Starting phenix.real_space_refine on Sat Jun 28 15:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqz_47119/06_2025/9dqz_47119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqz_47119/06_2025/9dqz_47119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dqz_47119/06_2025/9dqz_47119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqz_47119/06_2025/9dqz_47119.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqz_47119/06_2025/9dqz_47119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqz_47119/06_2025/9dqz_47119.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 244 5.16 5 C 21076 2.51 5 N 5745 2.21 5 O 6392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33465 Number of models: 1 Model: "" Number of chains: 28 Chain: "D" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "E" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "F" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "G" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "H" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "I" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "J" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "K" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "L" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "M" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "N" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "O" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain breaks: 1 Chain: "A" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3311 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 27, 'TRANS': 410} Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3201 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 28, 'TRANS': 380} Chain: "C" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "P" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.66, per 1000 atoms: 0.62 Number of scatterers: 33465 At special positions: 0 Unit cell: (188.68, 175.96, 204.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 244 16.00 O 6392 8.00 N 5745 7.00 C 21076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=80, symmetry=0 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.02 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.04 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.04 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.02 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 226 " distance=2.04 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.04 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.04 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.02 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.02 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.04 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 33 " - pdb=" SG CYS M 45 " distance=2.03 Simple disulfide: pdb=" SG CYS M 40 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 52 " - pdb=" SG CYS M 67 " distance=2.03 Simple disulfide: pdb=" SG CYS M 72 " - pdb=" SG CYS M 84 " distance=2.03 Simple disulfide: pdb=" SG CYS M 79 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS M 91 " - pdb=" SG CYS M 108 " distance=2.03 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 45 " distance=2.03 Simple disulfide: pdb=" SG CYS N 40 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 52 " - pdb=" SG CYS N 67 " distance=2.03 Simple disulfide: pdb=" SG CYS N 72 " - pdb=" SG CYS N 84 " distance=2.03 Simple disulfide: pdb=" SG CYS N 79 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 108 " distance=2.03 Simple disulfide: pdb=" SG CYS O 33 " - pdb=" SG CYS O 45 " distance=2.03 Simple disulfide: pdb=" SG CYS O 40 " - pdb=" SG CYS O 58 " distance=2.03 Simple disulfide: pdb=" SG CYS O 52 " - pdb=" SG CYS O 67 " distance=2.03 Simple disulfide: pdb=" SG CYS O 72 " - pdb=" SG CYS O 84 " distance=2.03 Simple disulfide: pdb=" SG CYS O 79 " - pdb=" SG CYS O 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 91 " - pdb=" SG CYS O 108 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 33 " - pdb=" SG CYS P 45 " distance=2.03 Simple disulfide: pdb=" SG CYS P 40 " - pdb=" SG CYS P 58 " distance=2.03 Simple disulfide: pdb=" SG CYS P 52 " - pdb=" SG CYS P 67 " distance=2.03 Simple disulfide: pdb=" SG CYS P 72 " - pdb=" SG CYS P 84 " distance=2.03 Simple disulfide: pdb=" SG CYS P 79 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 91 " - pdb=" SG CYS P 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 139 " " NAG A 502 " - " ASN A 245 " " NAG B 501 " - " ASN B 196 " " NAG B 502 " - " ASN B 318 " " NAG D 501 " - " ASN D 139 " " NAG D 502 " - " ASN D 245 " " NAG E 501 " - " ASN E 196 " " NAG E 502 " - " ASN E 318 " " NAG G 501 " - " ASN G 139 " " NAG G 502 " - " ASN G 245 " " NAG H 501 " - " ASN H 196 " " NAG H 502 " - " ASN H 318 " " NAG J 501 " - " ASN J 139 " " NAG J 502 " - " ASN J 245 " " NAG K 501 " - " ASN K 196 " " NAG K 502 " - " ASN K 318 " Time building additional restraints: 8.26 Conformation dependent library (CDL) restraints added in 4.8 seconds 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7982 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 97 sheets defined 13.3% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'D' and resid 111 through 116 removed outlier: 4.346A pdb=" N THR D 115 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 116 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.542A pdb=" N THR D 254 " --> pdb=" O LEU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.148A pdb=" N GLY D 258 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N CYS D 259 " --> pdb=" O PRO D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 259' Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.840A pdb=" N VAL D 402 " --> pdb=" O PHE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 438 Processing helix chain 'E' and resid 176 through 178 No H-bonds generated for 'chain 'E' and resid 176 through 178' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 363 through 402 Proline residue: E 399 - end of helix Processing helix chain 'F' and resid 7 through 11 Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.975A pdb=" N LYS F 73 " --> pdb=" O GLN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.646A pdb=" N GLY F 100 " --> pdb=" O TYR F 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.853A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 402 removed outlier: 3.949A pdb=" N VAL G 402 " --> pdb=" O PHE G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 438 Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 222 through 226 removed outlier: 3.564A pdb=" N GLN H 225 " --> pdb=" O LYS H 222 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS H 226 " --> pdb=" O ALA H 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 222 through 226' Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 363 through 402 removed outlier: 3.512A pdb=" N THR H 367 " --> pdb=" O HIS H 363 " (cutoff:3.500A) Proline residue: H 399 - end of helix removed outlier: 3.662A pdb=" N LEU H 402 " --> pdb=" O THR H 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 Processing helix chain 'I' and resid 47 through 52 removed outlier: 3.535A pdb=" N ALA I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 101 removed outlier: 4.123A pdb=" N GLY I 100 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 255 Processing helix chain 'J' and resid 256 through 259 Processing helix chain 'J' and resid 403 through 438 Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 363 through 402 Proline residue: K 399 - end of helix removed outlier: 3.572A pdb=" N LEU K 402 " --> pdb=" O THR K 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 12 Processing helix chain 'L' and resid 98 through 101 Processing helix chain 'M' and resid 49 through 51 No H-bonds generated for 'chain 'M' and resid 49 through 51' Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'M' and resid 100 through 104 removed outlier: 3.592A pdb=" N GLU M 103 " --> pdb=" O GLY M 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 100 through 104 removed outlier: 3.519A pdb=" N SER N 104 " --> pdb=" O SER N 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 51 No H-bonds generated for 'chain 'O' and resid 49 through 51' Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'O' and resid 100 through 104 removed outlier: 3.597A pdb=" N GLU O 103 " --> pdb=" O GLY O 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.051A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.817A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 438 Processing helix chain 'B' and resid 222 through 226 removed outlier: 3.715A pdb=" N CYS B 226 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.506A pdb=" N ILE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 402 Proline residue: B 399 - end of helix Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 47 through 52 removed outlier: 4.265A pdb=" N ALA C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 61 through 66 removed outlier: 3.698A pdb=" N ASN P 66 " --> pdb=" O SER P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 7 removed outlier: 4.068A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 19 removed outlier: 6.114A pdb=" N ILE D 13 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL D 33 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.814A pdb=" N VAL D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 47 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU D 45 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN D 43 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N THR D 126 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG D 134 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 33 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D 31 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.842A pdb=" N GLN D 59 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN D 102 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL D 80 " --> pdb=" O GLN D 102 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER D 104 " --> pdb=" O CYS D 78 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS D 78 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA D 106 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR D 76 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA D 74 " --> pdb=" O VAL D 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'D' and resid 296 through 304 removed outlier: 4.664A pdb=" N GLU D 298 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 321 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 315 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AB1, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AB2, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.511A pdb=" N HIS E 256 " --> pdb=" O THR E 3 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 35 removed outlier: 8.495A pdb=" N ILE E 31 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N SER E 48 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN E 33 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR E 99 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN E 104 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ARG E 93 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=AB6, first strand: chain 'E' and resid 83 through 86 removed outlier: 4.300A pdb=" N ASP E 109 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AB8, first strand: chain 'E' and resid 180 through 183 Processing sheet with id=AB9, first strand: chain 'E' and resid 206 through 211 removed outlier: 3.813A pdb=" N GLU E 200 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE E 227 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 276 through 279 Processing sheet with id=AC2, first strand: chain 'F' and resid 44 through 45 removed outlier: 3.540A pdb=" N GLY F 26 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N TYR F 27 " --> pdb=" O PRO F 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 88 through 89 Processing sheet with id=AC4, first strand: chain 'F' and resid 117 through 119 removed outlier: 8.163A pdb=" N ALA F 127 " --> pdb=" O TRP F 146 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N TRP F 146 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL F 129 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL F 144 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.936A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.503A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.811A pdb=" N VAL G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL G 47 " --> pdb=" O VAL G 120 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU G 45 " --> pdb=" O LEU G 122 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 35 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE G 31 " --> pdb=" O VAL G 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.792A pdb=" N GLN G 59 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN G 102 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL G 80 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER G 104 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS G 78 " --> pdb=" O SER G 104 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA G 106 " --> pdb=" O TYR G 76 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TYR G 76 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AD1, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD2, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD3, first strand: chain 'G' and resid 296 through 303 removed outlier: 3.838A pdb=" N GLU G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AD5, first strand: chain 'G' and resid 337 through 339 Processing sheet with id=AD6, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AD7, first strand: chain 'H' and resid 14 through 16 removed outlier: 3.748A pdb=" N CYS H 16 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS H 25 " --> pdb=" O CYS H 16 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 31 through 35 removed outlier: 8.443A pdb=" N ILE H 31 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 48 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN H 33 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 10.259A pdb=" N SER H 48 " --> pdb=" O MET H 67 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET H 67 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS H 63 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 31 through 35 removed outlier: 8.443A pdb=" N ILE H 31 " --> pdb=" O SER H 48 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER H 48 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN H 33 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR H 99 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA H 49 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LYS H 97 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N PHE H 51 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY H 95 " --> pdb=" O PHE H 51 " (cutoff:3.500A) removed outlier: 15.517A pdb=" N TYR H 53 " --> pdb=" O ARG H 93 " (cutoff:3.500A) removed outlier: 17.918A pdb=" N ARG H 93 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 83 through 86 removed outlier: 4.343A pdb=" N ASP H 109 