Starting phenix.real_space_refine on Fri Jan 17 23:27:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmw_38490/01_2025/8xmw_38490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmw_38490/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmw_38490/01_2025/8xmw_38490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmw_38490/01_2025/8xmw_38490.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmw_38490/01_2025/8xmw_38490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmw_38490/01_2025/8xmw_38490.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.95, per 1000 atoms: 0.62 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.04 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: 2.79 Time building geometry restraints manager: 2.79 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 23.650 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- 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 0.050 9763 Z= 0.314 Angle : 0.657 6.909 13257 Z= 0.351 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (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 TRP 0.012 0.002 TRP 2 310 HIS 0.016 0.001 HIS A 122 PHE 0.022 0.002 PHE A 46 TYR 0.019 0.002 TYR D 424 ARG 0.003 0.000 ARG G 392 *********************** 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 : 1.045 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: -0.0282 (p0) REVERT: 2 111 LYS cc_start: 0.0737 (mtmt) cc_final: 0.0324 (mtmt) REVERT: 2 128 THR cc_start: 0.1244 (p) cc_final: 0.0651 (p) REVERT: 2 306 GLU cc_start: 0.3789 (mp0) cc_final: 0.3531 (mp0) REVERT: 2 321 SER cc_start: -0.1027 (t) cc_final: -0.1423 (p) REVERT: D 159 MET cc_start: 0.6592 (ttp) cc_final: 0.6359 (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: 0.7785 (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: 0.6988 (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: 0.6649 (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: 1.5841 time to fit residues: 359.3312 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 : 0.956 ------------------------------------------------------------------------------- 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 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.0870 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.147860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109841 restraints weight = 10384.902| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.70 r_work: 0.3013 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9763 Z= 0.278 Angle : 0.602 6.353 13257 Z= 0.316 Chirality : 0.044 0.183 1440 Planarity : 0.004 0.044 1691 Dihedral : 7.347 80.054 1507 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 3.22 % Allowed : 11.57 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1198 helix: 1.34 (0.29), residues: 329 sheet: -0.98 (0.38), residues: 170 loop : -0.83 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 402 HIS 0.013 0.001 HIS A 122 PHE 0.012 0.001 PHE A 46 TYR 0.013 0.001 TYR 2 239 ARG 0.003 0.001 ARG 2 202 *********************** 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 187 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7701 (pt0) cc_final: 0.6533 (mm-30) REVERT: 2 266 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: 2 307 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: D 159 MET cc_start: 0.6752 (ttp) cc_final: 0.6353 (ttp) REVERT: D 167 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6677 (ttt) REVERT: D 187 ASN cc_start: 0.8106 (t0) cc_final: 0.7374 (t0) REVERT: D 245 LYS cc_start: 0.7697 (tmtt) cc_final: 0.6885 (mppt) REVERT: D 260 LYS cc_start: 0.8379 (tttp) cc_final: 0.7511 (ttpt) REVERT: D 344 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7455 (mt0) REVERT: D 435 THR cc_start: 0.8425 (t) cc_final: 0.8127 (m) REVERT: G 204 SER cc_start: 0.8261 (p) cc_final: 0.7864 (t) REVERT: G 218 SER cc_start: 0.8542 (t) cc_final: 0.8190 (m) REVERT: G 392 ARG cc_start: 0.7475 (tmm160) cc_final: 0.6804 (ttm-80) REVERT: A 42 TYR cc_start: 0.9278 (m-80) cc_final: 0.9062 (m-80) REVERT: A 56 LYS cc_start: 0.7681 (tttt) cc_final: 0.7406 (tptt) REVERT: A 60 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8561 (tptm) REVERT: A 127 LYS cc_start: 0.8644 (mttm) cc_final: 0.8430 (mtmm) REVERT: B 22 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7011 (mt-10) REVERT: B 65 LYS cc_start: 0.8524 (tttp) cc_final: 0.8277 (tttt) REVERT: B 121 GLU cc_start: 0.8516 (tt0) cc_final: 0.7966 (mt-10) outliers start: 32 outliers final: 9 residues processed: 173 average time/residue: 1.5025 time to fit residues: 275.8698 Evaluate side-chains 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 60 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.161936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127431 restraints weight = 10309.111| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.48 r_work: 0.3104 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2957 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2957 r_free = 0.2957 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2957 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9763 Z= 0.277 Angle : 0.590 6.320 13257 Z= 0.307 Chirality : 0.044 0.189 1440 Planarity : 0.004 0.042 1691 Dihedral : 6.873 77.389 1503 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 3.12 % Allowed : 15.79 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1198 helix: 1.40 (0.29), residues: 329 sheet: -1.24 (0.38), residues: 162 loop : -0.79 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 436 HIS 0.009 0.001 HIS A 122 PHE 0.012 0.001 PHE 2 280 TYR 0.013 0.002 TYR 2 239 ARG 0.006 0.001 ARG 2 202 *********************** 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 170 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7753 (pt0) cc_final: 0.6504 (mm-30) REVERT: 2 266 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8497 (mtpt) REVERT: 2 307 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7979 (pt0) REVERT: D 167 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6555 (ttt) REVERT: D 187 ASN cc_start: 0.8117 (t0) cc_final: 0.7321 (t0) REVERT: D 245 LYS cc_start: 0.7660 (tmtt) cc_final: 0.6830 (mppt) REVERT: D 260 LYS cc_start: 0.8381 (tttp) cc_final: 0.7515 (ttpt) REVERT: D 306 GLN cc_start: 0.7571 (tt0) cc_final: 0.7345 (tt0) REVERT: D 344 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: G 204 SER cc_start: 0.8241 (p) cc_final: 0.7853 (t) REVERT: G 218 SER cc_start: 0.8594 (t) cc_final: 0.8210 (m) REVERT: G 392 ARG cc_start: 0.7440 (tmm160) cc_final: 0.6747 (ttm-80) REVERT: A 56 LYS cc_start: 0.7668 (tttt) cc_final: 0.7334 (tptt) REVERT: A 78 ASN cc_start: 0.8695 (m-40) cc_final: 0.8353 (m-40) REVERT: A 127 LYS cc_start: 0.8514 (mttm) cc_final: 0.8281 (mtmm) REVERT: B 22 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6947 (mt-10) REVERT: B 65 LYS cc_start: 0.8419 (tttp) cc_final: 0.8152 (tttt) REVERT: B 121 GLU cc_start: 0.8478 (tt0) cc_final: 0.7952 (mt-10) outliers start: 31 outliers final: 13 residues processed: 160 average time/residue: 1.5698 time to fit residues: 265.7544 Evaluate side-chains 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117033 restraints weight = 10350.960| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.82 r_work: 0.3055 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 9763 Z= 0.301 Angle : 0.587 6.409 13257 Z= 0.306 Chirality : 0.044 0.185 1440 Planarity : 0.004 0.043 1691 Dihedral : 6.636 76.011 1503 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 3.32 % Allowed : 16.20 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.24), residues: 1198 helix: 1.39 (0.29), residues: 329 sheet: -1.44 (0.41), residues: 137 loop : -0.81 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 180 HIS 0.008 0.001 HIS A 122 PHE 0.012 0.001 PHE 2 280 TYR 0.015 0.002 TYR 2 183 ARG 0.008 0.001 ARG 2 202 *********************** 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 174 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7862 (pt0) cc_final: 0.6673 (mm-30) REVERT: 2 255 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: 2 266 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8594 (mtpt) REVERT: 2 307 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: D 167 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6600 (ttt) REVERT: D 187 ASN cc_start: 0.8179 (t0) cc_final: 0.7393 (t0) REVERT: D 245 LYS cc_start: 0.7640 (tmtt) cc_final: 0.6828 (mppt) REVERT: D 260 LYS cc_start: 0.8427 (tttp) cc_final: 0.7579 (ttpt) REVERT: D 306 GLN cc_start: 0.7650 (tt0) cc_final: 0.7449 (tt0) REVERT: D 344 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7197 (mt0) REVERT: G 204 SER cc_start: 0.8288 (p) cc_final: 0.7906 (t) REVERT: G 218 SER cc_start: 0.8612 (t) cc_final: 0.8248 (m) REVERT: G 249 ASP cc_start: 0.7736 (t0) cc_final: 0.7390 (t70) REVERT: G 344 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7447 (mm-40) REVERT: G 392 ARG cc_start: 0.7605 (tmm160) cc_final: 0.6825 (ttm-80) REVERT: A 56 LYS cc_start: 0.7822 (tttt) cc_final: 0.7332 (mttm) REVERT: A 61 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8200 (mtpt) REVERT: A 78 ASN cc_start: 0.8775 (m-40) cc_final: 0.8433 (m-40) REVERT: A 127 LYS cc_start: 0.8634 (mttm) cc_final: 0.8397 (mtmm) REVERT: B 22 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7088 (mt-10) REVERT: B 65 LYS cc_start: 0.8515 (tttp) cc_final: 0.8255 (tttt) REVERT: B 121 GLU cc_start: 0.8635 (tt0) cc_final: 0.8095 (mt-10) outliers start: 33 outliers final: 15 residues processed: 161 average time/residue: 1.5483 time to fit residues: 264.2695 Evaluate side-chains 147 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 266 LYS Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain 2 residue 331 VAL 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 D residue 461 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 61 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.153459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115668 restraints weight = 10385.401| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.72 r_work: 0.3067 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9763 Z= 0.280 Angle : 0.579 6.300 13257 Z= 0.300 Chirality : 0.044 0.185 1440 Planarity : 0.004 0.043 1691 Dihedral : 6.412 73.652 1503 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 3.32 % Allowed : 17.40 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1198 helix: 1.47 (0.29), residues: 329 sheet: -1.44 (0.41), residues: 137 loop : -0.79 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 180 HIS 0.006 0.001 HIS 2 124 PHE 0.011 0.001 PHE 2 280 TYR 0.014 0.002 TYR D 354 ARG 0.008 0.001 ARG 2 202 *********************** 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 173 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7912 (pt0) cc_final: 0.6783 (mm-30) REVERT: 2 213 TYR cc_start: 0.9239 (m-80) cc_final: 0.9002 (m-80) REVERT: 2 255 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: 2 307 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: D 245 LYS cc_start: 0.7658 (tmtt) cc_final: 0.6846 (mppt) REVERT: D 306 GLN cc_start: 0.7622 (tt0) cc_final: 0.7406 (tt0) REVERT: D 344 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: D 358 ASN cc_start: 0.7850 (m-40) cc_final: 0.7569 (m-40) REVERT: D 381 ARG cc_start: 0.7191 (ttp80) cc_final: 0.5578 (ptt180) REVERT: G 204 SER cc_start: 0.8274 (p) cc_final: 0.7888 (t) REVERT: G 218 SER cc_start: 0.8595 (t) cc_final: 0.8229 (m) REVERT: G 344 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7728 (mm-40) REVERT: G 392 ARG cc_start: 0.7540 (tmm160) cc_final: 0.6811 (ttm-80) REVERT: G 466 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 56 LYS cc_start: 0.7801 (tttt) cc_final: 0.7347 (mttm) REVERT: A 61 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8210 (mtpt) REVERT: A 78 ASN cc_start: 0.8771 (m-40) cc_final: 0.8437 (m-40) REVERT: A 127 LYS cc_start: 0.8648 (mttm) cc_final: 0.8400 (mtmm) REVERT: B 22 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7119 (mt-10) REVERT: B 65 LYS cc_start: 0.8534 (tttp) cc_final: 0.8279 (tttt) REVERT: B 120 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.7906 (pptt) REVERT: B 121 GLU cc_start: 0.8632 (tt0) cc_final: 0.8073 (mt-10) outliers start: 33 outliers final: 14 residues processed: 160 average time/residue: 1.4288 time to fit residues: 243.1934 Evaluate side-chains 142 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 344 GLN 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 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** D 199 GLN G 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.152158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112883 restraints weight = 10397.944| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.90 r_work: 0.3203 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9763 Z= 0.320 Angle : 0.594 6.503 13257 Z= 0.308 Chirality : 0.045 0.187 1440 Planarity : 0.004 0.046 1691 Dihedral : 6.363 72.114 1503 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 3.22 % Allowed : 18.61 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1198 helix: 1.40 (0.29), residues: 329 sheet: -1.63 (0.42), residues: 129 loop : -0.83 