Starting phenix.real_space_refine on Sat Aug 23 10:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmw_38490/08_2025/8xmw_38490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmw_38490/08_2025/8xmw_38490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmw_38490/08_2025/8xmw_38490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmw_38490/08_2025/8xmw_38490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmw_38490/08_2025/8xmw_38490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmw_38490/08_2025/8xmw_38490.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2255 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 2 7.16 5 S 70 5.16 5 C 5978 2.51 5 N 1662 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9538 Number of models: 1 Model: "" Number of chains: 13 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2442 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 3, 'TRANS': 316} Chain: "G" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2442 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 3, 'TRANS': 316} Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "C" 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: "F" 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: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.06, per 1000 atoms: 0.22 Number of scatterers: 9538 At special positions: 0 Unit cell: (89.88, 130.54, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 6 19.99 S 70 16.00 O 1820 8.00 N 1662 7.00 C 5978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.04 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.04 Simple disulfide: pdb=" SG CYS G 168 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 184 " - pdb=" SG CYS G 248 " distance=2.02 Simple disulfide: pdb=" SG CYS G 197 " - pdb=" SG CYS G 258 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 238 " distance=2.03 Simple disulfide: pdb=" SG CYS G 275 " - pdb=" SG CYS G 309 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 355 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 365 " distance=2.03 Simple disulfide: pdb=" SG CYS G 335 " - pdb=" SG CYS G 345 " distance=2.03 Simple disulfide: pdb=" SG CYS G 382 " - pdb=" SG CYS G 416 " distance=2.03 Simple disulfide: pdb=" SG CYS G 398 " - pdb=" SG CYS G 462 " distance=2.03 Simple disulfide: pdb=" SG CYS G 411 " - pdb=" SG CYS G 472 " distance=2.03 Simple disulfide: pdb=" SG CYS G 442 " - pdb=" SG CYS G 452 " 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG C 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG E 1 " - " ASN D 320 " " NAG F 1 " - " ASN G 320 " " NAG G1101 " - " ASN G 445 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 364.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 33.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 154 through 159 removed outlier: 3.505A pdb=" N ALA 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 259 through 263 removed outlier: 3.564A pdb=" N LYS 2 263 " --> pdb=" O PRO 2 260 " (cutoff:3.500A) Processing helix chain '2' and resid 333 through 346 removed outlier: 4.788A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU 2 346 " --> pdb=" O LYS 2 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.684A pdb=" N CYS D 238 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.658A pdb=" N ASP D 253 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 341 through 345 removed outlier: 3.600A pdb=" N GLN D 344 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS D 345 " --> pdb=" O ILE D 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 341 through 345' Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.535A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 259 through 263 Processing helix chain 'G' and resid 296 through 307 Processing helix chain 'G' and resid 356 through 360 Processing helix chain 'G' and resid 403 through 415 Processing helix chain 'G' and resid 448 through 452 Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.520A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.706A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.993A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 removed outlier: 4.106A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 removed outlier: 3.937A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.831A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.940A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.112A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.846A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA6, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.682A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.682A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N TRP D 287 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N LEU D 330 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR D 289 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 371 through 377 removed outlier: 3.983A pdb=" N LYS D 421 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 371 through 377 removed outlier: 6.059A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N