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AE3, first strand: chain 'H' and resid 237 through 238 removed outlier: 5.511A pdb=" N ILE H 257 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR H 165 " --> pdb=" O LEU H 255 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU H 255 " --> pdb=" O TYR H 165 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR H 167 " --> pdb=" O GLY H 253 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY H 253 " --> pdb=" O THR H 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 180 through 183 removed outlier: 4.126A pdb=" N ILE H 189 " --> pdb=" O THR H 215 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR H 215 " --> pdb=" O ILE H 189 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 206 through 211 Processing sheet with id=AE6, first strand: chain 'H' and resid 276 through 279 removed outlier: 3.657A pdb=" N GLY H 282 " --> pdb=" O TRP H 279 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 44 through 45 removed outlier: 3.667A pdb=" N GLY I 26 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N TYR I 27 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 94 through 95 removed outlier: 6.725A pdb=" N ILE I 118 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL I 126 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP I 146 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER I 142 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY I 132 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA I 140 " --> pdb=" O GLY I 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 94 through 95 removed outlier: 6.725A pdb=" N ILE I 118 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL I 126 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP I 146 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER I 142 " --> pdb=" O LEU I 130 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY I 132 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA I 140 " --> pdb=" O GLY I 132 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.885A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 12 through 20 removed outlier: 6.111A pdb=" N ILE J 13 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL J 33 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU J 29 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR J 137 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE J 31 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE J 135 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL J 33 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU J 133 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER J 35 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL J 131 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU J 37 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU J 129 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR J 39 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA J 127 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER J 41 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA J 119 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.623A pdb=" N ALA J 119 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL J 47 " --> pdb=" O ALA J 119 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA J 121 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER J 41 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA J 127 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR J 39 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU J 129 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLU J 37 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL J 131 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER J 35 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU J 133 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL J 33 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE J 135 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE J 31 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR J 137 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU J 29 " --> pdb=" O TYR J 137 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 59 through 62 removed outlier: 3.672A pdb=" N GLN J 59 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL J 108 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASP J 75 " --> pdb=" O VAL J 108 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 87 through 88 removed outlier: 3.514A pdb=" N GLY J 91 " --> pdb=" O MET J 88 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 203 through 205 Processing sheet with id=AF7, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AF8, first strand: chain 'J' and resid 299 through 304 removed outlier: 4.295A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 343 through 346 Processing sheet with id=AG1, first strand: chain 'J' and resid 387 through 388 removed outlier: 6.846A pdb=" N ARG K 291 " --> pdb=" O GLY K 313 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY K 313 " --> pdb=" O ARG K 291 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 14 through 16 Processing sheet with id=AG3, first strand: chain 'K' and resid 31 through 35 removed outlier: 8.514A pdb=" N ILE K 31 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER K 48 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 10.262A pdb=" N SER K 48 " --> pdb=" O MET K 67 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET K 67 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS K 63 " --> pdb=" O GLY K 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 31 through 35 removed outlier: 8.514A pdb=" N ILE K 31 " --> pdb=" O SER K 48 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER K 48 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR K 99 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA K 49 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LYS K 97 " --> pdb=" O ALA K 49 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE K 51 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.598A pdb=" N GLY K 95 " --> pdb=" O PHE K 51 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 83 through 86 removed outlier: 4.428A pdb=" N ASP K 109 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 150 through 155 Processing sheet with id=AG7, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AG8, first strand: chain 'K' and resid 180 through 182 Processing sheet with id=AG9, first strand: chain 'K' and resid 207 through 211 Processing sheet with id=AH1, first strand: chain 'K' and resid 276 through 279 Processing sheet with id=AH2, first strand: chain 'L' and resid 44 through 45 removed outlier: 6.672A pdb=" N PHE L 16 " --> pdb=" O TYR L 27 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR L 27 " --> pdb=" O PHE L 16 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE L 18 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR L 27 " --> pdb=" O PRO L 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 87 through 89 Processing sheet with id=AH4, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.695A pdb=" N ALA L 127 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AH6, first strand: chain 'M' and resid 76 through 78 Processing sheet with id=AH7, first strand: chain 'N' and resid 37 through 39 Processing sheet with id=AH8, first strand: chain 'N' and resid 76 through 78 Processing sheet with id=AH9, first strand: chain 'O' and resid 37 through 39 Processing sheet with id=AI1, first strand: chain 'O' and resid 76 through 78 Processing sheet with id=AI2, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.937A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'A' and resid 12 through 19 removed outlier: 5.972A pdb=" N ILE A 13 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL A 33 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 29 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR A 137 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 33 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 35 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 131 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 129 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA A 127 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER A 41 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.456A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER A 41 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ALA A 127 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU A 129 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 131 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N SER A 35 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 33 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR A 137 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 29 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 59 through 62 removed outlier: 3.870A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLN A 102 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL A 80 " --> pdb=" O GLN A 102 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 104 " --> pdb=" O CYS A 78 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS A 78 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 106 " --> pdb=" O TYR A 76 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR A 76 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 74 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.514A pdb=" N GLY A 91 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AI8, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AI9, first strand: chain 'A' and resid 296 through 304 Processing sheet with id=AJ1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AJ2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AJ3, first strand: chain 'B' and resid 14 through 16 removed outlier: 3.529A pdb=" N GLY B 14 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 27 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS B 25 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.796A pdb=" N GLN B 46 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 34 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 102 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'B' and resid 51 through 53 removed outlier: 4.783A pdb=" N GLY B 52 " --> pdb=" O ASP B 60 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AJ7, first strand: chain 'B' and resid 150 through 155 Processing sheet with id=AJ8, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AJ9, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AK1, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AK2, first strand: chain 'B' and resid 276 through 279 Processing sheet with id=AK3, first strand: chain 'C' and resid 44 through 45 removed outlier: 4.001A pdb=" N GLY C 26 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR C 27 " --> pdb=" O PRO C 38 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'C' and resid 88 through 90 removed outlier: 8.837A pdb=" N ALA C 94 " --> pdb=" O PRO C 105 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE C 102 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 140 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY C 132 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 142 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 127 " --> pdb=" O ILE C 118 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'C' and resid 88 through 90 removed outlier: 8.837A pdb=" N ALA C 94 " --> pdb=" O PRO C 105 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N PHE C 102 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 37 through 39 Processing sheet with id=AK7, first strand: chain 'P' and resid 76 through 78 1114 hydrogen bonds defined for protein. 2922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.26 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10881 1.34 - 1.47: 8339 1.47 - 1.60: 14766 1.60 - 1.73: 1 1.73 - 1.85: 304 Bond restraints: 34291 Sorted by residual: bond pdb=" CG LEU J 428 " pdb=" CD2 LEU J 428 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" CB ASP H 36 " pdb=" CG ASP H 36 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.40e+00 bond pdb=" CA GLU E 342 " pdb=" CB GLU E 342 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.22e-02 6.72e+03 2.07e+00 bond pdb=" CA ASN C 47 " pdb=" CB ASN C 47 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 1.99e+00 bond pdb=" CB ASN L 47 " pdb=" CG ASN L 47 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.89e+00 ... (remaining 34286 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 46045 2.96 - 5.91: 544 5.91 - 8.87: 51 8.87 - 11.82: 7 11.82 - 14.78: 4 Bond angle restraints: 46651 Sorted by residual: angle pdb=" C ASP C 46 " pdb=" N ASN C 47 " pdb=" CA ASN C 47 " ideal model delta sigma weight residual 121.54 132.61 -11.07 1.91e+00 2.74e-01 3.36e+01 angle pdb=" C VAL G 263 " pdb=" N GLU G 264 " pdb=" CA GLU G 264 " ideal model delta sigma weight residual 121.80 135.77 -13.97 2.44e+00 1.68e-01 3.28e+01 angle pdb=" CA CYS K 226 " pdb=" CB CYS K 226 " pdb=" SG CYS K 226 " ideal model delta sigma weight residual 114.40 126.96 -12.56 2.30e+00 1.89e-01 2.98e+01 angle pdb=" C LEU F 20 " pdb=" N ASN F 21 " pdb=" CA ASN F 21 " ideal model delta sigma weight residual 121.54 130.37 -8.83 1.91e+00 2.74e-01 2.14e+01 angle pdb=" CB MET C 19 " pdb=" CG MET C 19 " pdb=" SD MET C 19 " ideal model delta sigma weight residual 112.70 126.21 -13.51 3.00e+00 1.11e-01 2.03e+01 ... (remaining 46646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 19250 17.92 - 35.84: 1332 35.84 - 53.76: 231 53.76 - 71.68: 66 71.68 - 89.61: 24 Dihedral angle restraints: 20903 sinusoidal: 8448 harmonic: 12455 Sorted by residual: dihedral pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " pdb=" SG CYS A 370 " pdb=" CB CYS A 370 " ideal model delta sinusoidal sigma weight residual 93.00 -177.82 -89.18 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS K 152 " pdb=" SG CYS K 152 " pdb=" SG CYS K 266 " pdb=" CB CYS K 266 " ideal model delta sinusoidal sigma weight residual -86.00 -174.77 88.77 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 16 " pdb=" SG CYS B 16 " pdb=" SG CYS B 124 " pdb=" CB CYS B 124 " ideal model delta sinusoidal sigma weight residual -86.00 -174.28 88.28 1 1.00e+01 1.00e-02 9.31e+01 ... (remaining 20900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 4873 0.105 - 0.209: 360 0.209 - 0.314: 12 0.314 - 0.419: 0 0.419 - 0.523: 1 Chirality restraints: 5246 Sorted by residual: chirality pdb=" CB ILE G 307 " pdb=" CA ILE G 307 " pdb=" CG1 ILE G 307 " pdb=" CG2 ILE G 307 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" CB THR B 314 " pdb=" CA THR B 314 " pdb=" OG1 THR B 314 " pdb=" CG2 THR B 314 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL J 136 " pdb=" CA VAL J 136 " pdb=" CG1 VAL J 136 " pdb=" CG2 VAL J 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 5243 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 163 " -0.029 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP F 163 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP F 163 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP F 163 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 163 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 163 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 163 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 163 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 163 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP F 163 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 264 " -0.057 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO D 265 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 245 " -0.006 2.00e-02 2.50e+03 2.96e-02 1.10e+01 pdb=" CG ASN A 245 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 245 " -0.034 2.00e-02 2.50e+03 pdb=" ND2 ASN A 245 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A 502 " -0.028 2.00e-02 2.50e+03 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1355 2.72 - 3.27: 31987 3.27 - 3.81: 53874 3.81 - 4.36: 65505 4.36 - 4.90: 113325 Nonbonded interactions: 266046 Sorted by model distance: nonbonded pdb=" OE2 GLU G 30 " pdb=" OG1 THR G 32 " model vdw 2.175 3.040 nonbonded pdb=" OG SER B 27 " pdb=" O ILE B 29 " model vdw 2.211 3.040 nonbonded pdb=" O ASP F 113 " pdb=" NH1 ARG F 116 " model vdw 2.220 3.120 nonbonded pdb=" OG SER C 81 " pdb=" O ASN C 147 " model vdw 2.261 3.040 nonbonded pdb=" O ASP I 113 " pdb=" NH1 ARG I 116 " model vdw 2.262 3.120 ... (remaining 266041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 33 through 68 or resid 72 or resid 75 through 110 or resid \ 201 through 202)) selection = (chain 'N' and (resid 33 through 68 or resid 72 or resid 75 through 110 or resid \ 201 through 202)) selection = (chain 'O' and (resid 33 through 68 or resid 72 through 110 or resid 201 through \ 202)) selection = (chain 'P' and (resid 33 through 72 or resid 75 through 110 or resid 201 through \ 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.630 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 83.050 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.290 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:18.