BOND : angle 1.94720 ( 112) covalent geometry : bond 0.00284 (31692) covalent geometry : angle 0.70454 (43141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7926 Ramachandran restraints generated. 3963 Oldfield, 0 Emsley, 3963 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1177 time to evaluate : 3.306 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: 0.8262 (t0) cc_final: 0.7811 (t0) REVERT: J 24 TYR cc_start: 0.6922 (m-80) cc_final: 0.6503 (m-80) REVERT: J 61 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7459 (ttpt) REVERT: J 63 CYS cc_start: 0.5664 (OUTLIER) cc_final: 0.4435 (m) REVERT: J 99 GLU cc_start: 0.7347 (tt0) cc_final: 0.6789 (tt0) REVERT: J 180 ARG cc_start: 0.8537 (ttt-90) cc_final: 0.8136 (ttt-90) REVERT: J 191 GLU cc_start: 0.4652 (tt0) cc_final: 0.3611 (mt-10) REVERT: J 282 ILE cc_start: 0.8575 (mt) cc_final: 0.8149 (tp) REVERT: J 289 ARG cc_start: 0.7998 (mtt90) cc_final: 0.7528 (mtt90) REVERT: J 321 LYS cc_start: 0.5804 (mmmt) cc_final: 0.5538 (mmmt) REVERT: K 6 PHE cc_start: 0.7965 (m-80) cc_final: 0.7632 (m-80) REVERT: K 18 TYR cc_start: 0.7576 (t80) cc_final: 0.6819 (t80) REVERT: K 60 ASP cc_start: 0.7300 (t0) cc_final: 0.6748 (t0) REVERT: K 77 GLU cc_start: 0.8049 (pt0) cc_final: 0.7672 (pt0) REVERT: K 82 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8399 (mtpt) REVERT: K 155 TYR cc_start: 0.8674 (m-80) cc_final: 0.8419 (m-80) REVERT: K 159 LYS cc_start: 0.8735 (pttm) cc_final: 0.8474 (pttm) REVERT: K 176 TYR cc_start: 0.8193 (m-80) cc_final: 0.7841 (m-80) REVERT: K 181 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6892 (tm-30) REVERT: K 222 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8169 (mmtt) REVERT: K 324 GLU cc_start: 0.7769 (mp0) cc_final: 0.7331 (mp0) REVERT: K 353 HIS cc_start: 0.7329 (p90) cc_final: 0.6947 (p-80) REVERT: K 354 GLU cc_start: 0.7684 (mp0) cc_final: 0.7008 (mp0) REVERT: K 391 LYS cc_start: 0.8624 (tttm) cc_final: 0.8048 (tttm) REVERT: K 395 ASP cc_start: 0.8033 (m-30) cc_final: 0.7638 (m-30) REVERT: L 79 TYR cc_start: 0.7626 (p90) cc_final: 0.7415 (p90) REVERT: L 147 ASN cc_start: 0.7066 (p0) cc_final: 0.6745 (p0) REVERT: D 61 LYS cc_start: 0.7672 (pptt) cc_final: 0.7274 (ptmm) REVERT: D 76 TYR cc_start: 0.8152 (t80) cc_final: 0.7628 (t80) REVERT: D 99 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6052 (tm-30) REVERT: D 114 CYS cc_start: 0.7358 (m) cc_final: 0.7065 (m) REVERT: D 320 TYR cc_start: 0.7941 (p90) cc_final: 0.7377 (p90) REVERT: D 321 LYS cc_start: 0.8084 (ptpp) cc_final: 0.7782 (mtmm) REVERT: D 373 LYS cc_start: 0.8082 (mmtm) cc_final: 0.7767 (mmtm) REVERT: D 390 GLU cc_start: 0.7343 (pm20) cc_final: 0.6970 (pm20) REVERT: G 30 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6964 (mm-30) REVERT: G 76 TYR cc_start: 0.8356 (t80) cc_final: 0.7588 (t80) REVERT: G 105 GLU cc_start: 0.7359 (tt0) cc_final: 0.6812 (tt0) REVERT: G 174 ASP cc_start: 0.7890 (m-30) cc_final: 0.7326 (m-30) REVERT: G 218 ASP cc_start: 0.8142 (t0) cc_final: 0.7665 (t0) REVERT: G 241 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7583 (mm-30) REVERT: G 246 ASN cc_start: 0.7635 (t0) cc_final: 0.6957 (t0) REVERT: G 404 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7936 (ttmm) REVERT: A 9 ASN cc_start: 0.7469 (p0) cc_final: 0.7164 (p0) REVERT: A 30 GLU cc_start: 0.6710 (tp30) cc_final: 0.6347 (tp30) REVERT: A 107 TYR cc_start: 0.7689 (p90) cc_final: 0.7169 (p90) REVERT: A 117 ASP cc_start: 0.7118 (t0) cc_final: 0.6701 (t0) REVERT: A 188 ASP cc_start: 0.7754 (t0) cc_final: 0.7486 (t0) REVERT: A 223 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8167 (pttp) REVERT: A 234 THR cc_start: 0.7896 (m) cc_final: 0.7686 (m) REVERT: A 311 ASP cc_start: 0.7783 (m-30) cc_final: 0.7433 (m-30) REVERT: A 320 TYR cc_start: 0.7981 (p90) cc_final: 0.7108 (p90) REVERT: E 30 LYS cc_start: 0.8458 (tttt) cc_final: 0.8116 (tttm) REVERT: E 36 ASP cc_start: 0.7537 (p0) cc_final: 0.7277 (p0) REVERT: E 105 CYS cc_start: 0.7418 (m) cc_final: 0.7145 (m) REVERT: E 129 LYS cc_start: 0.8644 (tppt) cc_final: 0.8224 (tppt) REVERT: E 131 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7757 (mmt-90) REVERT: E 168 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7245 (tmm) REVERT: E 169 HIS cc_start: 0.7675 (m170) cc_final: 0.7300 (m170) REVERT: E 195 LYS cc_start: 0.8319 (mttt) cc_final: 0.7916 (mttt) REVERT: E 254 LYS cc_start: 0.8173 (mttt) cc_final: 0.7893 (mttt) REVERT: E 277 THR cc_start: 0.8445 (m) cc_final: 0.7931 (p) REVERT: E 278 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8215 (mtpp) REVERT: E 281 LYS cc_start: 0.8054 (mptt) cc_final: 0.7696 (mptt) REVERT: E 299 LYS cc_start: 0.8363 (mttt) cc_final: 0.7984 (mtpp) REVERT: E 321 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8447 (p) REVERT: E 393 ARG cc_start: 0.5161 (tpt170) cc_final: 0.4599 (tpt170) REVERT: H 25 CYS cc_start: 0.5319 (t) cc_final: 0.4926 (t) REVERT: H 60 ASP cc_start: 0.7900 (t0) cc_final: 0.7448 (t0) REVERT: H 80 MET cc_start: 0.8728 (tpp) cc_final: 0.8382 (tpp) REVERT: H 224 LYS cc_start: 