LEU D 439 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AB2, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AB3, first strand: chain 'G' and resid 265 through 269 removed outlier: 3.621A pdb=" N SER G 265 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 265 through 269 removed outlier: 3.621A pdb=" N SER G 265 " --> pdb=" O ARG G 282 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU G 279 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 290 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 286 " --> pdb=" O PHE G 283 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS G 327 " --> pdb=" O TRP G 287 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 371 through 380 removed outlier: 3.655A pdb=" N GLY G 378 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA G 383 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 371 through 380 removed outlier: 3.655A pdb=" N GLY G 378 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA G 383 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL G 386 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 397 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU G 437 " --> pdb=" O LEU G 394 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 396 " --> pdb=" O LEU G 437 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1122 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: 1.32 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3617 1.38 - 1.54: 6042 1.54 - 1.71: 15 1.71 - 1.88: 81 1.88 - 2.05: 8 Bond restraints: 9763 Sorted by residual: bond pdb=" C THR A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 1.334 1.366 -0.031 1.33e-02 5.65e+03 5.61e+00 bond pdb=" C LYS B 82 " pdb=" O LYS B 82 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.26e-02 6.30e+03 5.00e+00 bond pdb=" C LYS A 139 " pdb=" O LYS A 139 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.47e-02 4.63e+03 2.87e+00 bond pdb=" CA TYR A 140 " pdb=" C TYR A 140 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.30e-02 5.92e+03 2.70e+00 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.314 0.032 2.00e-02 2.50e+03 2.55e+00 ... (remaining 9758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 12646 1.38 - 2.76: 487 2.76 - 4.15: 94 4.15 - 5.53: 26 5.53 - 6.91: 4 Bond angle restraints: 13257 Sorted by residual: angle pdb=" N LYS A 139 " pdb=" CA LYS A 139 " pdb=" C LYS A 139 " ideal model delta sigma weight residual 113.15 108.59 4.56 1.19e+00 7.06e-01 1.47e+01 angle pdb=" N GLY 2 224 " pdb=" CA GLY 2 224 " pdb=" C GLY 2 224 " ideal model delta sigma weight residual 110.87 116.36 -5.49 1.54e+00 4.22e-01 1.27e+01 angle pdb=" C VAL D 319 " pdb=" N ASN D 320 " pdb=" CA ASN D 320 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N GLY G 210 " pdb=" CA GLY G 210 " pdb=" C GLY G 210 " ideal model delta sigma weight residual 113.18 120.09 -6.91 2.37e+00 1.78e-01 8.50e+00 angle pdb=" N LYS 2 94 " pdb=" CA LYS 2 94 " pdb=" C LYS 2 94 " ideal model delta sigma weight residual 111.02 107.47 3.55 1.22e+00 6.72e-01 8.48e+00 ... (remaining 13252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5244 17.46 - 34.92: 475 34.92 - 52.37: 88 52.37 - 69.83: 24 69.83 - 87.29: 8 Dihedral angle restraints: 5839 sinusoidal: 2426 harmonic: 3413 Sorted by residual: dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS G 184 " pdb=" SG CYS G 184 " pdb=" SG CYS G 248 " pdb=" CB CYS G 248 " ideal model delta sinusoidal sigma weight residual 93.00 148.18 -55.18 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS G 275 " pdb=" SG CYS G 275 " pdb=" SG CYS G 309 " pdb=" CB CYS G 309 " ideal model delta sinusoidal sigma weight residual -86.00 -136.02 50.02 1 1.00e+01 1.00e-02 3.43e+01 ... (remaining 5836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1311 0.080 - 0.159: 127 0.159 - 0.239: 1 0.239 - 0.319: 0 0.319 - 0.398: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.75e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN G 320 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA PRO G 310 " pdb=" N PRO G 310 " pdb=" C PRO G 310 " pdb=" CB PRO G 310 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1437 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.068 2.00e-02 2.50e+03 5.83e-02 4.25e+01 pdb=" C7 NAG F 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.095 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 138 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C SER A 138 " -0.085 2.00e-02 2.50e+03 pdb=" O SER A 138 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS A 139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.050 2.00e-02 2.50e+03 4.13e-02 2.14e+01 pdb=" C7 NAG F 2 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.066 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.011 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 137 2.62 - 3.19: 8504 3.19 - 3.76: 15702 3.76 - 4.33: 22701 4.33 - 4.90: 36622 Nonbonded interactions: 83666 Sorted by model distance: nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.047 3.040 nonbonded pdb=" OG SER