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34387 Z= 0.174 Angle : 0.820 18.456 46859 Z= 0.423 Chirality : 0.054 0.523 5246 Planarity : 0.007 0.103 6004 Dihedral : 12.293 89.605 12681 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.87 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 4291 helix: 0.15 (0.22), residues: 446 sheet: -0.07 (0.15), residues: 1256 loop : -1.01 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.002 TRP F 163 HIS 0.008 0.001 HIS D 125 PHE 0.021 0.002 PHE D 257 TYR 0.024 0.002 TYR D 273 ARG 0.015 0.001 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00800 ( 16) link_NAG-ASN : angle 4.78541 ( 48) hydrogen bonds : bond 0.12227 ( 1070) hydrogen bonds : angle 6.34231 ( 2922) SS BOND : bond 0.00425 ( 80) SS BOND : angle 1.98175 ( 160) covalent geometry : bond 0.00392 (34291) covalent geometry : angle 0.79926 (46651) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1083 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7519 (pp20) cc_final: 0.7258 (pp20) REVERT: D 99 GLU cc_start: 0.7760 (tp30) cc_final: 0.7554 (tp30) REVERT: D 202 ASP cc_start: 0.7714 (m-30) cc_final: 0.7270 (m-30) REVERT: D 234 THR cc_start: 0.8606 (m) cc_final: 0.8327 (t) REVERT: D 270 ASN cc_start: 0.8849 (m-40) cc_final: 0.8616 (m-40) REVERT: D 280 ILE cc_start: 0.8151 (mt) cc_final: 0.7674 (mp) REVERT: D 281 ASP cc_start: 0.7764 (t0) cc_final: 0.7525 (t0) REVERT: D 292 GLU cc_start: 0.8683 (mp0) cc_final: 0.8473 (mp0) REVERT: D 298 GLU cc_start: 0.6965 (tm-30) cc_final: 0.6505 (tm-30) REVERT: D 320 TYR cc_start: 0.7748 (p90) cc_final: 0.7403 (p90) REVERT: D 321 LYS cc_start: 0.7931 (mttm) cc_final: 0.7593 (mmmm) REVERT: D 404 LYS cc_start: 0.8265 (ttpt) cc_final: 0.8009 (ttpt) REVERT: E 63 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8081 (ttmm) REVERT: E 82 LYS cc_start: 0.7956 (mttm) cc_final: 0.7677 (mtmm) REVERT: E 129 LYS cc_start: 0.8721 (tptt) cc_final: 0.8456 (tptt) REVERT: E 138 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7307 (tm-30) REVERT: E 162 SER cc_start: 0.8359 (t) cc_final: 0.8122 (m) REVERT: E 176 TYR cc_start: 0.8782 (m-80) cc_final: 0.8348 (m-80) REVERT: E 178 SER cc_start: 0.8774 (t) cc_final: 0.8548 (t) REVERT: E 182 GLU cc_start: 0.7553 (tt0) cc_final: 0.7226 (tt0) REVERT: E 217 MET cc_start: 0.6365 (mmt) cc_final: 0.6093 (mmt) REVERT: E 222 LYS cc_start: 0.8295 (mtmm) cc_final: 0.7994 (mtmm) REVERT: E 235 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7709 (mmmm) REVERT: E 248 ASP cc_start: 0.8336 (t0) cc_final: 0.7872 (t0) REVERT: E 250 SER cc_start: 0.8646 (m) cc_final: 0.8288 (m) REVERT: E 254 LYS cc_start: 0.8542 (mttm) cc_final: 0.8289 (mttm) REVERT: E 324 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7920 (mt-10) REVERT: E 391 LYS cc_start: 0.8601 (tppp) cc_final: 0.8333 (tppp) REVERT: E 400 TYR cc_start: 0.8923 (m-80) cc_final: 0.8709 (m-80) REVERT: F 6 MET cc_start: 0.4202 (tpt) cc_final: 0.3958 (tpt) REVERT: F 44 LYS cc_start: 0.8179 (tppt) cc_final: 0.7806 (tppt) REVERT: G 101 THR cc_start: 0.7997 (t) cc_final: 0.7606 (p) REVERT: G 114 CYS cc_start: 0.7517 (m) cc_final: 0.7254 (m) REVERT: G 145 ASP cc_start: 0.7651 (m-30) cc_final: 0.7434 (m-30) REVERT: G 289 ARG cc_start: 0.8208 (mmm160) cc_final: 0.7729 (mmm160) REVERT: G 292 GLU cc_start: 0.8041 (mp0) cc_final: 0.7553 (mp0) REVERT: G 298 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6885 (tm-30) REVERT: G 341 GLU cc_start: 0.7992 (mp0) cc_final: 0.7739 (mp0) REVERT: H 61 VAL cc_start: 0.8140 (t) cc_final: 0.7935 (t) REVERT: H 129 LYS cc_start: 0.8459 (tptt) cc_final: 0.8163 (tmtt) REVERT: H 131 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7661 (mtm180) REVERT: H 134 PHE cc_start: 0.8615 (p90) cc_final: 0.8401 (p90) REVERT: H 178 SER cc_start: 0.8780 (m) cc_final: 0.8508 (m) REVERT: H 195 LYS cc_start: 0.8251 (mppt) cc_final: 0.7716 (mppt) REVERT: H 384 SER cc_start: 0.7982 (t) cc_final: 0.7507 (p) REVERT: H 391 LYS cc_start: 0.8426 (tppp) cc_final: 0.8095 (tppp) REVERT: H 393 ARG cc_start: 0.6283 (tpt170) cc_final: 0.5278 (tpt170) REVERT: I 62 ASP cc_start: 0.7941 (m-30) cc_final: 0.7660 (m-30) REVERT: I 72 MET cc_start: 0.7330 (mmp) cc_final: 0.6976 (mmp) REVERT: I 126 VAL cc_start: 0.8719 (p) cc_final: 0.8349 (t) REVERT: J 2 GLU cc_start: 0.7726 (pp20) cc_final: 0.7506 (pp20) REVERT: J 30 GLU cc_start: 0.7973 (pp20) cc_final: 0.7161 (pp20) REVERT: J 45 GLU cc_start: 0.7962 (tp30) cc_final: 0.7568 (tp30) REVERT: J 66 LEU cc_start: 0.8098 (tp) cc_final: 0.7742 (tp) REVERT: J 75 ASP cc_start: 0.8333 (t70) cc_final: 0.7991 (t0) REVERT: J 125 HIS cc_start: 0.7752 (m90) cc_final: 0.7446 (m170) REVERT: J 130 LYS cc_start: 0.8489 (tttt) cc_final: 0.8237 (ttmm) REVERT: J 202 ASP cc_start: 0.7571 (m-30) cc_final: 0.7147 (m-30) REVERT: J 218 ASP cc_start: 0.7121 (t0) cc_final: 0.6773 (t0) REVERT: J 241 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7801 (mm-30) REVERT: J 244 LYS cc_start: 0.8873 (mtmt) cc_final: 0.8459 (mtmt) REVERT: J 292 GLU cc_start: 0.7890 (mp0) cc_final: 0.7517 (mp0) REVERT: J 433 MET cc_start: 0.6788 (mmm) cc_final: 0.6416 (mmm) REVERT: K 37 GLU cc_start: 0.7462 (mp0) cc_final: 0.6934 (mp0) REVERT: K 128 LYS cc_start: 0.8781 (tptt) cc_final: 0.8576 (tptt) REVERT: K 139 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6964 (tm-30) REVERT: K 181 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7786 (ttpp) REVERT: K 245 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8262 (ttp-170) REVERT: K 347 ASP cc_start: 0.7603 (t70) cc_final: 0.7308 (t0) REVERT: K 391 LYS cc_start: 0.8475 (tptm) cc_final: 0.8204 (tptm) REVERT: K 393 ARG cc_start: 0.8633 (ttt-90) cc_final: 0.7865 (tpt170) REVERT: L 64 GLU cc_start: 0.7635 (mp0) cc_final: 0.7340 (mp0) REVERT: M 57 ASP cc_start: 0.7743 (m-30) cc_final: 0.7198 (m-30) REVERT: A 105 GLU cc_start: 0.8371 (tp30) cc_final: 0.7497 (mm-30) REVERT: A 114 CYS cc_start: 0.7391 (m) cc_final: 0.7119 (m) REVERT: A 130 LYS cc_start: 0.8394 (tttt) cc_final: 0.8102 (ttmm) REVERT: A 187 TYR cc_start: 0.8703 (t80) cc_final: 0.8490 (t80) REVERT: A 202 ASP cc_start: 0.7480 (m-30) cc_final: 0.7056 (m-30) REVERT: A 218 ASP cc_start: 0.7578 (t0) cc_final: 0.7354 (t70) REVERT: A 267 ARG cc_start: 0.8181 (pmt170) cc_final: 0.7980 (ptt-90) REVERT: A 289 ARG cc_start: 0.8023 (mtp85) cc_final: 0.7586 (mtp85) REVERT: A 292 GLU cc_start: 0.7759 (mp0) cc_final: 0.7413 (mp0) REVERT: A 335 THR cc_start: 0.8797 (p) cc_final: 0.8393 (t) REVERT: A 340 LYS cc_start: 0.8964 (tttp) cc_final: 0.8712 (tttp) REVERT: A 341 GLU cc_start: 0.7769 (mp0) cc_final: 0.7493 (mp0) REVERT: B 70 ASP cc_start: 0.6868 (p0) cc_final: 0.6625 (p0) REVERT: B 82 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8057 (mtpt) REVERT: B 138 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7324 (tm-30) REVERT: B 139 GLU cc_start: 0.7811 (tp30) cc_final: 0.7204 (tp30) REVERT: B 159 LYS cc_start: 0.8814 (pttt) cc_final: 0.8526 (ptmm) REVERT: B 217 MET cc_start: 0.7399 (mmp) cc_final: 0.6741 (mmt) REVERT: B 237 VAL cc_start: 0.7509 (t) cc_final: 0.7296 (p) REVERT: B 303 ARG cc_start: 0.8017 (mtm-85) cc_final: 0.7798 (mtm-85) REVERT: C 64 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 80 THR cc_start: 0.8568 (m) cc_final: 0.8366 (m) outliers start: 0 outliers final: 0 residues processed: 1083 average time/residue: 1.4866 time to fit residues: 1907.7279 Evaluate side-chains 902 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 902 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 1.9990 chunk 318 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 381 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 HIS D 143 HIS D 186 ASN D 408 ASN F 23 GLN F 91 HIS G 143 HIS G 319 GLN G 364 ASN ** H 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN J 345 HIS K 104 GLN K 225 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN A 125 HIS B 146 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118799 restraints weight = 49969.164| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.18 r_work: 0.3359 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34387 Z= 0.224 Angle : 0.665 13.908 46859 Z= 0.338 Chirality : 0.048 0.272 5246 Planarity : 0.005 0.071 6004 Dihedral : 5.969 76.021 4985 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % Rotamer: Outliers : 2.18 % Allowed : 10.96 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4291 helix: 0.97 (0.23), residues: 450 sheet: 0.08 (0.15), residues: 1236 loop : -0.88 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 163 HIS 0.006 0.001 HIS D 125 PHE 0.019 0.002 PHE B 134 TYR 0.029 0.002 TYR F 97 ARG 0.009 0.001 ARG B 132 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 16) link_NAG-ASN : angle 3.56330 ( 48) hydrogen bonds : bond 0.03586 ( 1070) hydrogen bonds : angle 5.18810 ( 2922) SS BOND : bond 0.00372 ( 80) SS BOND : angle 1.59976 ( 160) covalent geometry : bond 0.00514 (34291) covalent geometry : angle 0.64969 (46651) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 957 time to evaluate : 3.552 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: D 15 TYR cc_start: 0.8317 (t80) cc_final: 0.7877 (t80) REVERT: D 30 GLU cc_start: 0.7594 (pp20) cc_final: 0.7258 (pp20) REVERT: D 31 ILE cc_start: 0.8795 (mm) cc_final: 0.8447 (mp) REVERT: D 99 GLU cc_start: 0.7906 (tp30) cc_final: 0.7668 (tp30) REVERT: D 101 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8180 (t) REVERT: D 202 ASP cc_start: 0.7796 (m-30) cc_final: 0.7469 (m-30) REVERT: D 298 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6544 (tm-30) REVERT: D 320 TYR cc_start: 0.8055 (p90) cc_final: 0.7709 (p90) REVERT: D 404 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8075 (ttpt) REVERT: E 20 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7491 (ttt180) REVERT: E 76 LYS cc_start: 0.8645 (mttt) cc_final: 0.8361 (mtmm) REVERT: E 129 LYS cc_start: 0.8697 (tptt) cc_final: 0.8449 (tptt) REVERT: E 138 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 162 SER cc_start: 0.8440 (t) cc_final: 0.8142 (m) REVERT: E 177 LYS cc_start: 0.8519 (pttp) cc_final: 0.8263 (ttpp) REVERT: E 178 SER cc_start: 0.8854 (t) cc_final: 0.8644 (t) REVERT: E 182 GLU cc_start: 0.7718 (tt0) cc_final: 0.7359 (tt0) REVERT: E 195 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7508 (mmpt) REVERT: E 217 MET cc_start: 0.6775 (mmt) cc_final: 0.6384 (mmt) REVERT: E 248 ASP cc_start: 0.8383 (t0) cc_final: 0.7906 (t0) REVERT: E 250 SER cc_start: 0.8684 (m) cc_final: 0.8302 (m) REVERT: E 324 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 391 LYS cc_start: 0.8662 (tppp) cc_final: 0.8390 (tppp) REVERT: F 6 MET cc_start: 0.4342 (tpt) cc_final: 0.4060 (tpt) REVERT: F 44 LYS cc_start: 0.8297 (tppt) cc_final: 0.7900 (tppt) REVERT: F 78 GLN cc_start: 0.8330 (mp10) cc_final: 0.8065 (mp10) REVERT: F 99 ASN cc_start: 0.7994 (m-40) cc_final: 0.7551 (m-40) REVERT: F 149 LYS cc_start: 0.8539 (mppt) cc_final: 0.8308 (mppt) REVERT: G 63 CYS cc_start: 0.6625 (m) cc_final: 0.6395 (m) REVERT: G 114 CYS cc_start: 0.7583 (m) cc_final: 0.7303 (m) REVERT: G 145 ASP cc_start: 0.7828 (m-30) cc_final: 0.7620 (m-30) REVERT: G 292 GLU cc_start: 0.8188 (mp0) cc_final: 0.7586 (mp0) REVERT: G 298 GLU cc_start: 0.7478 (tm-30) cc_final: 0.6908 (tm-30) REVERT: G 327 HIS cc_start: 0.8097 (OUTLIER) cc_final: 0.7741 (m-70) REVERT: G 341 GLU cc_start: 0.7989 (mp0) cc_final: 0.7725 (mp0) REVERT: G 372 LYS cc_start: 0.8774 (tppp) cc_final: 0.8552 (tptm) REVERT: H 25 CYS cc_start: 0.7061 (p) cc_final: 0.6738 (p) REVERT: H 129 LYS cc_start: 0.8446 (tptt) cc_final: 0.8142 (tmtt) REVERT: H 131 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7645 (mtm180) REVERT: H 189 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7405 (pt) REVERT: H 224 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8153 (ttm-80) REVERT: H 239 ASN cc_start: 0.8088 (p0) cc_final: 0.7811 (p0) REVERT: H 391 LYS cc_start: 0.8378 (tppp) cc_final: 0.8155 (tppp) REVERT: H 393 ARG cc_start: 0.6441 (tpt170) cc_final: 0.5958 (tpt170) REVERT: I 62 ASP cc_start: 0.8039 (m-30) cc_final: 0.7737 (m-30) REVERT: J 2 GLU cc_start: 0.7829 (pp20) cc_final: 0.7590 (pp20) REVERT: J 30 GLU cc_start: 0.7784 (pp20) cc_final: 0.7207 (pp20) REVERT: J 45 GLU cc_start: 0.7915 (tp30) cc_final: 0.7584 (tp30) REVERT: J 116 ILE cc_start: 0.8753 (mp) cc_final: 0.8481 (mm) REVERT: J 125 HIS cc_start: 0.7884 (m90) cc_final: 0.7566 (m170) REVERT: J 149 ASN cc_start: 0.8729 (p0) cc_final: 0.8511 (p0) REVERT: J 195 MET cc_start: 0.7711 (ptt) cc_final: 0.7406 (ptt) REVERT: J 202 ASP cc_start: 0.7658 (m-30) cc_final: 0.7361 (m-30) REVERT: J 218 ASP cc_start: 0.7412 (t0) cc_final: 0.6918 (t0) REVERT: J 241 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7815 (mm-30) REVERT: J 260 LYS cc_start: 0.8309 (tmtt) cc_final: 0.7634 (tptp) REVERT: J 262 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7133 (mm-30) REVERT: J 289 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.7881 (mmm160) REVERT: J 292 GLU cc_start: 0.8074 (mp0) cc_final: 0.7554 (mp0) REVERT: J 306 CYS cc_start: 0.7396 (t) cc_final: 0.7057 (t) REVERT: J 397 GLU cc_start: 0.7693 (mp0) cc_final: 0.7379 (mp0) REVERT: J 402 VAL cc_start: 0.8781 (t) cc_final: 0.8523 (t) REVERT: J 433 MET cc_start: 