0.8186 (ptmm) cc_final: 0.7890 (ptmm) REVERT: H 239 ASN cc_start: 0.8255 (p0) cc_final: 0.8044 (p0) REVERT: H 347 ASP cc_start: 0.7501 (t0) cc_final: 0.6967 (t0) REVERT: H 393 ARG cc_start: 0.5647 (tpt170) cc_final: 0.4570 (tpt170) REVERT: H 397 LEU cc_start: 0.8395 (mm) cc_final: 0.8094 (mm) REVERT: B 67 MET cc_start: 0.6946 (mmm) cc_final: 0.6157 (mmm) REVERT: B 76 LYS cc_start: 0.7964 (tppp) cc_final: 0.7557 (tppp) REVERT: B 97 LYS cc_start: 0.7968 (tttp) cc_final: 0.7604 (tttp) REVERT: B 129 LYS cc_start: 0.8745 (tptt) cc_final: 0.8525 (tptt) REVERT: B 225 GLN cc_start: 0.6582 (tm-30) cc_final: 0.5989 (tm-30) REVERT: B 272 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7534 (t-90) REVERT: B 281 LYS cc_start: 0.8268 (mttt) cc_final: 0.7953 (mttt) REVERT: B 342 GLU cc_start: 0.6977 (pm20) cc_final: 0.6656 (pm20) REVERT: B 354 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7500 (mt-10) REVERT: F 56 LYS cc_start: 0.8301 (ptpp) cc_final: 0.7788 (ptpp) REVERT: F 97 TYR cc_start: 0.5681 (m-80) cc_final: 0.5204 (m-80) REVERT: F 143 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8304 (p) REVERT: I 14 LYS cc_start: 0.7994 (mmtp) cc_final: 0.7536 (mmtp) REVERT: I 25 ASN cc_start: 0.6927 (t0) cc_final: 0.6459 (t0) REVERT: I 111 LYS cc_start: 0.8539 (mtpp) cc_final: 0.8309 (mtpp) REVERT: I 124 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7254 (ptp90) REVERT: I 143 VAL cc_start: 0.8363 (p) cc_final: 0.8115 (m) REVERT: C 55 LEU cc_start: 0.7900 (mm) cc_final: 0.7641 (mt) REVERT: C 106 ARG cc_start: 0.8228 (ppt170) cc_final: 0.7979 (ppt170) outliers start: 125 outliers final: 100 residues processed: 1226 average time/residue: 0.4566 time to fit residues: 854.3695 Evaluate side-chains 1251 residues out of total 3376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1145 time to evaluate : 3.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain J residue 108 VAL Chi-restraints excluded: chain J residue 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 351 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 145 VAL Chi-restraints excluded: chain K residue 213 THR Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 268 VAL Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 83 LYS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain D residue 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 280 ILE Chi-restraints excluded: chain D residue 296 ILE Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 354 LEU 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 G residue 431 SER Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 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 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 223 LYS 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 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 135 VAL Chi-restraints excluded: chain E residue 168 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 287 LEU 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 101 LEU 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 255 LEU Chi-restraints excluded: chain H residue 257 ILE Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 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 C residue 20 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 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: 0.9980 chunk 175 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 174 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 chunk 363 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 329 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 319 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS G 52 HIS ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN G 345 HIS ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 332 ASN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.137445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120774 restraints weight = 56138.024| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.87 r_work: 0.3381 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 31760 Z= 0.142 Angle : 0.723 17.988 43289 Z= 0.357 Chirality : 0.048 0.307 4873 Planarity : 0.005 0.052 5520 Dihedral : 5.369 82.603 4563 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 3.32 % Allowed : 23.76 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3963 helix: 2.14 (0.25), residues: 400 sheet: -0.34 (0.16), residues: 1128 loop : -1.25 (0.13), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 339 HIS 0.012 0.001 HIS D 230 PHE 0.022 0.001 PHE E 51 TYR 0.031 0.001 TYR A 308 ARG 0.012 0.001 ARG J 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00229 ( 12) link_NAG-ASN : angle 1.42858 ( 36) hydrogen bonds : bond 0.03105 ( 1026) hydrogen bonds : angle 5.08659 ( 2733) SS BOND : bond 0.00498 ( 56) SS BOND : angle 2.32644 ( 112) covalent geometry : bond 0.00332 (31692) covalent geometry : angle 0.71302 (43141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19696.19 seconds wall clock time: 338 minutes 51.41 seconds (20331.41 seconds total)