G 366 " pdb=" OD1 ASP G 370 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP G 224 " pdb="CA CA G1103 " model vdw 2.227 2.510 nonbonded pdb=" NH2 ARG D 412 " pdb=" O GLY D 444 " model vdw 2.241 3.120 nonbonded pdb=" O PHE A 117 " pdb=" NH2 ARG B 30 " model vdw 2.242 3.120 ... (remaining 83661 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 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } 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=0.66 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.140 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 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 : 0.005 0.113 9803 Z= 0.211 Angle : 0.667 6.909 13343 Z= 0.354 Chirality : 0.046 0.398 1440 Planarity : 0.005 0.062 1691 Dihedral : 13.866 87.291 3577 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 0.30 % Allowed : 0.10 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.24), residues: 1198 helix: 1.12 (0.29), residues: 323 sheet: -0.72 (0.41), residues: 162 loop : -1.04 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 392 TYR 0.019 0.002 TYR D 424 PHE 0.022 0.002 PHE A 46 TRP 0.012 0.002 TRP 2 310 HIS 0.016 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9763) covalent geometry : angle 0.65697 (13257) SS BOND : bond 0.00322 ( 28) SS BOND : angle 1.47542 ( 56) hydrogen bonds : bond 0.16888 ( 377) hydrogen bonds : angle 7.10949 ( 1122) Misc. bond : bond 0.08787 ( 2) link_BETA1-4 : bond 0.00715 ( 3) link_BETA1-4 : angle 1.51673 ( 9) link_NAG-ASN : bond 0.00425 ( 7) link_NAG-ASN : angle 1.87625 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.1603 (pt0) cc_final: 0.1182 (mm-30) REVERT: 2 95 ASN cc_start: 0.0335 (p0) cc_final: -0.0285 (p0) REVERT: 2 111 LYS cc_start: 0.0737 (mtmt) cc_final: 0.0314 (mtmt) REVERT: 2 128 THR cc_start: 0.1244 (p) cc_final: 0.0659 (p) REVERT: 2 306 GLU cc_start: 0.3789 (mp0) cc_final: 0.3516 (mp0) REVERT: 2 321 SER cc_start: -0.1027 (t) cc_final: -0.1432 (p) REVERT: D 159 MET cc_start: 0.6592 (ttp) cc_final: 0.6360 (ttp) REVERT: D 187 ASN cc_start: 0.7924 (t0) cc_final: 0.7405 (t0) REVERT: D 245 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7253 (mppt) REVERT: D 260 LYS cc_start: 0.8388 (tttp) cc_final: 0.7786 (ttpt) REVERT: G 204 SER cc_start: 0.8549 (p) cc_final: 0.8129 (t) REVERT: G 218 SER cc_start: 0.8716 (t) cc_final: 0.8380 (m) REVERT: G 392 ARG cc_start: 0.7497 (tmm160) cc_final: 0.6991 (mtm180) REVERT: A 42 TYR cc_start: 0.9233 (m-80) cc_final: 0.8995 (m-80) REVERT: A 56 LYS cc_start: 0.7523 (tttt) cc_final: 0.7278 (tptt) REVERT: A 61 LYS cc_start: 0.8426 (mttt) cc_final: 0.8168 (mtpt) REVERT: A 141 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6648 (mtp-110) REVERT: B 22 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6887 (mt-10) REVERT: B 65 LYS cc_start: 0.8416 (tttp) cc_final: 0.8205 (tttt) REVERT: B 121 GLU cc_start: 0.8161 (tt0) cc_final: 0.7737 (mt-10) outliers start: 3 outliers final: 0 residues processed: 215 average time/residue: 0.6884 time to fit residues: 156.0399 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 288 GLN D 327 HIS G 348 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.146025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108099 restraints weight = 10402.520| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.66 r_work: 0.2996 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 9803 Z= 0.225 Angle : 0.640 6.836 13343 Z= 0.333 Chirality : 0.045 0.187 1440 Planarity : 0.004 0.046 1691 Dihedral : 7.443 80.215 1507 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 3.42 % Allowed : 11.67 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.24), residues: 1198 helix: 1.20 (0.29), residues: 329 sheet: -1.02 (0.38), residues: 170 loop : -0.88 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 2 252 TYR 0.016 0.002 TYR 2 239 PHE 0.014 0.002 PHE A 46 TRP 0.011 0.002 TRP D 402 HIS 0.014 0.002 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 9763) covalent geometry : angle 0.63212 (13257) SS BOND : bond 0.00405 ( 28) SS BOND : angle 1.36760 ( 56) hydrogen bonds : bond 0.04200 ( 377) hydrogen bonds : angle 5.33167 ( 1122) Misc. bond : bond 0.07437 ( 2) link_BETA1-4 : bond 0.00219 ( 3) link_BETA1-4 : angle 1.37151 ( 9) link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 1.57338 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7752 (pt0) cc_final: 0.6543 (mm-30) REVERT: 2 266 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8684 (mtpt) REVERT: 2 307 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7821 (pt0) REVERT: 2 308 ASP cc_start: 0.7659 (t0) cc_final: 0.7448 (t0) REVERT: D 159 MET cc_start: 0.6840 (ttp) cc_final: 0.6410 (ttp) REVERT: D 167 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6707 (ttt) REVERT: D 187 ASN cc_start: 0.8141 (t0) cc_final: 0.7472 (t0) REVERT: D 245 LYS cc_start: 0.7728 (tmtt) cc_final: 0.6896 (mppt) REVERT: D 260 LYS cc_start: 0.8385 (tttp) cc_final: 0.7513 (ttpt) REVERT: D 344 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: G 204 SER cc_start: 0.8284 (p) cc_final: 