0.6831 (mmm) cc_final: 0.6438 (mmm) REVERT: K 37 GLU cc_start: 0.7596 (mp0) cc_final: 0.7114 (mp0) REVERT: K 139 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7272 (tm-30) REVERT: K 146 GLN cc_start: 0.8638 (tt0) cc_final: 0.8302 (tt0) REVERT: K 181 LYS cc_start: 0.8418 (ttpp) cc_final: 0.7893 (ttmm) REVERT: K 217 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6872 (mtt) REVERT: K 260 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8246 (ttt90) REVERT: K 347 ASP cc_start: 0.7661 (t70) cc_final: 0.7274 (t70) REVERT: K 393 ARG cc_start: 0.8692 (ttt-90) cc_final: 0.8464 (ttp-170) REVERT: L 34 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7185 (mtp85) REVERT: L 64 GLU cc_start: 0.7785 (mp0) cc_final: 0.7434 (mp0) REVERT: L 83 LYS cc_start: 0.8868 (mtmm) cc_final: 0.8530 (mttm) REVERT: M 57 ASP cc_start: 0.7752 (m-30) cc_final: 0.7172 (m-30) REVERT: A 105 GLU cc_start: 0.8185 (tp30) cc_final: 0.7492 (mm-30) REVERT: A 114 CYS cc_start: 0.7449 (m) cc_final: 0.7228 (m) REVERT: A 130 LYS cc_start: 0.8396 (tttt) cc_final: 0.8111 (ttmm) REVERT: A 146 THR cc_start: 0.8390 (t) cc_final: 0.8176 (p) REVERT: A 202 ASP cc_start: 0.7533 (m-30) cc_final: 0.7208 (m-30) REVERT: A 218 ASP cc_start: 0.7661 (t0) cc_final: 0.7386 (t0) REVERT: A 241 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 267 ARG cc_start: 0.8258 (pmt170) cc_final: 0.7996 (ptt-90) REVERT: A 292 GLU cc_start: 0.8042 (mp0) cc_final: 0.7506 (mp0) REVERT: A 335 THR cc_start: 0.8831 (p) cc_final: 0.8423 (t) REVERT: A 340 LYS cc_start: 0.9023 (tttp) cc_final: 0.8749 (tttp) REVERT: A 341 GLU cc_start: 0.7799 (mp0) cc_final: 0.7509 (mp0) REVERT: B 60 ASP cc_start: 0.7796 (t0) cc_final: 0.7482 (t0) REVERT: B 70 ASP cc_start: 0.6926 (p0) cc_final: 0.6710 (p0) REVERT: B 80 MET cc_start: 0.8447 (ttp) cc_final: 0.8215 (ttp) REVERT: B 81 GLU cc_start: 0.7940 (mp0) cc_final: 0.7676 (mp0) REVERT: B 82 LYS cc_start: 0.8590 (mtpp) cc_final: 0.7976 (mtpt) REVERT: B 102 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8278 (tp) REVERT: B 157 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8288 (tpp-160) REVERT: B 199 TYR cc_start: 0.6357 (p90) cc_final: 0.6146 (p90) REVERT: B 217 MET cc_start: 0.7585 (mmp) cc_final: 0.6854 (mmp) REVERT: B 303 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7747 (mtm-85) REVERT: B 357 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8177 (mt) REVERT: C 11 GLU cc_start: 0.7134 (tt0) cc_final: 0.6924 (tt0) REVERT: C 64 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7747 (mt-10) outliers start: 80 outliers final: 39 residues processed: 988 average time/residue: 1.3777 time to fit residues: 1623.7167 Evaluate side-chains 966 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 919 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 300 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 34 ARG Chi-restraints excluded: chain L residue 113 ASP Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 18 TYR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 35 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 102 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 212 optimal weight: 0.0670 chunk 142 optimal weight: 0.8980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS D 186 ASN D 204 GLN E 286 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 HIS J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN J 246 ASN J 270 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.139377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.119749 restraints weight = 50191.335| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.19 r_work: 0.3375 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34387 Z= 0.133 Angle : 0.602 13.528 46859 Z= 0.305 Chirality : 0.046 0.311 5246 Planarity : 0.005 0.057 6004 Dihedral : 5.576 75.588 4985 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.31 % Favored : 94.57 % Rotamer: Outliers : 2.69 % Allowed : 13.74 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4291 helix: 1.34 (0.24), residues: 440 sheet: 0.10 (0.15), residues: 1256 loop : -0.77 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 163 HIS 0.005 0.001 HIS H 256 PHE 0.013 0.001 PHE H 134 TYR 0.020 0.001 TYR F 97 ARG 0.008 0.001 ARG G 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00587 ( 16) link_NAG-ASN : angle 3.40020 ( 48) hydrogen bonds : bond 0.03269 ( 1070) hydrogen bonds : angle 5.01558 ( 2922) SS BOND : bond 0.00280 ( 80) SS BOND : angle 1.30300 ( 160) covalent geometry : bond 0.00305 (34291) covalent geometry : angle 0.58838 (46651) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 936 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8303 (t80) cc_final: 0.7851 (t80) REVERT: D 30 GLU cc_start: 0.7489 (pp20) cc_final: 0.7185 (pp20) REVERT: D 99 GLU cc_start: 0.7948 (tp30) cc_final: 0.7661 (tp30) REVERT: D 101 THR cc_start: 0.8483 (m) cc_final: 0.8175 (t) REVERT: D 202 ASP cc_start: 0.7738 (m-30) cc_final: 0.7408 (m-30) REVERT: D 281 ASP cc_start: 0.7829 (t0) cc_final: 0.7579 (t0) REVERT: D 298 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6611 (tm-30) REVERT: D 306 CYS cc_start: 0.7567 (t) cc_final: 0.7134 (t) REVERT: D 320 TYR cc_start: 0.7997 (p90) cc_final: 0.7659 (p90) REVERT: D 404 LYS cc_start: 0.8309 (ttpt) cc_final: 0.8039 (ttpt) REVERT: E 20 ARG cc_start: 0.7760 (ttt180) cc_final: 0.7342 (ttt180) REVERT: E 70 ASP cc_start: 0.7329 (p0) cc_final: 0.7124 (p0) REVERT: E 76 LYS cc_start: 0.8655 (mttt) cc_final: 0.8342 (mtmm) REVERT: E 127 GLU cc_start: 0.8096 (tt0) cc_final: 0.7814 (tt0) REVERT: E 129 LYS cc_start: 0.8674 (tptt) cc_final: 0.8385 (tptt) REVERT: E 131 ARG cc_start: 0.8090 (mtp85) cc_final: 0.7874 (mtp85) REVERT: E 138 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7424 (tm-30) REVERT: E 162 SER cc_start: 0.8451 (t) cc_final: 0.8147 (m) REVERT: E 177 LYS cc_start: 0.8489 (pttp) cc_final: 0.8213 (ttpp) REVERT: E 178 SER cc_start: 0.8840 (t) cc_final: 0.8626 (t) REVERT: E 182 GLU cc_start: 0.7671 (tt0) cc_final: 0.7306 (tt0) REVERT: E 195 LYS cc_start: 0.8092 (mmmm) cc_final: 0.7497 (mmpt) REVERT: E 202 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7737 (tptt) REVERT: E 217 MET cc_start: 0.6907 (mmt) cc_final: 0.6560 (mmt) REVERT: E 248 ASP cc_start: 0.8336 (t0) cc_final: 0.7849 (t0) REVERT: E 250 SER cc_start: 0.8667 (m) cc_final: 0.8271 (m) REVERT: E 324 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7973 (mt-10) REVERT: E 391 LYS cc_start: 0.8647 (tppp) cc_final: 0.8369 (tppp) REVERT: F 6 MET cc_start: 0.4439 (tpt) cc_final: 0.4135 (tpt) REVERT: F 44 LYS cc_start: 0.8291 (tppt) cc_final: 0.7859 (tppt) REVERT: F 78 GLN cc_start: 0.8312 (mp10) cc_final: 0.8052 (mp10) REVERT: F 99 ASN cc_start: 0.7961 (m-40) cc_final: 0.7485 (m-40) REVERT: F 148 GLN cc_start: 0.7811 (mt0) cc_final: 0.7521 (mt0) REVERT: F 149 LYS cc_start: 0.8480 (mppt) cc_final: 0.8247 (mppt) REVERT: G 114 CYS cc_start: 0.7621 (m) cc_final: 0.7333 (m) REVERT: G 134 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7890 (ttp80) REVERT: G 145 ASP cc_start: 0.7816 (m-30) cc_final: 0.7604 (m-30) REVERT: G 246 ASN cc_start: 0.7926 (m-40) cc_final: 0.7676 (m-40) REVERT: G 292 GLU cc_start: 0.8151 (mp0) cc_final: 0.7587 (mp0) REVERT: G 298 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6884 (tm-30) REVERT: G 327 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7653 (m-70) REVERT: G 341 GLU cc_start: 0.7995 (mp0) cc_final: 0.7747 (mp0) REVERT: H 25 CYS cc_start: 0.7035 (p) cc_final: 0.6711 (p) REVERT: H 60 ASP cc_start: 0.8077 (t0) cc_final: 0.7830 (t0) REVERT: H 129 LYS cc_start: 0.8447 (tptt) cc_final: 0.8179 (tmtt) REVERT: H 131 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7693 (mtm180) REVERT: H 189 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7455 (pt) REVERT: H 239 ASN cc_start: 0.8037 (p0) cc_final: 0.7753 (p0) REVERT: H 393 ARG cc_start: 0.6419 (tpt170) cc_final: 0.5952 (tpt170) REVERT: I 62 ASP cc_start: 0.7989 (m-30) cc_final: 0.7632 (m-30) REVERT: J 2 GLU cc_start: 0.7808 (pp20) cc_final: 0.7505 (pp20) REVERT: J 30 GLU cc_start: 0.7779 (pp20) cc_final: 0.7194 (pp20) REVERT: J 45 GLU cc_start: 0.7888 (tp30) cc_final: 0.7536 (tp30) REVERT: J 75 ASP cc_start: 0.8345 (t70) cc_final: 0.8139 (t0) REVERT: J 114 CYS cc_start: 0.7349 (m) cc_final: 0.7075 (m) REVERT: J 116 ILE cc_start: 0.8848 (mp) cc_final: 0.8570 (mm) REVERT: J 125 HIS cc_start: 0.7858 (m90) cc_final: 0.7543 (m170) REVERT: J 191 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7786 (mm-30) REVERT: J 202 ASP cc_start: 0.7667 (m-30) cc_final: 0.7339 (m-30) REVERT: J 218 ASP cc_start: 0.7410 (t0) cc_final: 0.6906 (t0) REVERT: J 241 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7862 (mm-30) REVERT: J 260 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7638 (tptp) REVERT: J 289 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7951 (mmm160) REVERT: J 292 GLU cc_start: 0.8077 (mp0) cc_final: 0.7534 (mp0) REVERT: J 295 THR cc_start: 0.8517 (p) cc_final: 0.8255 (p) REVERT: J 306 CYS cc_start: 0.7299 (t) cc_final: 0.6975 (t) REVERT: J 397 GLU cc_start: 0.7665 (mp0) cc_final: 0.7384 (mp0) REVERT: J 402 VAL cc_start: 0.8741 (t) cc_final: 0.8500 (t) REVERT: J 433 MET cc_start: 0.6765 (mmm) cc_final: 0.6429 (mmm) REVERT: K 37 GLU cc_start: 0.7601 (mp0) cc_final: 0.7166 (mp0) REVERT: K 60 ASP cc_start: 0.7927 (t0) cc_final: 0.7666 (t0) REVERT: K 70 ASP cc_start: 0.7711 (p0) cc_final: 0.7444 (p0) REVERT: K 139 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7276 (tm-30) REVERT: K 146 GLN cc_start: 0.8604 (tt0) cc_final: 0.8287 (tt0) REVERT: K 181 LYS cc_start: 0.8414 (ttpp) cc_final: 0.7866 (ttmm) REVERT: K 217 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6814 (mtt) REVERT: K 347 ASP cc_start: 0.7612 (t70) cc_final: 0.7181 (t70) REVERT: K 393 ARG cc_start: 0.8662 (ttt-90) cc_final: 0.8432 (ttp-170) REVERT: L 64 GLU cc_start: 0.7742 (mp0) cc_final: 0.7389 (mp0) REVERT: L 83 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8557 (mttm) REVERT: L 135 GLU cc_start: 0.5081 (tp30) cc_final: 0.4778 (tp30) REVERT: M 57 ASP cc_start: 0.7700 (m-30) cc_final: 0.7131 (m-30) REVERT: A 105 GLU cc_start: 0.8084 (tp30) cc_final: 0.7661 (tp30) REVERT: A 114 CYS cc_start: 0.7513 (m) cc_final: 0.7292 (m) REVERT: A 130 LYS cc_start: 0.8405 (tttt) cc_final: 0.8121 (ttmm) REVERT: A 202 ASP cc_start: 0.7500 (m-30) cc_final: 0.7078 (m-30) REVERT: A 212 ASP cc_start: 0.7871 (m-30) cc_final: 0.7669 (m-30) REVERT: A 218 ASP cc_start: 0.7671 (t0) cc_final: 0.7393 (t0) REVERT: A 289 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7923 (mtp85) REVERT: B 60 ASP cc_start: 0.7734 (t0) cc_final: 0.7360 (t0) REVERT: B 70 ASP cc_start: 0.6809 (p0) cc_final: 0.6582 (p0) REVERT: B 81 GLU cc_start: 0.7931 (mp0) cc_final: 0.7670 (mp0) REVERT: B 82 LYS cc_start: 0.8551 (mtpp) cc_final: 0.7931 (mtpt) REVERT: B 102 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8299 (tp) REVERT: B 157 ARG cc_start: 0.8511 (tpp80) cc_final: 0.8276 (tpp-160) REVERT: B 159 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8527 (ptpt) REVERT: B 199 TYR cc_start: 0.6282 (p90) cc_final: 0.6026 (p90) REVERT: B 217 MET cc_start: 0.7525 (mmp) cc_final: 0.6757 (mmt) REVERT: B 303 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7798 (mtm-85) REVERT: B 324 GLU cc_start: 0.7991 (mp0) cc_final: 0.7783 (mp0) REVERT: B 357 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8160 (mt) REVERT: C 11 GLU cc_start: 0.7138 (tt0) cc_final: 0.6923 (tt0) REVERT: C 19 MET cc_start: 0.8336 (mmm) cc_final: 0.8077 (mmm) REVERT: C 64 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 155 ASP cc_start: 0.7555 (m-30) cc_final: 0.7316 (m-30) outliers start: 99 outliers final: 61 residues processed: 978 average time/residue: 1.4519 time to fit residues: 1696.1595 Evaluate side-chains 968 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 900 time to evaluate : 3.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 237 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 226 CYS Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 151 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 202 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 300 optimal weight: 0.0970 chunk 296 optimal weight: 10.0000 chunk 121 optimal weight: 0.0370 chunk 259 optimal weight: 10.0000 chunk 411 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 chunk 415 optimal weight: 1.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS D 204 GLN E 21 HIS E 146 GLN E 286 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** B 249 HIS ** 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 = 0.3779 r_free = 0.3779 target = 0.138861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119287 restraints weight = 50320.013| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.18 r_work: 0.3371 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34387 Z= 0.146 Angle : 0.599 13.016 46859 Z= 0.303 Chirality : 0.046 0.328 5246 Planarity : 0.005 0.067 6004 Dihedral : 5.401 74.785 4985 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 3.10 % Allowed : 15.32 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4291 helix: 1.48 (0.24), residues: 440 sheet: 0.29 (0.15), residues: 1188 loop : -0.73 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 163 HIS 0.004 0.001 HIS B 96 PHE 0.018 0.001 PHE H 134 TYR 0.019 0.001 TYR A 308 ARG 0.008 0.000 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 16) link_NAG-ASN : angle 3.29476 ( 48) hydrogen bonds : bond 0.03190 ( 1070) hydrogen bonds : angle 4.89915 ( 2922) SS BOND : bond 0.00284 ( 80) SS BOND : angle 1.38126 ( 160) covalent geometry : bond 0.00336 (34291) covalent geometry : angle 0.58528 (46651) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 912 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8285 (t80) cc_final: 0.7772 (t80) REVERT: D 30 GLU cc_start: 0.7499 (pp20) cc_final: 0.7205 (pp20) REVERT: D 99 GLU cc_start: 0.7908 (tp30) cc_final: 0.7618 (tp30) REVERT: D 101 THR cc_start: 0.8441 (m) cc_final: 0.8089 (m) REVERT: D 202 ASP cc_start: 0.7736 (m-30) cc_final: 0.7404 (m-30) REVERT: D 298 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6651 (tm-30) REVERT: D 306 CYS cc_start: 0.7542 (t) cc_final: 0.7120 (t) REVERT: D 308 TYR cc_start: 0.8624 (p90) cc_final: 0.8423 (p90) REVERT: D 320 TYR cc_start: 0.7995 (p90) cc_final: 0.7575 (p90) REVERT: D 393 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8845 (mmtt) REVERT: D 404 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8016 (ttpt) REVERT: E 70 ASP cc_start: 0.7297 (p0) cc_final: 0.7043 (p0) REVERT: E 76 LYS cc_start: 0.8708 (mttt) cc_final: 0.8363 (mtmm) REVERT: E 127 GLU cc_start: 0.8109 (tt0) cc_final: 0.7817 (tt0) REVERT: E 129 LYS cc_start: 0.8701 (tptt) cc_final: 0.8449 (tptt) REVERT: E 138 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7404 (tm-30) REVERT: E 162 SER cc_start: 0.8481 (t) cc_final: 0.8169 (m) REVERT: E 177 LYS cc_start: 0.8506 (pttp) cc_final: 0.8199 (ttpp) REVERT: E 178 SER cc_start: 0.8838 (t) cc_final: 0.8613 (t) REVERT: E 182 GLU cc_start: 0.7674 (tt0) cc_final: 0.7314 (tt0) REVERT: E 195 LYS cc_start: 0.8077 (mmmm) cc_final: 0.7528 (mmpt) REVERT: E 217 