0.7883 (t) REVERT: G 218 SER cc_start: 0.8556 (t) cc_final: 0.8206 (m) REVERT: G 392 ARG cc_start: 0.7536 (tmm160) cc_final: 0.6834 (ttm-80) REVERT: A 42 TYR cc_start: 0.9295 (m-80) cc_final: 0.9006 (m-80) REVERT: A 56 LYS cc_start: 0.7733 (tttt) cc_final: 0.7446 (tptt) REVERT: A 78 ASN cc_start: 0.8715 (m-40) cc_final: 0.8388 (m-40) REVERT: A 127 LYS cc_start: 0.8641 (mttm) cc_final: 0.8395 (mtmm) REVERT: B 22 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7014 (mt-10) REVERT: B 65 LYS cc_start: 0.8550 (tttp) cc_final: 0.8312 (tttt) REVERT: B 121 GLU cc_start: 0.8547 (tt0) cc_final: 0.7996 (mt-10) outliers start: 34 outliers final: 10 residues processed: 165 average time/residue: 0.6293 time to fit residues: 109.8665 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 266 LYS Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 447 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.154466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.116211 restraints weight = 10370.994| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.80 r_work: 0.3226 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 9803 Z= 0.212 Angle : 0.626 6.860 13343 Z= 0.324 Chirality : 0.045 0.195 1440 Planarity : 0.004 0.045 1691 Dihedral : 7.050 78.940 1503 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 3.32 % Allowed : 15.69 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.24), residues: 1198 helix: 1.25 (0.29), residues: 329 sheet: -1.27 (0.38), residues: 162 loop : -0.84 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 202 TYR 0.014 0.002 TYR 2 239 PHE 0.024 0.002 PHE D 176 TRP 0.011 0.001 TRP D 402 HIS 0.010 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9763) covalent geometry : angle 0.61716 (13257) SS BOND : bond 0.00381 ( 28) SS BOND : angle 1.39563 ( 56) hydrogen bonds : bond 0.03726 ( 377) hydrogen bonds : angle 5.10064 ( 1122) Misc. bond : bond 0.07655 ( 2) link_BETA1-4 : bond 0.00243 ( 3) link_BETA1-4 : angle 1.40433 ( 9) link_NAG-ASN : bond 0.00280 ( 7) link_NAG-ASN : angle 1.68019 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7895 (pt0) cc_final: 0.6813 (mm-30) REVERT: 2 266 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8638 (mtpt) REVERT: 2 307 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8037 (pt0) REVERT: 2 308 ASP cc_start: 0.7861 (t0) cc_final: 0.7606 (t0) REVERT: D 159 MET cc_start: 0.6992 (ttp) cc_final: 0.6453 (ttp) REVERT: D 167 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6720 (ttt) REVERT: D 245 LYS cc_start: 0.7743 (tmtt) cc_final: 0.6958 (mppt) REVERT: D 260 LYS cc_start: 0.8460 (tttp) cc_final: 0.7599 (ttpt) REVERT: D 306 GLN cc_start: 0.7839 (tt0) cc_final: 0.7602 (tt0) REVERT: D 344 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7466 (mt0) REVERT: D 462 CYS cc_start: 0.6543 (t) cc_final: 0.6334 (t) REVERT: G 204 SER cc_start: 0.8319 (p) cc_final: 0.7934 (t) REVERT: G 218 SER cc_start: 0.8642 (t) cc_final: 0.8294 (m) REVERT: G 344 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: G 392 ARG cc_start: 0.7690 (tmm160) cc_final: 0.6891 (ttm-80) REVERT: A 56 LYS cc_start: 0.7842 (tttt) cc_final: 0.7575 (tptt) REVERT: A 60 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8628 (tptm) REVERT: A 61 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8216 (mtpt) REVERT: A 78 ASN cc_start: 0.8766 (m-40) cc_final: 0.8440 (m-40) REVERT: A 127 LYS cc_start: 0.8697 (mttm) cc_final: 0.8465 (mtmm) REVERT: B 22 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7158 (mt-10) REVERT: B 65 LYS cc_start: 0.8577 (tttp) cc_final: 0.8330 (tttt) REVERT: B 121 GLU cc_start: 0.8614 (tt0) cc_final: 0.8092 (mt-10) outliers start: 33 outliers final: 14 residues processed: 156 average time/residue: 0.6741 time to fit residues: 111.1281 Evaluate side-chains 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 266 LYS Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 61 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 105 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 106 optimal weight: 0.0020 overall best weight: 0.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS G 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.162283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.127082 restraints weight = 10437.072| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.59 r_work: 0.3158 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9803 Z= 0.113 Angle : 0.546 5.773 13343 Z= 0.282 Chirality : 0.042 0.181 1440 Planarity : 0.004 0.041 1691 Dihedral : 6.379 76.111 1503 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.22 % Allowed : 17.00 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.24), residues: 1198 helix: 1.59 (0.29), residues: 329 sheet: -1.32 (0.39), residues: 147 loop : -0.79 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 381 TYR 0.015 0.001 TYR D 354 PHE 0.028 0.001 PHE D 176 TRP 0.012 0.001 TRP G 180 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9763) covalent geometry : angle 0.54057 (13257) SS BOND : bond 0.00229 ( 28) SS BOND : angle 0.96574 ( 56) hydrogen bonds : bond 0.03023 ( 377) hydrogen bonds : angle 4.76486 ( 1122) Misc. bond : bond 0.05112 ( 2) link_BETA1-4 : bond 0.00272 ( 3) link_BETA1-4 : angle 1.04405 ( 9) link_NAG-ASN : bond 0.00195 ( 7) link_NAG-ASN : angle 1.36676 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7894 (pt0) cc_final: 0.6760 (mm-30) REVERT: 2 255 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: 2 266 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8537 (ttpp) REVERT: 2 308 ASP cc_start: 0.7861 (t0) cc_final: 0.7659 (t0) REVERT: D 167 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6522 (ttt) REVERT: D 245 LYS cc_start: 0.7664 (tmtt) cc_final: 0.6980 (mppt) REVERT: D 344 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7324 (mt0) REVERT: D 358 ASN cc_start: 0.7913 (m-40) cc_final: 0.7574 (m-40) REVERT: G 204 SER cc_start: 0.8215 (p) cc_final: 0.7825 (t) REVERT: G 218 SER cc_start: 0.8574 (t) cc_final: 0.8211 (m) REVERT: G 249 ASP cc_start: 0.7500 (t70) cc_final: 0.7133 (t70) REVERT: G 298 TYR cc_start: 0.7799 (m-80) cc_final: 0.7569 (m-80) REVERT: G 392 ARG cc_start: 0.7449 (tmm160) cc_final: 0.6960 (mtm180) REVERT: G 466 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 56 LYS cc_start: 0.7798 (tttt) cc_final: 0.7423 (mmtm) REVERT: B 22 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7116 (mt-10) REVERT: B 65 LYS cc_start: 0.8508 (tttp) cc_final: 0.8244 (tttt) REVERT: B 121 GLU cc_start: 0.8621 (tt0) cc_final: 0.8127 (mt-10) outliers start: 32 outliers final: 11 residues processed: 180 average time/residue: 0.5937 time to fit residues: 114.0166 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 266 LYS Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN D 306 GLN D 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.154073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.115121 restraints weight = 10550.175| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.93 r_work: 0.3234 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9803 Z= 0.170 Angle : 0.589 6.824 13343 Z= 0.304 Chirality : 0.044 0.185 1440 Planarity : 0.004 0.042 1691 Dihedral : 6.333 73.763 1503 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 3.22 % Allowed : 18.91 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.24), residues: 1198 helix: 1.52 (0.29), residues: 329 sheet: -1.37 (0.39), residues: 147 loop : -0.81 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 202 TYR 0.013 0.002 TYR 2 183 PHE 0.025 0.001 PHE D 176 TRP 0.014 0.001 TRP G 180 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 9763) covalent geometry : angle 0.57875 (13257) SS BOND : bond 0.00407 ( 28) SS BOND : angle 1.51750 ( 56) hydrogen bonds : bond 0.03255 ( 377) hydrogen bonds : angle 4.80389 ( 1122) Misc. bond : bond 0.06654 ( 2) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 1.34380 ( 9) link_NAG-ASN : bond 0.00208 ( 7) link_NAG-ASN : angle 1.53212 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7938 (pt0) cc_final: 0.6634 (mm-30) REVERT: 2 255 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: 2 308 ASP cc_start: 0.7990 (t0) cc_final: 0.7714 (t0) REVERT: D 159 MET cc_start: 0.7251 (ttp) cc_final: 0.6829 (ttp) REVERT: D 245 LYS cc_start: 0.7593 (tmtt) cc_final: 0.6786 (mppt) REVERT: D 344 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6550 (mt0) REVERT: D 358 ASN cc_start: 0.7902 (m-40) cc_final: 0.7549 (m-40) REVERT: G 204 SER cc_start: 0.8213 (p) cc_final: 0.7823 (t) REVERT: G 218 SER cc_start: 0.8626 (t) cc_final: 0.8233 (m) REVERT: G 344 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: G 392 ARG cc_start: 0.7533 (tmm160) cc_final: 0.6814 (ttm-80) REVERT: G 466 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 56 LYS cc_start: 0.7775 (tttt) cc_final: 0.7269 (mttm) REVERT: A 78 ASN cc_start: 0.8739 (m-40) cc_final: 0.8370 (m-40) REVERT: B 22 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6997 (mt-10) REVERT: B 65 LYS cc_start: 0.8451 (tttp) cc_final: 0.8177 (tttt) REVERT: B 121 GLU cc_start: 0.8615 (tt0) cc_final: 0.8019 (mt-10) outliers start: 32 outliers final: 15 residues processed: 152 average time/residue: 0.5794 time to fit residues: 93.9980 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.154493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115811 restraints weight = 10561.948| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.89 r_work: 0.3300 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9803 Z= 0.158 Angle : 0.575 5.934 13343 Z= 0.296 Chirality : 0.043 0.181 1440 Planarity : 0.004 0.044 1691 Dihedral : 6.154 72.322 1503 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.08 % Rotamer: Outliers : 3.22 % Allowed : 19.82 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.24), residues: 1198 helix: 1.58 (0.29), residues: 329 sheet: -1.33 (0.40), residues: 147 loop : -0.79 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 202 TYR 0.013 0.002 TYR 2 183 PHE 0.022 0.001 PHE D 176 TRP 0.014 0.001 TRP G 180 HIS 0.005 0.001 HIS 2 124 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9763) covalent geometry : angle 0.56692 (13257) SS BOND : bond 0.00292 ( 28) SS BOND : angle 1.20586 ( 56) hydrogen bonds : bond 0.03209 ( 377) hydrogen bonds : angle 4.75478 ( 1122) Misc. bond : bond 0.06382 ( 2) link_BETA1-4 : bond 0.00496 ( 3) link_BETA1-4 : angle 1.33787 ( 9) link_NAG-ASN : bond 0.00174 ( 7) link_NAG-ASN : angle 1.47289 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.8007 (pt0) cc_final: 0.6825 (mm-30) REVERT: 2 213 TYR cc_start: 0.9226 (m-80) cc_final: 0.9010 (m-80) REVERT: 2 255 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: 2 308 ASP cc_start: 0.8004 (t0) cc_final: 0.7744 (t0) REVERT: D 190 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7314 (mp) REVERT: D 245 LYS cc_start: 0.7631 (tmtt) cc_final: 0.6862 (mppt) REVERT: D 344 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6627 (mt0) REVERT: D 352 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8171 (tmtm) REVERT: D 358 ASN cc_start: 0.7873 (m-40) cc_final: 0.7553 (m-40) REVERT: G 204 SER cc_start: 0.8249 (p) cc_final: 0.7860 (t) REVERT: G 218 SER cc_start: 0.8639 (t) cc_final: 0.8255 (m) REVERT: G 344 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: G 392 ARG cc_start: 0.7572 (tmm160) cc_final: 0.6893 (ttm-80) REVERT: A 56 LYS cc_start: 0.7885 (tttt) cc_final: 0.7403 (mttm) REVERT: A 78 ASN cc_start: 0.8743 (m-40) cc_final: 0.8410 (m-40) REVERT: B 22 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7098 (mt-10) REVERT: B 65 LYS cc_start: 0.8529 (tttp) cc_final: 0.8262 (tttt) REVERT: B 120 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.7900 (pptt) REVERT: B 121 GLU cc_start: 0.8667 (tt0) cc_final: 0.8071 (mt-10) outliers start: 32 outliers final: 15 residues processed: 148 average time/residue: 0.5932 time to fit residues: 93.8709 Evaluate side-chains 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 40 optimal weight: 0.1980 chunk 105 optimal weight: 0.0870 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.169419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135986 restraints weight = 10266.776| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.49 r_work: 0.3146 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9803 Z= 0.126 Angle : 0.550 5.626 13343 Z= 0.285 Chirality : 0.042 0.173 1440 Planarity : 0.004 0.050 1691 Dihedral : 5.945 71.491 1503 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.91 % Rotamer: Outliers : 2.82 % Allowed : 20.22 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1198 helix: 1.70 (0.30), residues: 329 sheet: -1.21 (0.39), residues: 159 loop : -0.75 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 202 TYR 0.012 0.001 TYR 2 183 PHE 0.020 0.001 PHE D 176 TRP 0.014 0.001 TRP G 180 HIS 0.004 0.001 HIS 2 124 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9763) covalent geometry : angle 0.54466 (13257) SS BOND : bond 0.00232 ( 28) SS BOND : angle 1.00901 ( 56) hydrogen bonds : bond 0.03042 ( 377) hydrogen bonds : angle 4.65639 ( 1122) Misc. bond : bond 0.05182 ( 2) link_BETA1-4 : bond 0.00347 ( 3) link_BETA1-4 : angle 1.22032 ( 9) link_NAG-ASN : bond 0.00152 ( 7) link_NAG-ASN : angle 1.38281 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7842 (pt0) cc_final: 0.6678 (mm-30) REVERT: 2 255 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7698 (mt-10) REVERT: 2 308 ASP cc_start: 0.7878 (t0) cc_final: 0.7632 (t0) REVERT: D 167 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6454 (ttt) REVERT: D 190 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7241 (mp) REVERT: D 245 LYS cc_start: 0.7604 (tmtt) cc_final: 0.6824 (mppt) REVERT: D 344 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6505 (mt0) REVERT: D 352 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8192 (tmtm) REVERT: D 357 HIS cc_start: 0.8349 (m-70) cc_final: 0.8076 (m-70) REVERT: D 358 ASN cc_start: 0.7762 (m-40) cc_final: 0.7424 (m-40) REVERT: D 381 ARG cc_start: 0.7396 (ttp80) cc_final: 0.5581 (ptt180) REVERT: G 204 SER cc_start: 0.8193 (p) cc_final: 0.7815 (t) REVERT: G 218 SER cc_start: 0.8614 (t) cc_final: 0.8202 (m) REVERT: G 249 ASP cc_start: 0.7304 (t70) cc_final: 0.6907 (p0) REVERT: G 286 GLU cc_start: 0.8323 (pt0) cc_final: 0.8037 (pt0) REVERT: G 344 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7467 (mm-40) REVERT: G 381 ARG cc_start: 0.8159 (tmm-80) cc_final: 0.7552 (ttp80) REVERT: G 392 ARG cc_start: 0.7383 (tmm160) cc_final: 0.6824 (mtm180) REVERT: A 40 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8669 (mtmt) REVERT: A 56 LYS cc_start: 0.7780 (tttt) cc_final: 0.7314 (mttm) REVERT: B 22 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7017 (mt-10) REVERT: B 65 LYS cc_start: 0.8449 (tttp) cc_final: 0.8172 (tttt) REVERT: B 120 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7877 (pptt) REVERT: B 121 GLU cc_start: 0.8582 (tt0) cc_final: 0.8018 (mt-10) outliers start: 28 outliers final: 13 residues processed: 151 average time/residue: 0.5879 time to fit residues: 94.3248 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.154100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.115201 restraints weight = 