MET cc_start: 0.7020 (mmt) cc_final: 0.6712 (mmp) REVERT: E 248 ASP cc_start: 0.8294 (t0) cc_final: 0.7862 (t0) REVERT: E 250 SER cc_start: 0.8686 (m) cc_final: 0.8287 (m) REVERT: E 324 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7993 (mt-10) REVERT: E 391 LYS cc_start: 0.8640 (tppp) cc_final: 0.8363 (tppp) REVERT: F 6 MET cc_start: 0.4513 (tpt) cc_final: 0.4188 (tpt) REVERT: F 44 LYS cc_start: 0.8231 (tppt) cc_final: 0.7801 (tppt) REVERT: F 78 GLN cc_start: 0.8345 (mp10) cc_final: 0.8080 (mp10) REVERT: F 99 ASN cc_start: 0.7955 (m-40) cc_final: 0.7494 (m-40) REVERT: F 148 GLN cc_start: 0.7821 (mt0) cc_final: 0.7508 (mt0) REVERT: F 149 LYS cc_start: 0.8493 (mppt) cc_final: 0.8275 (mppt) REVERT: G 114 CYS cc_start: 0.7620 (m) cc_final: 0.7349 (m) REVERT: G 246 ASN cc_start: 0.7930 (m-40) cc_final: 0.7674 (m-40) REVERT: G 292 GLU cc_start: 0.8234 (mp0) cc_final: 0.7688 (mp0) REVERT: G 298 GLU cc_start: 0.7447 (tm-30) cc_final: 0.6866 (tm-30) REVERT: G 327 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7644 (m-70) REVERT: G 341 GLU cc_start: 0.8003 (mp0) cc_final: 0.7715 (mp0) REVERT: G 404 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7958 (ttpt) REVERT: H 25 CYS cc_start: 0.7088 (p) cc_final: 0.6764 (p) REVERT: H 60 ASP cc_start: 0.8084 (t0) cc_final: 0.7827 (t0) REVERT: H 129 LYS cc_start: 0.8461 (tptt) cc_final: 0.8196 (tmtt) REVERT: H 131 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7741 (mtm180) REVERT: H 189 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7493 (pt) REVERT: H 239 ASN cc_start: 0.8015 (p0) cc_final: 0.7699 (p0) REVERT: H 393 ARG cc_start: 0.6439 (tpt170) cc_final: 0.5997 (tpt170) REVERT: I 62 ASP cc_start: 0.7995 (m-30) cc_final: 0.7659 (m-30) REVERT: J 2 GLU cc_start: 0.7829 (pp20) cc_final: 0.7519 (pp20) REVERT: J 30 GLU cc_start: 0.7768 (pp20) cc_final: 0.7226 (pp20) REVERT: J 61 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7707 (ttpt) REVERT: J 102 GLN cc_start: 0.8856 (tt0) cc_final: 0.8623 (tt0) REVERT: J 114 CYS cc_start: 0.7375 (m) cc_final: 0.7119 (m) REVERT: J 116 ILE cc_start: 0.8881 (mp) cc_final: 0.8610 (mm) REVERT: J 125 HIS cc_start: 0.7847 (m90) cc_final: 0.7548 (m170) REVERT: J 149 ASN cc_start: 0.8698 (p0) cc_final: 0.8390 (p0) REVERT: J 174 ASP cc_start: 0.8229 (m-30) cc_final: 0.8007 (m-30) REVERT: J 191 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7804 (mm-30) REVERT: J 195 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7158 (mtm) REVERT: J 214 VAL cc_start: 0.8810 (m) cc_final: 0.8537 (p) REVERT: J 241 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7843 (mm-30) REVERT: J 260 LYS cc_start: 0.8199 (tmtt) cc_final: 0.7808 (tptp) REVERT: J 262 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7192 (mm-30) REVERT: J 289 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.7893 (mmt90) REVERT: J 292 GLU cc_start: 0.8092 (mp0) cc_final: 0.7545 (mp0) REVERT: J 295 THR cc_start: 0.8519 (p) cc_final: 0.8246 (p) REVERT: J 306 CYS cc_start: 0.7349 (t) cc_final: 0.7014 (t) REVERT: J 397 GLU cc_start: 0.7650 (mp0) cc_final: 0.7369 (mp0) REVERT: J 402 VAL cc_start: 0.8755 (t) cc_final: 0.8493 (t) REVERT: J 433 MET cc_start: 0.6715 (mmm) cc_final: 0.6365 (mmm) REVERT: K 37 GLU cc_start: 0.7652 (mp0) cc_final: 0.7195 (mp0) REVERT: K 60 ASP cc_start: 0.7926 (t0) cc_final: 0.7663 (t0) REVERT: K 70 ASP cc_start: 0.7774 (p0) cc_final: 0.7536 (p0) REVERT: K 139 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7316 (tm-30) REVERT: K 146 GLN cc_start: 0.8628 (tt0) cc_final: 0.8336 (tt0) REVERT: K 181 LYS cc_start: 0.8397 (ttpp) cc_final: 0.7819 (ttmm) REVERT: K 217 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6821 (mtt) REVERT: K 347 ASP cc_start: 0.7608 (t70) cc_final: 0.7242 (t70) REVERT: K 393 ARG cc_start: 0.8647 (ttt-90) cc_final: 0.8399 (ttp-170) REVERT: L 64 GLU cc_start: 0.7786 (mp0) cc_final: 0.7344 (mp0) REVERT: M 57 ASP cc_start: 0.7666 (m-30) cc_final: 0.7073 (m-30) REVERT: A 105 GLU cc_start: 0.8167 (tp30) cc_final: 0.7828 (tp30) REVERT: A 114 CYS cc_start: 0.7534 (m) cc_final: 0.7329 (m) REVERT: A 202 ASP cc_start: 0.7575 (m-30) cc_final: 0.7232 (m-30) REVERT: A 212 ASP cc_start: 0.7887 (m-30) cc_final: 0.7686 (m-30) REVERT: A 218 ASP cc_start: 0.7688 (t0) cc_final: 0.7400 (t70) REVERT: A 289 ARG cc_start: 0.8193 (mtp85) cc_final: 0.7880 (mtp85) REVERT: A 379 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 60 ASP cc_start: 0.7772 (t0) cc_final: 0.7391 (t0) REVERT: B 70 ASP cc_start: 0.6786 (p0) cc_final: 0.6524 (p0) REVERT: B 81 GLU cc_start: 0.7924 (mp0) cc_final: 0.7673 (mp0) REVERT: B 82 LYS cc_start: 0.8510 (mtpp) cc_final: 0.7914 (mtpt) REVERT: B 102 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8333 (tp) REVERT: B 159 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8492 (ptpt) REVERT: B 177 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8174 (ttmm) REVERT: B 199 TYR cc_start: 0.6306 (p90) cc_final: 0.6072 (p90) REVERT: B 217 MET cc_start: 0.7491 (mmp) cc_final: 0.6753 (mmt) REVERT: B 303 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7805 (mtm-85) REVERT: B 324 GLU cc_start: 0.7981 (mp0) cc_final: 0.7767 (mp0) REVERT: B 357 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8222 (mt) REVERT: C 11 GLU cc_start: 0.7174 (tt0) cc_final: 0.6950 (tt0) REVERT: C 19 MET cc_start: 0.8322 (mmm) cc_final: 0.8073 (mmm) REVERT: C 64 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 155 ASP cc_start: 0.7547 (m-30) cc_final: 0.7317 (m-30) outliers start: 114 outliers final: 71 residues processed: 962 average time/residue: 1.4470 time to fit residues: 1658.6219 Evaluate side-chains 989 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 909 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 10 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 chunk 141 optimal weight: 0.0570 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 159 optimal weight: 0.9990 chunk 365 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 381 optimal weight: 4.9990 chunk 296 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS D 186 ASN D 204 GLN E 21 HIS E 286 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 ASN I 148 GLN J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.120370 restraints weight = 50090.126| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.18 r_work: 0.3385 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34387 Z= 0.114 Angle : 0.583 12.718 46859 Z= 0.295 Chirality : 0.045 0.342 5246 Planarity : 0.004 0.057 6004 Dihedral : 5.178 73.814 4985 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 3.05 % Allowed : 16.02 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4291 helix: 1.60 (0.24), residues: 440 sheet: 0.18 (0.15), residues: 1256 loop : -0.67 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 163 HIS 0.007 0.001 HIS B 96 PHE 0.019 0.001 PHE H 134 TYR 0.019 0.001 TYR F 97 ARG 0.012 0.000 ARG K 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 16) link_NAG-ASN : angle 3.18416 ( 48) hydrogen bonds : bond 0.03014 ( 1070) hydrogen bonds : angle 4.80066 ( 2922) SS BOND : bond 0.00269 ( 80) SS BOND : angle 1.26307 ( 160) covalent geometry : bond 0.00262 (34291) covalent geometry : angle 0.57053 (46651) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 926 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7464 (pp20) cc_final: 0.7204 (pp20) REVERT: D 99 GLU cc_start: 0.7988 (tp30) cc_final: 0.7652 (tp30) REVERT: D 101 THR cc_start: 0.8403 (m) cc_final: 0.8055 (m) REVERT: D 102 GLN cc_start: 0.8844 (tt0) cc_final: 0.8621 (tt0) REVERT: D 202 ASP cc_start: 0.7724 (m-30) cc_final: 0.7399 (m-30) REVERT: D 298 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6658 (tm-30) REVERT: D 306 CYS cc_start: 0.7450 (t) cc_final: 0.7040 (t) REVERT: D 320 TYR cc_start: 0.7892 (p90) cc_final: 0.7413 (p90) REVERT: D 404 LYS cc_start: 0.8276 (ttpt) cc_final: 0.8006 (ttpt) REVERT: E 70 ASP cc_start: 0.7099 (p0) cc_final: 0.6735 (p0) REVERT: E 72 ASP cc_start: 0.7609 (p0) cc_final: 0.6977 (p0) REVERT: E 76 LYS cc_start: 0.8689 (mttt) cc_final: 0.8348 (mtmm) REVERT: E 127 GLU cc_start: 0.8080 (tt0) cc_final: 0.7796 (tt0) REVERT: E 129 LYS cc_start: 0.8702 (tptt) cc_final: 0.8457 (tptp) REVERT: E 131 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7890 (mtp85) REVERT: E 138 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7414 (tm-30) REVERT: E 139 GLU cc_start: 0.7764 (tp30) cc_final: 0.7132 (tp30) REVERT: E 162 SER cc_start: 0.8484 (t) cc_final: 0.8174 (m) REVERT: E 177 LYS cc_start: 0.8531 (pttp) cc_final: 0.8245 (ttpp) REVERT: E 178 SER cc_start: 0.8806 (t) cc_final: 0.8597 (t) REVERT: E 182 GLU cc_start: 0.7601 (tt0) cc_final: 0.7232 (tt0) REVERT: E 195 LYS cc_start: 0.8081 (mmmm) cc_final: 0.7531 (mmpt) REVERT: E 217 MET cc_start: 0.6991 (mmt) cc_final: 0.6534 (mmp) REVERT: E 248 ASP cc_start: 0.8286 (t0) cc_final: 0.7873 (t0) REVERT: E 250 SER cc_start: 0.8680 (m) cc_final: 0.8272 (m) REVERT: E 324 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7994 (mt-10) REVERT: E 391 LYS cc_start: 0.8650 (tppp) cc_final: 0.8399 (tppp) REVERT: F 6 MET cc_start: 0.4285 (tpt) cc_final: 0.4015 (tpt) REVERT: F 78 GLN cc_start: 0.8318 (mp10) cc_final: 0.8057 (mp10) REVERT: F 148 GLN cc_start: 0.7842 (mt0) cc_final: 0.7527 (mt0) REVERT: F 149 LYS cc_start: 0.8549 (mppt) cc_final: 0.8321 (mppt) REVERT: G 2 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: G 114 CYS cc_start: 0.7584 (m) cc_final: 0.7323 (m) REVERT: G 134 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7834 (ttp80) REVERT: G 246 ASN cc_start: 0.7920 (m-40) cc_final: 0.7618 (m-40) REVERT: G 292 GLU cc_start: 0.8233 (mp0) cc_final: 0.7729 (mp0) REVERT: G 298 GLU cc_start: 0.7430 (tm-30) cc_final: 0.6864 (tm-30) REVERT: G 327 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7607 (m-70) REVERT: G 341 GLU cc_start: 0.7986 (mp0) cc_final: 0.7698 (mp0) REVERT: G 404 LYS cc_start: 0.8277 (ttpt) cc_final: 0.7994 (ttpt) REVERT: H 25 CYS cc_start: 0.7102 (p) cc_final: 0.6776 (p) REVERT: H 60 ASP cc_start: 0.8028 (t0) cc_final: 0.7760 (t0) REVERT: H 78 ASP cc_start: 0.8199 (t0) cc_final: 0.7965 (t0) REVERT: H 129 LYS cc_start: 0.8424 (tptt) cc_final: 0.8209 (tmtt) REVERT: H 131 ARG cc_start: 0.7989 (mtm180) cc_final: 0.7698 (mtm180) REVERT: H 224 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8056 (ptm-80) REVERT: H 239 ASN cc_start: 0.7967 (p0) cc_final: 0.7633 (p0) REVERT: H 393 ARG cc_start: 0.6418 (tpt170) cc_final: 0.5990 (tpt170) REVERT: I 62 ASP cc_start: 0.7923 (m-30) cc_final: 0.7639 (m-30) REVERT: I 72 MET cc_start: 0.6907 (mmp) cc_final: 0.6693 (mmp) REVERT: I 118 ILE cc_start: 0.8755 (mt) cc_final: 0.8524 (mp) REVERT: J 2 GLU cc_start: 0.7828 (pp20) cc_final: 0.7523 (pp20) REVERT: J 30 GLU cc_start: 0.7749 (pp20) cc_final: 0.7223 (pp20) REVERT: J 61 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7647 (ttpt) REVERT: J 102 GLN cc_start: 0.8849 (tt0) cc_final: 0.8647 (tt0) REVERT: J 114 CYS cc_start: 0.7395 (m) cc_final: 0.7152 (m) REVERT: J 116 ILE cc_start: 0.8905 (mp) cc_final: 0.8642 (mm) REVERT: J 125 HIS cc_start: 0.7837 (m90) cc_final: 0.7543 (m170) REVERT: J 149 ASN cc_start: 0.8642 (p0) cc_final: 0.8380 (p0) REVERT: J 191 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7833 (mm-30) REVERT: J 214 VAL cc_start: 0.8829 (m) cc_final: 0.8490 (p) REVERT: J 241 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7870 (mm-30) REVERT: J 289 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.7920 (mmt90) REVERT: J 292 GLU cc_start: 0.8097 (mp0) cc_final: 0.7581 (mp0) REVERT: J 295 THR cc_start: 0.8533 (p) cc_final: 0.8265 (p) REVERT: J 306 CYS cc_start: 0.7317 (t) cc_final: 0.6967 (t) REVERT: J 397 GLU cc_start: 0.7629 (mp0) cc_final: 0.7343 (mp0) REVERT: J 402 VAL cc_start: 0.8714 (t) cc_final: 0.8458 (t) REVERT: J 433 MET cc_start: 0.6770 (mmm) cc_final: 0.6419 (mmm) REVERT: K 37 GLU cc_start: 0.7646 (mp0) cc_final: 0.7184 (mp0) REVERT: K 60 ASP cc_start: 0.7905 (t0) cc_final: 0.7638 (t0) REVERT: K 70 ASP cc_start: 0.7721 (p0) cc_final: 0.7469 (p0) REVERT: K 139 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7303 (tm-30) REVERT: K 146 GLN cc_start: 0.8621 (tt0) cc_final: 0.8327 (tt0) REVERT: K 181 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7859 (ttmm) REVERT: K 347 ASP cc_start: 0.7578 (t70) cc_final: 0.7213 (t70) REVERT: K 393 ARG cc_start: 0.8596 (ttt-90) cc_final: 0.7596 (tpm170) REVERT: L 83 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8620 (mttm) REVERT: M 57 ASP cc_start: 0.7666 (m-30) cc_final: 0.7070 (m-30) REVERT: A 202 ASP cc_start: 0.7547 (m-30) cc_final: 0.7170 (m-30) REVERT: A 212 ASP cc_start: 0.7893 (m-30) cc_final: 0.7691 (m-30) REVERT: A 218 ASP cc_start: 0.7693 (t0) cc_final: 0.7392 (t70) REVERT: A 240 TYR cc_start: 0.8370 (t80) cc_final: 0.7971 (t80) REVERT: A 289 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7889 (mtp85) REVERT: B 60 ASP cc_start: 0.7760 (t0) cc_final: 0.7366 (t0) REVERT: B 70 ASP cc_start: 0.6712 (p0) cc_final: 0.6454 (p0) REVERT: B 82 LYS cc_start: 0.8337 (mtpp) cc_final: 0.7776 (mtpt) REVERT: B 96 HIS cc_start: 0.7811 (p90) cc_final: 0.7358 (p90) REVERT: B 157 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8286 (tpp-160) REVERT: B 159 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8400 (ptpt) REVERT: B 177 LYS cc_start: 0.8398 (ttpt) cc_final: 0.8121 (ttmm) REVERT: B 199 TYR cc_start: 0.6253 (p90) cc_final: 0.6043 (p90) REVERT: B 217 MET cc_start: 0.7486 (mmp) cc_final: 0.6760 (mmt) REVERT: B 303 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7773 (mtm-85) REVERT: B 324 GLU cc_start: 0.7988 (mp0) cc_final: 0.7765 (mp0) REVERT: B 357 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8153 (mt) REVERT: C 11 GLU cc_start: 0.7218 (tt0) cc_final: 0.7003 (tt0) REVERT: C 19 MET cc_start: 0.8301 (mmm) cc_final: 0.8077 (mmm) REVERT: C 37 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8775 (ptmm) REVERT: C 64 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7605 (mt-10) REVERT: C 155 ASP cc_start: 0.7540 (m-30) cc_final: 0.7300 (m-30) outliers start: 112 outliers final: 71 residues processed: 972 average time/residue: 1.4029 time to fit residues: 1630.9411 Evaluate side-chains 995 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 917 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 137 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 411 optimal weight: 0.9980 chunk 363 optimal weight: 3.9990 chunk 412 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS E 21 HIS E 146 GLN E 286 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN J 228 ASN J 246 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS A 355 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.118981 restraints weight = 49988.339| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.17 r_work: 0.3366 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34387 Z= 0.156 Angle : 0.604 12.082 46859 Z= 0.305 Chirality : 0.047 0.343 5246 Planarity : 0.005 0.094 6004 Dihedral : 5.183 72.271 4985 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 3.43 % Allowed : 16.70 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4291 helix: 1.64 (0.24), residues: 440 sheet: 0.18 (0.15), residues: 1256 loop : -0.65 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 163 HIS 0.006 0.001 HIS B 96 PHE 0.022 0.001 PHE H 134 TYR 0.021 0.001 TYR F 97 ARG 0.010 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00574 ( 16) link_NAG-ASN : angle 3.10010 ( 48) hydrogen bonds : bond 0.03102 ( 1070) hydrogen bonds : angle 4.76154 ( 2922) SS BOND : bond 0.00295 ( 80) SS BOND : angle 1.44887 ( 160) covalent geometry : bond 0.00359 (34291) covalent geometry : angle 0.59060 (46651) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1078 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 952 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7469 (pp20) cc_final: 0.7161 (pp20) REVERT: D 99 GLU cc_start: 0.7961 (tp30) cc_final: 0.7642 (tp30) REVERT: D 101 THR cc_start: 0.8408 (m) cc_final: 0.8066 (m) REVERT: D 102 GLN cc_start: 0.8871 (tt0) cc_final: 0.8608 (tt0) REVERT: D 202 ASP cc_start: 0.7724 (m-30) cc_final: 0.7405 (m-30) REVERT: D 260 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8328 (mtpm) REVERT: D 298 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6663 (tm-30) REVERT: D 306 CYS cc_start: 0.7497 (t) cc_final: 0.7127 (t) REVERT: D 308 TYR cc_start: 0.8603 (p90) cc_final: 0.8383 (p90) REVERT: D 320 TYR cc_start: 0.8002 (p90) cc_final: 0.7394 (p90) REVERT: E 20 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7340 (ttt180) REVERT: E 63 LYS cc_start: 0.8473 (mtpp) cc_final: 0.8171 (ttmm) REVERT: E 70 ASP cc_start: 0.6888 (p0) cc_final: 0.6483 (p0) REVERT: E 72 ASP cc_start: 0.7536 (p0) cc_final: 0.6849 (p0) REVERT: E 76 LYS cc_start: 0.8703 (mttt) cc_final: 0.8332 (mtmm) REVERT: E 127 GLU cc_start: 0.8049 (tt0) cc_final: 0.7776 (tt0) REVERT: E 129 LYS cc_start: 0.8695 (tptt) cc_final: 0.8490 (tptt) REVERT: E 131 ARG cc_start: 0.8084 (mtp85) cc_final: 0.7883 (mtp85) REVERT: E 138 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 139 GLU cc_start: 0.7797 (tp30) cc_final: 0.6999 (tp30) REVERT: E 162 SER cc_start: 0.8508 (t) cc_final: 0.8200 (m) REVERT: E 177 LYS cc_start: 0.8528 (pttp) cc_final: 0.8236 (ttpp) REVERT: E 178 SER cc_start: 0.8823 (t) cc_final: 0.8611 (t) REVERT: E 182 GLU cc_start: 0.7604 (tt0) cc_final: 0.7257 (tt0) REVERT: E 217 MET cc_start: 0.7209 (mmt) cc_final: 0.6678 (mmp) REVERT: E 248 ASP cc_start: 0.8268 (t0) cc_final: 0.7860 (t0) REVERT: E 250 SER cc_start: 0.8701 (m) cc_final: 0.8284 (m) REVERT: E 324 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8002 (mt-10) REVERT: E 391 LYS cc_start: 0.8652 (tppp) cc_final: 0.8397 (tppp) REVERT: F 6 MET cc_start: 0.4417 (tpt) cc_final: 0.4116 (tpt) REVERT: F 78 GLN cc_start: 0.8330 (mp10) cc_final: 0.8081 (mp10) REVERT: F 149 LYS cc_start: 0.8575 (mppt) cc_final: 0.8331 (mppt) REVERT: G 75 ASP cc_start: 0.8286 (t0) cc_final: 0.7970 (t0) REVERT: G 99 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6699 (tm-30) REVERT: G 114 CYS cc_start: 0.7600 (m) cc_final: 0.7362 (m) REVERT: G 246 ASN cc_start: 0.7933 (m-40) cc_final: 0.7640 (m-40) REVERT: G 292 GLU cc_start: 0.8242 (mp0) cc_final: 0.7757 (mp0) REVERT: G 298 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6914 (tm-30) REVERT: G 327 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7599 (m-70) REVERT: G 341 GLU cc_start: 0.8002 (mp0) cc_final: 0.7693 (mp0) REVERT: G 404 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7976 (ttpt) REVERT: H 25 CYS cc_start: 0.7040 (p) cc_final: 0.6699 (p) REVERT: H 60 ASP cc_start: 0.7982 (t0) cc_final: 0.7684 (t0) REVERT: H 78 ASP cc_start: 0.8219 (t0) cc_final: 0.7981 (t0) REVERT: H 129 LYS cc_start: 0.8426 (tptt) cc_final: 0.8205 (tmtt) REVERT: H 131 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7696 (mtm180) REVERT: H 224 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8262 (ptm-80) REVERT: H 239 ASN cc_start: 0.7969 (p0) cc_final: 0.7668 (p0) REVERT: H 393 ARG cc_start: 0.6459 (tpt170) cc_final: 0.5011 (ttm170) REVERT: I 72 MET cc_start: 0.7042 (mmp) cc_final: 0.6739 (mmp) REVERT: I 118 ILE cc_start: 0.8785 (mt) cc_final: 0.8555 (mp) REVERT: J 2 GLU cc_start: 0.7823 (pp20) cc_final: 0.7524 (pp20) REVERT: J 30 GLU cc_start: 0.7759 (pp20) cc_final: 0.7256 (pp20) REVERT: J 61 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7712 (ttpt) REVERT: J 102 GLN cc_start: 0.8843 (tt0) cc_final: 0.8583 (tt0) REVERT: J 114 CYS cc_start: 0.7395 (m) cc_final: 0.7165 (m) REVERT: J 116 ILE cc_start: 0.8948 (mp) cc_final: 0.8687 (mm) REVERT: J 125 HIS cc_start: 0.7850 (m90) cc_final: 0.7538 (m170) REVERT: J 149 ASN cc_start: 0.8692 (p0) cc_final: 0.8417 (p0) REVERT: J 191 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7826 (mm-30) REVERT: J 195 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7280 (mtm) REVERT: J 212 ASP cc_start: 0.7851 (t0) cc_final: 0.7527 (t0) REVERT: J 241 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7942 (mm-30) REVERT: J 289 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8055 (mmt90) REVERT: J 292 GLU cc_start: 0.8123 (mp0) cc_final: 0.7737 (mp0) REVERT: J 295 THR cc_start: 0.8517 (p) cc_final: 0.8247 (p) REVERT: J 306 CYS cc_start: 0.7374 (t) cc_final: 0.7025 (t) REVERT: J 397 GLU cc_start: 0.7625 (mp0) cc_final: 0.7329 (mp0) REVERT: J 402 VAL cc_start: 0.8724 (t) cc_final: 0.8477 (t) REVERT: J 433 MET cc_start: 0.6756 (mmm) cc_final: 0.6424 (mmm) REVERT: K 37 GLU cc_start: 0.7693 (mp0) cc_final: 0.7207 (mp0) REVERT: K 60 ASP cc_start: 0.7915 (t0) cc_final: 0.7640 (t0) REVERT: K 139 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7367 (tm-30) REVERT: K 146 GLN cc_start: 0.8656 (tt0) cc_final: 0.8373 (tt0) REVERT: K 181 LYS cc_start: 0.8366 (ttpp) cc_final: 0.7813 (ttmm) REVERT: K 342 GLU cc_start: 0.7769 (tt0) cc_final: 0.7481 (tm-30) REVERT: K 347 ASP cc_start: 0.7599 (t70) cc_final: 0.7225 (t70) REVERT: K 393 ARG cc_start: 0.8617 (ttt-90) cc_final: 0.7581 (tpm170) REVERT: M 57 ASP cc_start: 0.7697 (m-30) cc_final: 0.7110 (m-30) REVERT: A 105 GLU cc_start: 0.8140 (tp30) cc_final: 0.7783 (tp30) REVERT: A 202 ASP cc_start: 0.7575 (m-30) cc_final: 0.7191 (m-30) REVERT: A 212 ASP cc_start: 0.7889 (m-30) cc_final: 0.7686 (m-30) REVERT: A 218 ASP cc_start: 0.7701 (t0) cc_final: 0.7399 (t70) REVERT: A 240 TYR cc_start: 0.8428 (t80) cc_final: 0.8120 (t80) REVERT: A 292 GLU cc_start: 0.8150 (mp0) cc_final: 0.7611 (mp0) REVERT: A 327 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7740 (t70) REVERT: B 60 ASP cc_start: 0.7746 (t0) cc_final: 0.7335 (t0) REVERT: B 70 ASP cc_start: 0.6721 (p0) cc_final: 0.6475 (p0) REVERT: B 81 GLU cc_start: 0.7889 (mp0) cc_final: 0.7655 (mp0) REVERT: B 157 ARG cc_start: 0.8503 (tpp80) cc_final: 0.8243 (tpp-160) REVERT: B 177 LYS cc_start: 0.8419 (ttpt) cc_final: 0.8143 (ttmm) REVERT: B 199 TYR cc_start: 0.6340 (p90) cc_final: 0.6055 (p90) REVERT: B 217 MET cc_start: 0.7556 (mmp) cc_final: 0.6808 (mmt) REVERT: B 303 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7804 (mtm-85) REVERT: B 357 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 11 GLU cc_start: 0.7217 (tt0) cc_final: 0.6983 (tt0) REVERT: C 19 MET cc_start: 0.8336 (mmm) cc_final: 0.8070 (mmm) REVERT: C 37 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8773 (ptmm) REVERT: C 64 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 71 ASN cc_start: 0.8392 (p0) cc_final: 0.8155 (p0) REVERT: C 155 ASP cc_start: 0.7567 (m-30) cc_final: 0.7332 (m-30) REVERT: P 79 CYS cc_start: 0.0682 (OUTLIER) cc_final: -0.1887 (t) outliers start: 126 outliers final: 94 residues processed: 1002 average time/residue: 1.3895 time to fit residues: 1668.6532 Evaluate side-chains 1040 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 938 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 70 GLN Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 244 ILE Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 77 optimal weight: 0.9980 chunk 143 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 350 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 277 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS D 186 ASN E 21 HIS E 286 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS J 186 ASN J 204 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS A 362 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118539 restraints weight = 50281.789| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.16 r_work: 0.3353 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 34387 Z= 0.176 Angle : 0.630 12.652 46859 Z= 0.318 Chirality : 0.047 0.345 5246 Planarity : 0.005 0.087 6004 Dihedral : 5.244 70.394 4985 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 3.45 % Allowed : 17.76 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4291 helix: 1.60 (0.24), residues: 440 sheet: 0.17 (0.15), residues: 1256 loop : -0.65 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 163 HIS 0.004 0.001 HIS C 92 PHE 0.023 0.001 PHE H 134 TYR 0.020 0.001 TYR D 233 ARG 0.009 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 16) link_NAG-ASN : angle 3.02231 ( 48) hydrogen bonds : bond 0.03167 ( 1070) hydrogen bonds : angle 4.79561 ( 2922) SS BOND : bond 0.00341 ( 80) SS BOND : angle 1.73093 ( 160) covalent geometry : bond 0.00406 (34291) covalent geometry : angle 0.61551 (46651) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 931 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7471 (pp20) cc_final: 0.7174 (pp20) REVERT: D 49 CYS cc_start: 0.7845 (p) cc_final: 0.7352 (p) REVERT: D 99 GLU cc_start: 0.8001 (tp30) cc_final: 0.7652 (tp30) REVERT: D 101 THR cc_start: 0.8394 (m) cc_final: 0.8070 (m) REVERT: D 102 GLN cc_start: 0.8894 (tt0) cc_final: 0.8611 (tt0) REVERT: D 202 ASP cc_start: 0.7734 (m-30) cc_final: 0.7398 (m-30) REVERT: D 298 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6702 (tm-30) REVERT: D 306 CYS cc_start: 0.7477 (t) cc_final: 0.7104 (t) REVERT: D 320 TYR cc_start: 0.8000 (p90) cc_final: 0.7423 (p90) REVERT: E 20 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7382 (ttt180) REVERT: E 63 LYS cc_start: 0.8487 (mtpp) cc_final: 0.8175 (ttmm) REVERT: E 70 ASP cc_start: 0.6759 (p0) cc_final: 0.6346 (p0) REVERT: E 72 ASP cc_start: 0.7510 (p0) cc_final: 0.6787 (p0) REVERT: E 76 LYS cc_start: 0.8705 (mttt) cc_final: 0.8323 (mtmm) REVERT: E 81 GLU cc_start: 0.7843 (pm20) cc_final: 0.7527 (pm20) REVERT: E 127 GLU cc_start: 0.8061 (tt0) cc_final: 0.7781 (tt0) REVERT: E 129 LYS cc_start: 0.8689 (tptt) cc_final: 0.8480 (tptt) REVERT: E 138 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7387 (tm-30) REVERT: E 139 GLU cc_start: 0.7811 (tp30) cc_final: 0.7028 (tp30) REVERT: E 162 SER cc_start: 0.8512 (t) cc_final: 0.8199 (m) REVERT: E 177 LYS cc_start: 0.8510 (pttp) cc_final: 0.8229 (ttpp) REVERT: E 178 SER cc_start: 0.8838 (t) cc_final: 0.8634 (t) REVERT: E 182 GLU cc_start: 0.7601 (tt0) cc_final: 0.7253 (tt0) REVERT: E 195 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7914 (mtpp) REVERT: E 217 MET cc_start: 0.7309 (mmt) cc_final: 0.6828 (mmp) REVERT: E 248 ASP cc_start: 0.8264 (t0) cc_final: 0.7853 (t0) REVERT: E 250 SER cc_start: 0.8710 (m) cc_final: 0.8278 (m) REVERT: E 324 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7997 (mt-10) REVERT: E 391 LYS cc_start: 0.8658 (tppp) cc_final: 0.8383 (tppp) REVERT: F 6 MET cc_start: 0.4310 (tpt) cc_final: 0.4043 (tpt) REVERT: F 30 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7178 (t) REVERT: F 78 GLN cc_start: 0.8317 (mp10) cc_final: 0.8072 (mp10) REVERT: F 149 LYS cc_start: 0.8584 (mppt) cc_final: 0.8349 (mppt) REVERT: G 75 ASP cc_start: 0.8269 (t0) cc_final: 0.7997 (t0) REVERT: G 99 GLU cc_start: 0.7485 (tm-30) cc_final: 0.6657 (tm-30) REVERT: G 114 CYS cc_start: 0.7531 (m) cc_final: 0.7295 (m) REVERT: G 246 ASN cc_start: 0.7954 (m-40) cc_final: 0.7659 (m-40) REVERT: G 292 GLU cc_start: 0.8239 (mp0) cc_final: 0.7748 (mp0) REVERT: G 298 GLU cc_start: 0.7463 (tm-30) cc_final: 0.6887 (tm-30) REVERT: G 327 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7586 (m-70) REVERT: G 341 GLU cc_start: 0.8001 (mp0) cc_final: 0.7685 (mp0) REVERT: G 404 LYS cc_start: 0.8289 (ttpt) cc_final: 0.8026 (ttpt) REVERT: H 25 CYS cc_start: 0.7052 (p) cc_final: 0.6711 (p) REVERT: H 60 ASP cc_start: 0.7976 (t0) cc_final: 0.7660 (t0) REVERT: H 78 ASP cc_start: 0.8225 (t0) cc_final: 0.7981 (t0) REVERT: H 129 LYS cc_start: 0.8425 (tptt) cc_final: 0.8208 (tmtt) REVERT: H 131 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7684 (mtm180) REVERT: H 224 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8165 (ptm-80) REVERT: H 239 ASN cc_start: 0.7970 (p0) cc_final: 0.7661 (p0) REVERT: H 393 ARG cc_start: 0.6504 (tpt170) cc_final: 0.5067 (ttm170) REVERT: H 408 VAL cc_start: 0.7274 (t) cc_final: 0.6958 (m) REVERT: I 72 MET cc_start: 0.7086 (mmp) cc_final: 0.6745 (mmp) REVERT: I 118 ILE cc_start: 0.8805 (mt) cc_final: 0.8573 (mp) REVERT: J 2 GLU cc_start: 0.7850 (pp20) cc_final: 0.7548 (pp20) REVERT: J 30 GLU cc_start: 0.7792 (pp20) cc_final: 0.7278 (pp20) REVERT: J 102 GLN cc_start: 0.8860 (tt0) cc_final: 0.8602 (tt0) REVERT: J 114 CYS cc_start: 0.7390 (m) cc_final: 0.7167 (m) REVERT: J 116 ILE cc_start: 0.8944 (mp) cc_final: 0.8688 (mm) REVERT: J 125 HIS cc_start: 0.7861 (m90) cc_final: 0.7537 (m170) REVERT: J 191 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7835 (mm-30) REVERT: J 195 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7529 (mtm) REVERT: J 212 ASP cc_start: 0.7831 (t0) cc_final: 0.7498 (t0) REVERT: J 214 VAL cc_start: 0.8813 (m) cc_final: 0.8520 (p) REVERT: J 241 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7982 (mm-30) REVERT: J 289 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8172 (mmm160) REVERT: J 292 GLU cc_start: 0.8140 (mp0) cc_final: 0.7767 (mp0) REVERT: J 295 THR cc_start: 0.8490 (p) cc_final: 0.8240 (p) REVERT: J 306 CYS cc_start: 0.7347 (t) cc_final: 0.7007 (t) REVERT: J 397 GLU cc_start: 0.7597 (mp0) cc_final: 0.7239 (mp0) REVERT: J 402 VAL cc_start: 0.8721 (t) cc_final: 0.8482 (t) REVERT: J 410 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8355 (mp) REVERT: J 433 MET cc_start: 0.6774 (mmm) cc_final: 0.6443 (mmm) REVERT: K 37 GLU cc_start: 0.7685 (mp0) cc_final: 0.7216 (mp0) REVERT: K 60 ASP cc_start: 0.7909 (t0) cc_final: 0.7617 (t0) REVERT: K 139 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7408 (tm-30) REVERT: K 146 GLN cc_start: 0.8675 (tt0) cc_final: 0.8392 (tt0) REVERT: K 181 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7799 (ttmm) REVERT: K 342 GLU cc_start: 0.7755 (tt0) cc_final: 0.7541 (tm-30) REVERT: K 347 ASP cc_start: 0.7625 (t70) cc_final: 0.7244 (t70) REVERT: K 393 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.7575 (tpm170) REVERT: L 83 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8515 (mttm) REVERT: M 57 ASP cc_start: 0.7714 (m-30) cc_final: 0.7116 (m-30) REVERT: A 105 GLU cc_start: 0.8144 (tp30) cc_final: 0.7834 (tp30) REVERT: A 202 ASP cc_start: 0.7562 (m-30) cc_final: 0.7208 (m-30) REVERT: A 212 ASP cc_start: 0.7894 (m-30) cc_final: 0.7689 (m-30) REVERT: A 218 ASP cc_start: 0.7683 (t0) cc_final: 0.7386 (t70) REVERT: A 240 TYR cc_start: 0.8427 (t80) cc_final: 0.8068 (t80) REVERT: A 241 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7680 (mm-30) REVERT: A 292 GLU cc_start: 0.8184 (mp0) cc_final: 0.7643 (mp0) REVERT: B 60 ASP cc_start: 0.7715 (t0) cc_final: 0.7316 (t0) REVERT: B 70 ASP cc_start: 0.6737 (p0) cc_final: 0.6484 (p0) REVERT: B 81 GLU cc_start: 0.7896 (mp0) cc_final: 0.7688 (mp0) REVERT: B 82 LYS cc_start: 0.8422 (mtmt) cc_final: 0.7928 (mtpt) REVERT: B 112 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8273 (p) REVERT: B 157 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8274 (tpp-160) REVERT: B 177 LYS cc_start: 0.8428 (ttpt) cc_final: 0.8109 (ttmm) REVERT: B 199 TYR cc_start: 0.6333 (p90) cc_final: 0.6048 (p90) REVERT: B 217 MET cc_start: 0.7590 (mmp) cc_final: 0.6866 (mmt) REVERT: B 303 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7798 (mtm-85) REVERT: B 357 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8211 (mt) REVERT: C 19 MET cc_start: 0.8353 (mmm) cc_final: 0.8089 (mmm) REVERT: C 37 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8830 (ptmm) REVERT: C 64 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 155 ASP cc_start: 0.7540 (m-30) cc_final: 0.7304 (m-30) REVERT: P 79 CYS cc_start: 0.0823 (OUTLIER) cc_final: -0.1746 (t) outliers start: 127 outliers final: 95 residues processed: 983 average time/residue: 1.3752 time to fit residues: 1620.8675 Evaluate side-chains 1024 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 920 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 328 CYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 105 GLU Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 195 MET Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 410 LEU Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 382 optimal weight: 2.9990 chunk 304 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN D 143 HIS E 21 HIS E 286 HIS F 92 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS J 204 GLN J 228 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.137519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.118124 restraints weight = 50037.788| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.17 r_work: 0.3348 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34387 Z= 0.177 Angle : 0.634 13.359 46859 Z= 0.322 Chirality : 0.047 0.339 5246 Planarity : 0.005 0.081 6004 Dihedral : 5.266 67.271 4985 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.99 % Favored : 93.94 % Rotamer: Outliers : 3.56 % Allowed : 17.98 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 4291 helix: 1.64 (0.24), residues: 440 sheet: 0.11 (0.15), residues: 1280 loop : -0.65 (0.12), residues: 2571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 163 HIS 0.006 0.001 HIS B 96 PHE 0.025 0.001 PHE H 134 TYR 0.020 0.001 TYR I 79 ARG 0.011 0.001 ARG C 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 16) link_NAG-ASN : angle 2.90263 ( 48) hydrogen bonds : bond 0.03160 ( 1070) hydrogen bonds : angle 4.80351 ( 2922) SS BOND : bond 0.00344 ( 80) SS BOND : angle 1.64452 ( 160) covalent geometry : bond 0.00409 (34291) covalent geometry : angle 0.62124 (46651) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 930 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8397 (t80) cc_final: 0.7898 (t80) REVERT: D 30 GLU cc_start: 0.7507 (pp20) cc_final: 0.7186 (pp20) REVERT: D 99 GLU cc_start: 0.7956 (tp30) cc_final: 0.7623 (tp30) REVERT: D 101 THR cc_start: 0.8410 (m) cc_final: 0.8093 (m) REVERT: D 102 GLN cc_start: 0.8917 (tt0) cc_final: 0.8639 (tt0) REVERT: D 202 ASP cc_start: 0.7743 (m-30) cc_final: 0.7409 (m-30) REVERT: D 298 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6741 (tm-30) REVERT: D 306 CYS cc_start: 0.7434 (t) cc_final: 0.7051 (t) REVERT: D 320 TYR cc_start: 0.8012 (p90) cc_final: 0.7233 (p90) REVERT: E 70 ASP cc_start: 0.6730 (p0) cc_final: 0.6252 (p0) REVERT: E 72 ASP cc_start: 0.7485 (p0) cc_final: 0.6731 (p0) REVERT: E 76 LYS cc_start: 0.8723 (mttt) cc_final: 0.8326 (mtmm) REVERT: E 81 GLU cc_start: 0.7852 (pm20) cc_final: 0.7488 (pm20) REVERT: E 127 GLU cc_start: 0.8057 (tt0) cc_final: 0.7780 (tt0) REVERT: E 129 LYS cc_start: 0.8686 (tptt) cc_final: 0.8391 (tptt) REVERT: E 138 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7381 (tm-30) REVERT: E 139 GLU cc_start: 0.7826 (tp30) cc_final: 0.6994 (tp30) REVERT: E 162 SER cc_start: 0.8488 (t) cc_final: 0.8184 (m) REVERT: E 177 LYS cc_start: 0.8520 (pttp) cc_final: 0.8238 (ttpp) REVERT: E 182 GLU cc_start: 0.7646 (tt0) cc_final: 0.7303 (tt0) REVERT: E 195 LYS cc_start: 0.8189 (mmmm) cc_final: 0.7930 (mtpp) REVERT: E 217 MET cc_start: 0.7400 (mmt) cc_final: 0.6880 (mmp) REVERT: E 248 ASP cc_start: 0.8244 (t0) cc_final: 0.7880 (t0) REVERT: E 250 SER cc_start: 0.8720 (m) cc_final: 0.8292 (m) REVERT: E 324 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8011 (mt-10) REVERT: E 391 LYS cc_start: 0.8680 (tppp) cc_final: 0.8399 (tppp) REVERT: F 6 MET cc_start: 0.4478 (tpt) cc_final: 0.4168 (tpt) REVERT: F 30 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7193 (t) REVERT: F 78 GLN cc_start: 0.8369 (mp10) cc_final: 0.8126 (mp10) REVERT: F 149 LYS cc_start: 0.8560 (mppt) cc_final: 0.8324 (mppt) REVERT: G 75 ASP cc_start: 0.8249 (t0) cc_final: 0.7969 (t0) REVERT: G 99 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6692 (tm-30) REVERT: G 114 CYS cc_start: 0.7528 (m) cc_final: 0.7286 (m) REVERT: G 204 GLN cc_start: 0.8615 (mt0) cc_final: 0.8413 (mt0) REVERT: G 246 ASN cc_start: 0.7948 (m-40) cc_final: 0.7643 (m-40) REVERT: G 292 GLU cc_start: 0.8251 (mp0) cc_final: 0.7729 (mp0) REVERT: G 298 GLU cc_start: 0.7517 (tm-30) cc_final: 0.6926 (tm-30) REVERT: G 327 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7596 (m-70) REVERT: G 341 GLU cc_start: 0.7989 (mp0) cc_final: 0.7658 (mp0) REVERT: G 404 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8060 (ttpt) REVERT: H 20 ARG cc_start: 0.7994 (tpt90) cc_final: 0.7555 (tpt90) REVERT: H 25 CYS cc_start: 0.7076 (p) cc_final: 0.6742 (p) REVERT: H 60 ASP cc_start: 0.7997 (t0) cc_final: 0.7643 (t0) REVERT: H 78 ASP cc_start: 0.8222 (t0) cc_final: 0.7979 (t0) REVERT: H 129 LYS cc_start: 0.8415 (tptt) cc_final: 0.8191 (tmtt) REVERT: H 131 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7687 (mtm180) REVERT: H 239 ASN cc_start: 0.7952 (p0) cc_final: 0.7692 (p0) REVERT: H 393 ARG cc_start: 0.6509 (tpt170) cc_final: 0.5118 (ttm170) REVERT: H 408 VAL cc_start: 0.7313 (t) cc_final: 0.7034 (m) REVERT: I 118 ILE cc_start: 0.8826 (mt) cc_final: 0.8593 (mp) REVERT: J 2 GLU cc_start: 0.7837 (pp20) cc_final: 0.7517 (pp20) REVERT: J 30 GLU cc_start: 0.7771 (pp20) cc_final: 0.7261 (pp20) REVERT: J 102 GLN cc_start: 0.8855 (tt0) cc_final: 0.8607 (tt0) REVERT: J 114 CYS cc_start: 0.7411 (m) cc_final: 0.7202 (m) REVERT: J 116 ILE cc_start: 0.8947 (mp) cc_final: 0.8700 (mm) REVERT: J 125 HIS cc_start: 0.7849 (m90) cc_final: 0.7537 (m170) REVERT: J 191 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7835 (mm-30) REVERT: J 212 ASP cc_start: 0.7881 (t0) cc_final: 0.7544 (t0) REVERT: J 214 VAL cc_start: 0.8787 (m) cc_final: 0.8508 (p) REVERT: J 241 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7994 (mm-30) REVERT: J 289 ARG cc_start: 0.8470 (mmm-85) cc_final: 0.8194 (mmm160) REVERT: J 292 GLU cc_start: 0.8174 (mp0) cc_final: 0.7771 (mp0) REVERT: J 295 THR cc_start: 0.8479 (p) cc_final: 0.8226 (p) REVERT: J 306 CYS cc_start: 0.7316 (t) cc_final: 0.6963 (t) REVERT: J 311 ASP cc_start: 0.7466 (t0) cc_final: 0.7262 (t0) REVERT: J 397 GLU cc_start: 0.7585 (mp0) cc_final: 0.7232 (mp0) REVERT: J 402 VAL cc_start: 0.8727 (t) cc_final: 0.8488 (t) REVERT: J 433 MET cc_start: 0.6727 (mmm) cc_final: 0.6407 (mmm) REVERT: K 37 GLU cc_start: 0.7669 (mp0) cc_final: 0.7187 (mp0) REVERT: K 60 ASP cc_start: 0.7895 (t0) cc_final: 0.7624 (t0) REVERT: K 80 MET cc_start: 0.8663 (tpt) cc_final: 0.8448 (tpp) REVERT: K 139 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7403 (tm-30) REVERT: K 146 GLN cc_start: 0.8692 (tt0) cc_final: 0.8397 (tt0) REVERT: K 181 LYS cc_start: 0.8344 (ttpp) cc_final: 0.7789 (ttmm) REVERT: K 347 ASP cc_start: 0.7614 (t70) cc_final: 0.7256 (t70) REVERT: K 393 ARG cc_start: 0.8595 (ttt-90) cc_final: 0.7559 (tpm170) REVERT: L 83 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8513 (mttm) REVERT: M 57 ASP cc_start: 0.7688 (m-30) cc_final: 0.7061 (m-30) REVERT: A 202 ASP cc_start: 0.7577 (m-30) cc_final: 0.7193 (m-30) REVERT: A 212 ASP cc_start: 0.7888 (m-30) cc_final: 0.7682 (m-30) REVERT: A 218 ASP cc_start: 0.7671 (t0) cc_final: 0.7385 (t70) REVERT: A 240 TYR cc_start: 0.8415 (t80) cc_final: 0.8018 (t80) REVERT: A 292 GLU cc_start: 0.8202 (mp0) cc_final: 0.7650 (mp0) REVERT: A 321 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8347 (mtpp) REVERT: B 22 SER cc_start: 0.8936 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 60 ASP cc_start: 0.7688 (t0) cc_final: 0.7295 (t0) REVERT: B 70 ASP cc_start: 0.6722 (p0) cc_final: 0.6445 (p0) REVERT: B 78 ASP cc_start: 0.8385 (t0) cc_final: 0.8069 (t0) REVERT: B 81 GLU cc_start: 0.7841 (mp0) cc_final: 0.7602 (mp0) REVERT: B 112 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 157 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8259 (tpp-160) REVERT: B 177 LYS cc_start: 0.8431 (ttpt) cc_final: 0.8107 (ttmm) REVERT: B 199 TYR cc_start: 0.6374 (p90) cc_final: 0.6005 (p90) REVERT: B 217 MET cc_start: 0.7592 (mmp) cc_final: 0.6873 (mmt) REVERT: B 303 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7827 (mtm-85) REVERT: B 357 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 19 MET cc_start: 0.8365 (mmm) cc_final: 0.8056 (mmm) REVERT: C 37 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8828 (ptmm) REVERT: C 64 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7548 (mt-10) REVERT: C 155 ASP cc_start: 0.7533 (m-30) cc_final: 0.7295 (m-30) REVERT: P 79 CYS cc_start: 0.1059 (OUTLIER) cc_final: -0.1480 (t) outliers start: 131 outliers final: 97 residues processed: 985 average time/residue: 1.4204 time to fit residues: 1686.0117 Evaluate side-chains 1023 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 919 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain G residue 381 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 211 VAL Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 11 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 158 optimal weight: 0.0030 chunk 142 optimal weight: 0.8980 chunk 396 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 193 optimal weight: 10.0000 overall best weight: 1.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN D 143 HIS E 286 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 364 ASN ** H 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS J 204 GLN J 228 ASN K 71 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** 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 = 0.3766 r_free = 0.3766 target = 0.137817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118470 restraints weight = 50288.359| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.17 r_work: 0.3353 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 34387 Z= 0.156 Angle : 0.637 13.771 46859 Z= 0.322 Chirality : 0.047 0.333 5246 Planarity : 0.005 0.077 6004 Dihedral : 5.234 64.950 4985 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 3.07 % Allowed : 19.26 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4291 helix: 1.70 (0.24), residues: 440 sheet: 0.15 (0.15), residues: 1256 loop : -0.64 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 409 HIS 0.010 0.001 HIS B 96 PHE 0.025 0.001 PHE H 134 TYR 0.020 0.001 TYR I 79 ARG 0.012 0.001 ARG F 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 16) link_NAG-ASN : angle 2.80920 ( 48) hydrogen bonds : bond 0.03094 ( 1070) hydrogen bonds : angle 4.78186 ( 2922) SS BOND : bond 0.00310 ( 80) SS BOND : angle 1.55336 ( 160) covalent geometry : bond 0.00361 (34291) covalent geometry : angle 0.62579 (46651) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 939 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 TYR cc_start: 0.8365 (t80) cc_final: 0.7844 (t80) REVERT: D 30 GLU cc_start: 0.7488 (pp20) cc_final: 0.7185 (pp20) REVERT: D 75 ASP cc_start: 0.8450 (t0) cc_final: 0.8103 (t0) REVERT: D 99 GLU cc_start: 0.8022 (tp30) cc_final: 0.7629 (tp30) REVERT: D 101 THR cc_start: 0.8411 (m) cc_final: 0.8074 (m) REVERT: D 102 GLN cc_start: 0.8901 (tt0) cc_final: 0.8621 (tt0) REVERT: D 135 ILE cc_start: 0.8577 (mt) cc_final: 0.8165 (tt) REVERT: D 202 ASP cc_start: 0.7743 (m-30) cc_final: 0.7398 (m-30) REVERT: D 298 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6768 (tm-30) REVERT: D 306 CYS cc_start: 0.7428 (t) cc_final: 0.7039 (t) REVERT: D 320 TYR cc_start: 0.7982 (p90) cc_final: 0.7216 (p90) REVERT: E 70 ASP cc_start: 0.6709 (p0) cc_final: 0.6239 (p0) REVERT: E 72 ASP cc_start: 0.7461 (p0) cc_final: 0.6725 (p0) REVERT: E 76 LYS cc_start: 0.8732 (mttt) cc_final: 0.8324 (mtmm) REVERT: E 81 GLU cc_start: 0.7872 (pm20) cc_final: 0.7507 (pm20) REVERT: E 127 GLU cc_start: 0.8057 (tt0) cc_final: 0.7725 (tt0) REVERT: E 129 LYS cc_start: 0.8670 (tptt) cc_final: 0.8369 (tptt) REVERT: E 138 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 139 GLU cc_start: 0.7830 (tp30) cc_final: 0.7013 (tp30) REVERT: E 162 SER cc_start: 0.8488 (t) cc_final: 0.8185 (m) REVERT: E 177 LYS cc_start: 0.8498 (pttp) cc_final: 0.8234 (ttpp) REVERT: E 182 GLU cc_start: 0.7657 (tt0) cc_final: 0.7311 (tt0) REVERT: E 195 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7955 (mtpp) REVERT: E 217 MET cc_start: 0.7411 (mmt) cc_final: 0.6974 (mmp) REVERT: E 248 ASP cc_start: 0.8235 (t0) cc_final: 0.7870 (t0) REVERT: E 250 SER cc_start: 0.8710 (m) cc_final: 0.8273 (m) REVERT: E 391 LYS cc_start: 0.8657 (tppp) cc_final: 0.8373 (tppp) REVERT: F 6 MET cc_start: 0.4454 (tpt) cc_final: 0.4152 (tpt) REVERT: F 30 VAL cc_start: 0.7593 (OUTLIER) cc_final: 0.7194 (t) REVERT: F 78 GLN cc_start: 0.8382 (mp10) cc_final: 0.8151 (mp10) REVERT: F 149 LYS cc_start: 0.8516 (mppt) cc_final: 0.8275 (mppt) REVERT: G 114 CYS cc_start: 0.7526 (m) cc_final: 0.7274 (m) REVERT: G 134 ARG cc_start: 0.8378 (ttp80) cc_final: 0.7802 (ttp80) REVERT: G 246 ASN cc_start: 0.7942 (m-40) cc_final: 0.7631 (m-40) REVERT: G 292 GLU cc_start: 0.8247 (mp0) cc_final: 0.7735 (mp0) REVERT: G 298 GLU cc_start: 0.7508 (tm-30) cc_final: 0.6901 (tm-30) REVERT: G 327 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7614 (m-70) REVERT: G 341 GLU cc_start: 0.8005 (mp0) cc_final: 0.7665 (mp0) REVERT: G 404 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8082 (ttpt) REVERT: H 20 ARG cc_start: 0.7994 (tpt90) cc_final: 0.7549 (tpt90) REVERT: H 25 CYS cc_start: 0.7072 (p) cc_final: 0.6753 (p) REVERT: H 60 ASP cc_start: 0.7978 (t0) cc_final: 0.7631 (t0) REVERT: H 78 ASP cc_start: 0.8215 (t0) cc_final: 0.7969 (t0) REVERT: H 129 LYS cc_start: 0.8448 (tptt) cc_final: 0.8216 (tmtt) REVERT: H 131 ARG cc_start: 0.7984 (mtm180) cc_final: 0.7707 (mtm180) REVERT: H 239 ASN cc_start: 0.7903 (p0) cc_final: 0.7643 (p0) REVERT: H 393 ARG cc_start: 0.6551 (tpt170) cc_final: 0.5183 (ttm170) REVERT: H 408 VAL cc_start: 0.7284 (t) cc_final: 0.7012 (m) REVERT: I 118 ILE cc_start: 0.8829 (mt) cc_final: 0.8601 (mp) REVERT: J 2 GLU cc_start: 0.7881 (pp20) cc_final: 0.7562 (pp20) REVERT: J 30 GLU cc_start: 0.7745 (pp20) cc_final: 0.7248 (pp20) REVERT: J 102 GLN cc_start: 0.8860 (tt0) cc_final: 0.8593 (tt0) REVERT: J 114 CYS cc_start: 0.7385 (m) cc_final: 0.7170 (m) REVERT: J 116 ILE cc_start: 0.8942 (mp) cc_final: 0.8694 (mm) REVERT: J 125 HIS cc_start: 0.7846 (m90) cc_final: 0.7533 (m170) REVERT: J 191 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7850 (mm-30) REVERT: J 195 MET cc_start: 0.7958 (mtm) cc_final: 0.7630 (mtm) REVERT: J 212 ASP cc_start: 0.7886 (t0) cc_final: 0.7559 (t0) REVERT: J 241 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8012 (mm-30) REVERT: J 289 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8196 (mmm160) REVERT: J 292 GLU cc_start: 0.8173 (mp0) cc_final: 0.7773 (mp0) REVERT: J 295 THR cc_start: 0.8488 (p) cc_final: 0.8247 (p) REVERT: J 306 CYS cc_start: 0.7388 (t) cc_final: 0.7033 (t) REVERT: J 311 ASP cc_start: 0.7442 (t0) cc_final: 0.7203 (t0) REVERT: J 397 GLU cc_start: 0.7547 (mp0) cc_final: 0.7217 (mp0) REVERT: J 402 VAL cc_start: 0.8720 (t) cc_final: 0.8475 (t) REVERT: J 433 MET cc_start: 0.6745 (mmm) cc_final: 0.6421 (mmm) REVERT: K 37 GLU cc_start: 0.7648 (mp0) cc_final: 0.7161 (mp0) REVERT: K 80 MET cc_start: 0.8648 (tpt) cc_final: 0.8434 (tpp) REVERT: K 139 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7389 (tm-30) REVERT: K 146 GLN cc_start: 0.8685 (tt0) cc_final: 0.8386 (tt0) REVERT: K 181 LYS cc_start: 0.8340 (ttpp) cc_final: 0.7787 (ttmm) REVERT: K 342 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6953 (tm-30) REVERT: K 347 ASP cc_start: 0.7629 (t70) cc_final: 0.7268 (t70) REVERT: K 393 ARG cc_start: 0.8586 (ttt-90) cc_final: 0.7557 (tpm170) REVERT: M 57 ASP cc_start: 0.7668 (m-30) cc_final: 0.7029 (m-30) REVERT: A 202 ASP cc_start: 0.7569 (m-30) cc_final: 0.7181 (m-30) REVERT: A 212 ASP cc_start: 0.7885 (m-30) cc_final: 0.7680 (m-30) REVERT: A 218 ASP cc_start: 0.7668 (t0) cc_final: 0.7396 (t70) REVERT: A 240 TYR cc_start: 0.8420 (t80) cc_final: 0.8006 (t80) REVERT: A 241 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 262 GLU cc_start: 0.7559 (mp0) cc_final: 0.7330 (mp0) REVERT: A 292 GLU cc_start: 0.8195 (mp0) cc_final: 0.7637 (mp0) REVERT: A 321 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8334 (mtpp) REVERT: B 22 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8738 (p) REVERT: B 60 ASP cc_start: 0.7650 (t0) cc_final: 0.7280 (t0) REVERT: B 70 ASP cc_start: 0.6707 (p0) cc_final: 0.6465 (p0) REVERT: B 78 ASP cc_start: 0.8399 (t0) cc_final: 0.8002 (t0) REVERT: B 112 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8206 (p) REVERT: B 157 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8250 (tpp-160) REVERT: B 177 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8058 (ttmm) REVERT: B 199 TYR cc_start: 0.6485 (p90) cc_final: 0.6082 (p90) REVERT: B 217 MET cc_start: 0.7593 (mmp) cc_final: 0.6883 (mmt) REVERT: B 303 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: B 357 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8171 (mt) REVERT: C 19 MET cc_start: 0.8383 (mmm) cc_final: 0.8116 (mmm) REVERT: C 37 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8809 (ptmm) REVERT: C 64 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 155 ASP cc_start: 0.7514 (m-30) cc_final: 0.7278 (m-30) REVERT: P 79 CYS cc_start: 0.0768 (OUTLIER) cc_final: -0.1788 (t) outliers start: 113 outliers final: 96 residues processed: 988 average time/residue: 1.4862 time to fit residues: 1769.6318 Evaluate side-chains 1034 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 931 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain F residue 163 TRP Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 227 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 HIS Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 374 THR Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 200 GLU Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 377 ASN Chi-restraints excluded: chain J residue 379 GLU Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 97 LYS Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 46 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 336 optimal weight: 0.5980 chunk 282 optimal weight: 3.9990 chunk 360 optimal weight: 0.0980 chunk 194 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 213 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 400 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS E 286 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 HIS J 9 ASN J 52 HIS J 228 ASN J 396 GLN K 21 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120292 restraints weight = 50259.371| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.19 r_work: 0.3383 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 34387 Z= 0.112 Angle : 0.613 13.211 46859 Z= 0.309 Chirality : 0.046 0.328 5246 Planarity : 0.005 0.072 6004 Dihedral : 5.068 64.374 4985 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 2.48 % Allowed : 19.94 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.13), residues: 4291 helix: 1.79 (0.24), residues: 440 sheet: 0.12 (0.15), residues: 1288 loop : -0.56 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 409 HIS 0.007 0.001 HIS B 96 PHE 0.019 0.001 PHE H 134 TYR 0.019 0.001 TYR I 79 ARG 0.010 0.001 ARG J 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 16) link_NAG-ASN : angle 2.67955 ( 48) hydrogen bonds : bond 0.02918 ( 1070) hydrogen bonds : angle 4.68861 ( 2922) SS BOND : bond 0.00238 ( 80) SS BOND : angle 1.35422 ( 160) covalent geometry : bond 0.00260 (34291) covalent geometry : angle 0.60267 (46651) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8582 Ramachandran restraints generated. 4291 Oldfield, 0 Emsley, 4291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 940 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 GLU cc_start: 0.7475 (pp20) cc_final: 0.7200 (pp20) REVERT: D 75 ASP cc_start: 0.8473 (t0) cc_final: 0.8122 (t0) REVERT: D 99 GLU cc_start: 0.7959 (tp30) cc_final: 0.7587 (tp30) REVERT: D 101 THR cc_start: 0.8389 (m) cc_final: 0.8058 (m) REVERT: D 102 GLN cc_start: 0.8873 (tt0) cc_final: 0.8600 (tt0) REVERT: D 135 ILE cc_start: 0.8467 (mt) cc_final: 0.8067 (tt) REVERT: D 202 ASP cc_start: 0.7740 (m-30) cc_final: 0.7391 (m-30) REVERT: D 298 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6734 (tm-30) REVERT: D 306 CYS cc_start: 0.7360 (t) cc_final: 0.6956 (t) REVERT: D 308 TYR cc_start: 0.8599 (p90) cc_final: 0.8394 (p90) REVERT: D 320 TYR cc_start: 0.7860 (p90) cc_final: 0.6976 (p90) REVERT: E 70 ASP cc_start: 0.6667 (p0) cc_final: 0.6202 (p0) REVERT: E 72 ASP cc_start: 0.7428 (p0) cc_final: 0.6710 (p0) REVERT: E 76 LYS cc_start: 0.8704 (mttt) cc_final: 0.8494 (mtpt) REVERT: E 81 GLU cc_start: 0.7902 (pm20) cc_final: 0.7573 (pm20) REVERT: E 127 GLU cc_start: 0.8039 (tt0) cc_final: 0.7714 (tt0) REVERT: E 129 LYS cc_start: 0.8670 (tptt) cc_final: 0.8420 (tptp) REVERT: E 138 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7465 (tm-30) REVERT: E 139 GLU cc_start: 0.7821 (tp30) cc_final: 0.7000 (tp30) REVERT: E 162 SER cc_start: 0.8516 (t) cc_final: 0.8198 (m) REVERT: E 177 LYS cc_start: 0.8492 (pttp) cc_final: 0.8231 (ttpp) REVERT: E 182 GLU cc_start: 0.7587 (tt0) cc_final: 0.7185 (tt0) REVERT: E 195 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7585 (mmpt) REVERT: E 217 MET cc_start: 0.7359 (mmt) cc_final: 0.6840 (mmp) REVERT: E 248 ASP cc_start: 0.8225 (t0) cc_final: 0.7911 (t0) REVERT: E 250 SER cc_start: 0.8663 (m) cc_final: 0.8168 (m) REVERT: E 391 LYS cc_start: 0.8653 (tppp) cc_final: 0.8392 (tppp) REVERT: F 6 MET cc_start: 0.4461 (tpt) cc_final: 0.4172 (tpt) REVERT: F 30 VAL cc_start: 0.7580 (OUTLIER) cc_final: 0.7192 (t) REVERT: F 78 GLN cc_start: 0.8351 (mp10) cc_final: 0.8150 (mp10) REVERT: F 149 LYS cc_start: 0.8446 (mppt) cc_final: 0.8200 (mppt) REVERT: G 114 CYS cc_start: 0.7565 (m) cc_final: 0.7331 (m) REVERT: G 246 ASN cc_start: 0.7925 (m-40) cc_final: 0.7620 (m-40) REVERT: G 292 GLU cc_start: 0.8207 (mp0) cc_final: 0.7788 (mp0) REVERT: G 298 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6853 (tm-30) REVERT: G 341 GLU cc_start: 0.8018 (mp0) cc_final: 0.7699 (mp0) REVERT: G 404 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8113 (ttpt) REVERT: H 20 ARG cc_start: 0.7981 (tpt90) cc_final: 0.7619 (tpt90) REVERT: H 25 CYS cc_start: 0.7053 (p) cc_final: 0.6744 (p) REVERT: H 60 ASP cc_start: 0.7957 (t0) cc_final: 0.7652 (t0) REVERT: H 78 ASP cc_start: 0.8178 (t0) cc_final: 0.7924 (t0) REVERT: H 129 LYS cc_start: 0.8452 (tptt) cc_final: 0.8207 (tmtt) REVERT: H 131 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7680 (mtm180) REVERT: H 239 ASN cc_start: 0.7770 (p0) cc_final: 0.7518 (p0) REVERT: H 393 ARG cc_start: 0.6484 (tpt170) cc_final: 0.5123 (ttm170) REVERT: H 408 VAL cc_start: 0.7141 (t) cc_final: 0.6857 (m) REVERT: I 72 MET cc_start: 0.6901 (mmp) cc_final: 0.6667 (mmp) REVERT: I 118 ILE cc_start: 0.8791 (mt) cc_final: 0.8579 (mp) REVERT: J 2 GLU cc_start: 0.7889 (pp20) cc_final: 0.7571 (pp20) REVERT: J 30 GLU cc_start: 0.7802 (pp20) cc_final: 0.7304 (pp20) REVERT: J 75 ASP cc_start: 0.7912 (t0) cc_final: 0.7449 (t0) REVERT: J 102 GLN cc_start: 0.8820 (tt0) cc_final: 0.8607 (tt0) REVERT: J 114 CYS cc_start: 0.7378 (m) cc_final: 0.7160 (m) REVERT: J 125 HIS cc_start: 0.7854 (m90) cc_final: 0.7541 (m170) REVERT: J 191 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7828 (mm-30) REVERT: J 195 MET cc_start: 0.7915 (mtm) cc_final: 0.7574 (mtm) REVERT: J 212 ASP cc_start: 0.7879 (t0) cc_final: 0.7556 (t0) REVERT: J 241 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7966 (mm-30) REVERT: J 289 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8203 (mmm160) REVERT: J 292 GLU cc_start: 0.8131 (mp0) cc_final: 0.7805 (mp0) REVERT: J 306 CYS cc_start: 0.7432 (t) cc_final: 0.7123 (t) REVERT: J 397 GLU cc_start: 0.7505 (mp0) cc_final: 0.7179 (mp0) REVERT: J 402 VAL cc_start: 0.8670 (t) cc_final: 0.8456 (t) REVERT: J 433 MET cc_start: 0.6721 (mmm) cc_final: 0.6400 (mmm) REVERT: K 37 GLU cc_start: 0.7590 (mp0) cc_final: 0.6972 (mp0) REVERT: K 60 ASP cc_start: 0.7967 (t0) cc_final: 0.7663 (t0) REVERT: K 80 MET cc_start: 0.8599 (tpt) cc_final: 0.8379 (tpp) REVERT: K 139 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7396 (tm-30) REVERT: K 146 GLN cc_start: 0.8669 (tt0) cc_final: 0.8395 (tt0) REVERT: K 181 LYS cc_start: 0.8349 (ttpp) cc_final: 0.7786 (ttmm) REVERT: K 342 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6961 (tm-30) REVERT: K 347 ASP cc_start: 0.7577 (t70) cc_final: 0.7232 (t70) REVERT: K 393 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.7553 (tpm170) REVERT: M 57 ASP cc_start: 0.7604 (m-30) cc_final: 0.6975 (m-30) REVERT: A 202 ASP cc_start: 0.7559 (m-30) cc_final: 0.7164 (m-30) REVERT: A 212 ASP cc_start: 0.7889 (m-30) cc_final: 0.7684 (m-30) REVERT: A 218 ASP cc_start: 0.7595 (t0) cc_final: 0.7299 (t70) REVERT: A 241 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 292 GLU cc_start: 0.8150 (mp0) cc_final: 0.7608 (mp0) REVERT: A 321 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8272 (mtpp) REVERT: B 22 SER cc_start: 0.8928 (OUTLIER) cc_final: 0.8724 (p) REVERT: B 60 ASP cc_start: 0.7754 (t0) cc_final: 0.7421 (t0) REVERT: B 70 ASP cc_start: 0.6604 (p0) cc_final: 0.6392 (p0) REVERT: B 112 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8182 (p) REVERT: B 157 ARG cc_start: 0.8507 (tpp80) cc_final: 0.8225 (tpp-160) REVERT: B 177 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8013 (ttmm) REVERT: B 199 TYR cc_start: 0.6428 (p90) cc_final: 0.6121 (p90) REVERT: B 217 MET cc_start: 0.7572 (mmp) cc_final: 0.6906 (mmt) REVERT: B 303 ARG cc_start: 0.8066 (mtm-85) cc_final: 0.7818 (mtm-85) REVERT: B 324 GLU cc_start: 0.7978 (mp0) cc_final: 0.7747 (mp0) REVERT: B 357 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8089 (mt) REVERT: C 19 MET cc_start: 0.8376 (mmm) cc_final: 0.8076 (mmm) REVERT: C 37 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8806 (ptmm) REVERT: C 64 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 155 ASP cc_start: 0.7478 (m-30) cc_final: 0.7248 (m-30) REVERT: P 79 CYS cc_start: 0.0980 (OUTLIER) cc_final: -0.1537 (t) outliers start: 91 outliers final: 71 residues processed: 981 average time/residue: 1.4474 time to fit residues: 1721.9693 Evaluate side-chains 1011 residues out of total 3676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 934 time to evaluate : 5.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 327 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 144 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 152 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 328 CYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 288 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 327 GLU Chi-restraints excluded: chain H residue 371 LEU Chi-restraints excluded: chain H residue 394 ARG Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 60 MET Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 62 CYS Chi-restraints excluded: chain J residue 99 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 307 ILE Chi-restraints excluded: chain J residue 347 THR Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 404 LYS Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain J residue 431 SER Chi-restraints excluded: chain K residue 224 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 374 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 29 CYS Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 79 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 121 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 341 optimal weight: 0.0870 chunk 322 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 376 optimal weight: 0.0000 chunk 276 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS G 143 HIS ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 327 HIS G 345 HIS J 52 HIS J 59 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 204 GLN J 228 ASN J 246 ASN J 327 HIS J 396 GLN K 21 HIS ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121009 restraints weight = 50309.994| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.17 r_work: 0.3413 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 34387 Z= 0.110 Angle : 0.616 12.794 46859 Z= 0.311 Chirality : 0.046 0.330 5246 Planarity : 0.004 0.071 6004 Dihedral : 5.000 65.364 4985 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.50 % Favored : 94.43 % Rotamer: Outliers : 2.39 % Allowed : 20.40 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 4291 helix: 1.85 (0.24), residues: 440 sheet: 0.18 (0.15), residues: 1264 loop : -0.55 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 409 HIS 0.007 0.001 HIS B 96 PHE 0.021 0.001 PHE H 134 TYR 0.020 0.001 TYR I 79 ARG 0.010 0.001 ARG A 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 16) link_NAG-ASN : angle 2.63224 ( 48) hydrogen bonds : bond 0.02878 ( 1070) hydrogen bonds : angle 4.62977 ( 2922) SS BOND : bond 0.00239 ( 80) SS BOND : angle 1.33207 ( 160) covalent geometry : bond 0.00258 (34291) covalent geometry : angle 0.60689 (46651) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37175.96 seconds wall clock time: 637 minutes 51.57 seconds (38271.57 seconds total)