10541.778| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.92 r_work: 0.3251 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 9803 Z= 0.172 Angle : 0.580 5.802 13343 Z= 0.300 Chirality : 0.044 0.188 1440 Planarity : 0.004 0.046 1691 Dihedral : 6.072 73.657 1503 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 3.02 % Allowed : 20.22 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.25), residues: 1198 helix: 1.63 (0.29), residues: 329 sheet: -1.24 (0.39), residues: 159 loop : -0.74 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 2 202 TYR 0.013 0.002 TYR 2 239 PHE 0.019 0.001 PHE D 176 TRP 0.016 0.001 TRP G 180 HIS 0.006 0.001 HIS D 464 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9763) covalent geometry : angle 0.57260 (13257) SS BOND : bond 0.00337 ( 28) SS BOND : angle 1.20166 ( 56) hydrogen bonds : bond 0.03221 ( 377) hydrogen bonds : angle 4.73039 ( 1122) Misc. bond : bond 0.06928 ( 2) link_BETA1-4 : bond 0.00328 ( 3) link_BETA1-4 : angle 1.43671 ( 9) link_NAG-ASN : bond 0.00189 ( 7) link_NAG-ASN : angle 1.51904 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7967 (pt0) cc_final: 0.6835 (mm-30) REVERT: 2 255 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: 2 308 ASP cc_start: 0.8037 (t0) cc_final: 0.7768 (t0) REVERT: D 167 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6561 (ttt) REVERT: D 190 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7207 (mp) REVERT: D 245 LYS cc_start: 0.7641 (tmtt) cc_final: 0.6952 (mppt) REVERT: D 344 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.6576 (mt0) REVERT: D 352 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8220 (tmtm) REVERT: D 358 ASN cc_start: 0.7861 (m-40) cc_final: 0.7575 (m-40) REVERT: D 381 ARG cc_start: 0.7385 (ttp80) cc_final: 0.5646 (ptt180) REVERT: G 204 SER cc_start: 0.8255 (p) cc_final: 0.7857 (t) REVERT: G 218 SER cc_start: 0.8661 (t) cc_final: 0.8254 (m) REVERT: G 249 ASP cc_start: 0.7506 (t70) cc_final: 0.7004 (p0) REVERT: G 286 GLU cc_start: 0.8493 (pt0) cc_final: 0.8271 (pt0) REVERT: G 344 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: G 381 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7643 (ttp80) REVERT: G 392 ARG cc_start: 0.7606 (tmm160) cc_final: 0.6888 (mtm180) REVERT: A 56 LYS cc_start: 0.7853 (tttt) cc_final: 0.7372 (mttm) REVERT: B 22 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7098 (mt-10) REVERT: B 65 LYS cc_start: 0.8509 (tttp) cc_final: 0.8237 (tttt) REVERT: B 120 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7929 (pptt) REVERT: B 121 GLU cc_start: 0.8668 (tt0) cc_final: 0.8078 (mt-10) outliers start: 30 outliers final: 17 residues processed: 143 average time/residue: 0.5114 time to fit residues: 78.1342 Evaluate side-chains 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 126 LEU Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131506 restraints weight = 10323.175| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.47 r_work: 0.3045 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 9803 Z= 0.159 Angle : 0.575 5.970 13343 Z= 0.297 Chirality : 0.044 0.180 1440 Planarity : 0.004 0.048 1691 Dihedral : 6.035 73.930 1503 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.91 % Rotamer: Outliers : 2.52 % Allowed : 20.72 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.25), residues: 1198 helix: 1.62 (0.29), residues: 329 sheet: -1.24 (0.39), residues: 159 loop : -0.72 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 202 TYR 0.012 0.002 TYR 2 239 PHE 0.018 0.001 PHE D 176 TRP 0.018 0.001 TRP D 180 HIS 0.006 0.001 HIS D 464 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 9763) covalent geometry : angle 0.56665 (13257) SS BOND : bond 0.00292 ( 28) SS BOND : angle 1.25011 ( 56) hydrogen bonds : bond 0.03186 ( 377) hydrogen bonds : angle 4.71610 ( 1122) Misc. bond : bond 0.06270 ( 2) link_BETA1-4 : bond 0.00231 ( 3) link_BETA1-4 : angle 1.36836 ( 9) link_NAG-ASN : bond 0.00175 ( 7) link_NAG-ASN : angle 1.50531 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7828 (pt0) cc_final: 0.6641 (mm-30) REVERT: 2 255 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7704 (mt-10) REVERT: 2 308 ASP cc_start: 0.7943 (t0) cc_final: 0.7679 (t0) REVERT: D 167 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6379 (ttt) REVERT: D 190 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7041 (mt) REVERT: D 245 LYS cc_start: 0.7608 (tmtt) cc_final: 0.6771 (mppt) REVERT: D 344 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6449 (mt0) REVERT: D 352 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8231 (tmtm) REVERT: D 358 ASN cc_start: 0.7791 (m-40) cc_final: 0.7490 (m-40) REVERT: D 381 ARG cc_start: 0.7291 (ttp80) cc_final: 0.5526 (ptt180) REVERT: G 204 SER cc_start: 0.8247 (p) cc_final: 0.7845 (t) REVERT: G 218 SER cc_start: 0.8616 (t) cc_final: 0.8196 (m) REVERT: G 249 ASP cc_start: 0.7363 (t70) cc_final: 0.6843 (p0) REVERT: G 286 GLU cc_start: 0.8412 (pt0) cc_final: 0.8166 (pt0) REVERT: G 344 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7484 (mm-40) REVERT: G 381 ARG cc_start: 0.8174 (tmm-80) cc_final: 0.7637 (ttp80) REVERT: G 392 ARG cc_start: 0.7438 (tmm160) cc_final: 0.6815 (mtm180) REVERT: A 56 LYS cc_start: 0.7745 (tttt) cc_final: 0.7256 (mttm) REVERT: B 22 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6974 (mt-10) REVERT: B 65 LYS cc_start: 0.8430 (tttp) cc_final: 0.8157 (tttt) REVERT: B 120 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7925 (pptt) REVERT: B 121 GLU cc_start: 0.8570 (tt0) cc_final: 0.7974 (mt-10) outliers start: 25 outliers final: 15 residues processed: 139 average time/residue: 0.5924 time to fit residues: 87.9420 Evaluate side-chains 136 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 126 LEU Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 247 GLN 2 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.150269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.113187 restraints weight = 10530.999| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.80 r_work: 0.3014 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 9803 Z= 0.200 Angle : 0.609 6.499 13343 Z= 0.314 Chirality : 0.045 0.185 1440 Planarity : 0.004 0.050 1691 Dihedral : 6.197 75.557 1503 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 2.52 % Allowed : 21.23 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.24), residues: 1198 helix: 1.49 (0.29), residues: 329 sheet: -1.34 (0.41), residues: 149 loop : -0.70 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 202 TYR 0.014 0.002 TYR 2 239 PHE 0.017 0.002 PHE D 176 TRP 0.022 0.002 TRP G 180 HIS 0.007 0.001 HIS D 464 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 9763) covalent geometry : angle 0.60008 (13257) SS BOND : bond 0.00370 ( 28) SS BOND : angle 1.29218 ( 56) hydrogen bonds : bond 0.03366 ( 377) hydrogen bonds : angle 4.83952 ( 1122) Misc. bond : bond 0.07840 ( 2) link_BETA1-4 : bond 0.00267 ( 3) link_BETA1-4 : angle 1.54459 ( 9) link_NAG-ASN : bond 0.00228 ( 7) link_NAG-ASN : angle 1.66283 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.8032 (pt0) cc_final: 0.6880 (mm-30) REVERT: 2 255 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: 2 308 ASP cc_start: 0.8059 (t0) cc_final: 0.7768 (t0) REVERT: D 190 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7088 (mt) REVERT: D 245 LYS cc_start: 0.7680 (tmtt) cc_final: 0.6826 (mppt) REVERT: D 344 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6538 (mt0) REVERT: D 352 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8208 (tmtm) REVERT: D 358 ASN cc_start: 0.7904 (m-40) cc_final: 0.7634 (m-40) REVERT: D 381 ARG cc_start: 0.7370 (ttp80) cc_final: 0.5647 (ptt180) REVERT: G 204 SER cc_start: 0.8322 (p) cc_final: 0.7923 (t) REVERT: G 218 SER cc_start: 0.8633 (t) cc_final: 0.8236 (m) REVERT: G 249 ASP cc_start: 0.7582 (t70) cc_final: 0.6995 (p0) REVERT: G 286 GLU cc_start: 0.8535 (pt0) cc_final: 0.8318 (pt0) REVERT: G 344 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: G 381 ARG cc_start: 0.8235 (tmm-80) cc_final: 0.7726 (ttp80) REVERT: G 392 ARG cc_start: 0.7688 (tmm160) cc_final: 0.6991 (ttm-80) REVERT: A 56 LYS cc_start: 0.7904 (tttt) cc_final: 0.7423 (mttm) REVERT: B 22 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7174 (mt-10) REVERT: B 65 LYS cc_start: 0.8539 (tttp) cc_final: 0.8286 (tttt) REVERT: B 120 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8048 (pptt) REVERT: B 121 GLU cc_start: 0.8693 (tt0) cc_final: 0.8104 (mt-10) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.5693 time to fit residues: 79.6070 Evaluate side-chains 134 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 126 LEU Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 275 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 352 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 98 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.150162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111692 restraints weight = 10554.109| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.80 r_work: 0.3231 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9803 Z= 0.199 Angle : 0.609 6.636 13343 Z= 0.315 Chirality : 0.045 0.184 1440 Planarity : 0.004 0.050 1691 Dihedral : 6.201 75.524 1503 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 2.92 % Allowed : 20.62 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.24), residues: 1198 helix: 1.42 (0.29), residues: 329 sheet: -1.35 (0.41), residues: 149 loop : -0.70 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 202 TYR 0.013 0.002 TYR 2 239 PHE 0.011 0.002 PHE 2 280 TRP 0.022 0.002 TRP G 180 HIS 0.006 0.001 HIS D 464 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9763) covalent geometry : angle 0.59984 (13257) SS BOND : bond 0.00366 ( 28) SS BOND : angle 1.31780 ( 56) hydrogen bonds : bond 0.03394 ( 377) hydrogen bonds : angle 4.87003 ( 1122) Misc. bond : bond 0.07593 ( 2) link_BETA1-4 : bond 0.00252 ( 3) link_BETA1-4 : angle 1.48268 ( 9) link_NAG-ASN : bond 0.00218 ( 7) link_NAG-ASN : angle 1.66411 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3632.40 seconds wall clock time: 62 minutes 36.02 seconds (3756.02 seconds total)