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 180 HIS 0.007 0.001 HIS A 122 PHE 0.014 0.002 PHE D 176 TYR 0.014 0.002 TYR 2 239 ARG 0.011 0.001 ARG 2 202 *********************** 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 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7889 (pt0) cc_final: 0.6665 (mm-30) REVERT: 2 213 TYR cc_start: 0.9252 (m-80) cc_final: 0.9012 (m-80) REVERT: 2 307 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: 2 342 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.8033 (pttt) REVERT: D 167 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6528 (ttt) REVERT: D 245 LYS cc_start: 0.7599 (tmtt) cc_final: 0.6856 (mppt) REVERT: D 344 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6507 (mt0) REVERT: D 358 ASN cc_start: 0.7853 (m-40) cc_final: 0.7549 (m-40) REVERT: G 204 SER cc_start: 0.8246 (p) cc_final: 0.7863 (t) REVERT: G 218 SER cc_start: 0.8618 (t) cc_final: 0.8230 (m) REVERT: G 249 ASP cc_start: 0.7811 (t0) cc_final: 0.7459 (t70) REVERT: G 344 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7691 (mm-40) REVERT: G 392 ARG cc_start: 0.7523 (tmm160) cc_final: 0.6728 (ttm-80) REVERT: G 466 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 56 LYS cc_start: 0.7760 (tttt) cc_final: 0.7232 (mttm) REVERT: A 61 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: A 78 ASN cc_start: 0.8731 (m-40) cc_final: 0.8370 (m-40) REVERT: A 127 LYS cc_start: 0.8575 (mttm) cc_final: 0.8313 (mtmm) REVERT: A 141 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7560 (ptm-80) REVERT: B 22 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7025 (mt-10) REVERT: B 65 LYS cc_start: 0.8425 (tttp) cc_final: 0.8157 (tttt) REVERT: B 120 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7859 (pptt) REVERT: B 121 GLU cc_start: 0.8629 (tt0) cc_final: 0.8003 (mt-10) outliers start: 32 outliers final: 16 residues processed: 152 average time/residue: 1.5004 time to fit residues: 242.2463 Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain 2 residue 342 LYS 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 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 75 LEU 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 37 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.152569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114802 restraints weight = 10562.945| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.73 r_work: 0.3054 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9763 Z= 0.290 Angle : 0.580 6.430 13257 Z= 0.302 Chirality : 0.044 0.184 1440 Planarity : 0.004 0.046 1691 Dihedral : 6.235 72.570 1503 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 3.12 % Allowed : 19.11 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1198 helix: 1.47 (0.29), residues: 329 sheet: -1.53 (0.41), residues: 139 loop : -0.78 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 180 HIS 0.006 0.001 HIS A 122 PHE 0.025 0.002 PHE D 176 TYR 0.013 0.002 TYR 2 239 ARG 0.009 0.001 ARG 2 202 *********************** 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 164 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7917 (pt0) cc_final: 0.6810 (mm-30) REVERT: 2 213 TYR cc_start: 0.9239 (m-80) cc_final: 0.9010 (m-80) REVERT: 2 255 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: D 245 LYS cc_start: 0.7627 (tmtt) cc_final: 0.7022 (mppt) REVERT: D 344 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6540 (mt0) REVERT: D 358 ASN cc_start: 0.7852 (m-40) cc_final: 0.7535 (m-40) REVERT: D 381 ARG cc_start: 0.7178 (ttp80) cc_final: 0.5552 (ptt180) REVERT: G 204 SER cc_start: 0.8281 (p) cc_final: 0.7893 (t) REVERT: G 218 SER cc_start: 0.8628 (t) cc_final: 0.8249 (m) REVERT: G 344 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: G 392 ARG cc_start: 0.7592 (tmm160) cc_final: 0.6836 (mtm180) REVERT: G 466 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7562 (mm-30) REVERT: A 56 LYS cc_start: 0.7860 (tttt) cc_final: 0.7355 (mttm) REVERT: A 61 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8221 (mtpt) REVERT: A 78 ASN cc_start: 0.8770 (m-40) cc_final: 0.8445 (m-40) REVERT: B 22 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7136 (mt-10) REVERT: B 65 LYS cc_start: 0.8521 (tttp) cc_final: 0.8266 (tttt) REVERT: B 120 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.7989 (pptt) REVERT: B 121 GLU cc_start: 0.8695 (tt0) cc_final: 0.8095 (mt-10) outliers start: 31 outliers final: 16 residues processed: 154 average time/residue: 1.4183 time to fit residues: 232.9631 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 : 1.021 ------------------------------------------------------------------------------- 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 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 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain B residue 75 LEU 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 70 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 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 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.152948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.115244 restraints weight = 10558.356| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.73 r_work: 0.3033 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9763 Z= 0.271 Angle : 0.579 6.284 13257 Z= 0.301 Chirality : 0.044 0.180 1440 Planarity : 0.004 0.047 1691 Dihedral : 6.176 73.232 1503 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 2.82 % Allowed : 19.52 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1198 helix: 1.48 (0.29), residues: 329 sheet: -1.37 (0.40), residues: 149 loop : -0.78 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 180 HIS 0.005 0.001 HIS A 122 PHE 0.025 0.001 PHE D 176 TYR 0.013 0.002 TYR 2 239 ARG 0.011 0.001 ARG 2 202 *********************** 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 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.8026 (pt0) cc_final: 0.6883 (mm-30) REVERT: 2 213 TYR cc_start: 0.9242 (m-80) cc_final: 0.9008 (m-80) REVERT: 2 255 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: D 245 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7038 (mppt) REVERT: D 344 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6536 (mt0) REVERT: D 358 ASN cc_start: 0.7850 (m-40) cc_final: 0.7566 (m110) REVERT: D 381 ARG cc_start: 0.7197 (ttp80) cc_final: 0.5562 (ptt180) REVERT: G 204 SER cc_start: 0.8275 (p) cc_final: 0.7889 (t) REVERT: G 218 SER cc_start: 0.8628 (t) cc_final: 0.8243 (m) REVERT: G 381 ARG cc_start: 0.8223 (tmm-80) cc_final: 0.7649 (ttp80) REVERT: G 392 ARG cc_start: 0.7569 (tmm160) cc_final: 0.6901 (mtm180) REVERT: A 16 LYS cc_start: 0.8389 (tppt) cc_final: 0.8055 (mmtt) REVERT: A 56 LYS cc_start: 0.7850 (tttt) cc_final: 0.7371 (mttm) REVERT: A 61 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8211 (mtpt) REVERT: A 141 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7666 (ptm-80) REVERT: B 22 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7153 (mt-10) REVERT: B 65 LYS cc_start: 0.8511 (tttp) cc_final: 0.8254 (tttt) REVERT: B 120 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8010 (pptt) REVERT: B 121 GLU cc_start: 0.8671 (tt0) cc_final: 0.8109 (mt-10) outliers start: 28 outliers final: 15 residues processed: 145 average time/residue: 1.4029 time to fit residues: 216.5978 Evaluate side-chains 136 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 255 GLU 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 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 141 ARG 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 66 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 0.0060 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 327 HIS D 356 ASN D 464 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.161793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127907 restraints weight = 10254.288| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.44 r_work: 0.3112 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9763 Z= 0.236 Angle : 0.568 6.018 13257 Z= 0.295 Chirality : 0.043 0.177 1440 Planarity : 0.004 0.049 1691 Dihedral : 6.087 73.381 1503 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 2.41 % Allowed : 20.22 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.25), residues: 1198 helix: 1.54 (0.29), residues: 329 sheet: -1.35 (0.38), residues: 159 loop : -0.79 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 180 HIS 0.005 0.001 HIS D 327 PHE 0.022 0.001 PHE D 176 TYR 0.012 0.001 TYR 2 239 ARG 0.011 0.001 ARG 2 202 *********************** 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 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7866 (pt0) cc_final: 0.6660 (mm-30) REVERT: 2 213 TYR cc_start: 0.9194 (m-80) cc_final: 0.8955 (m-80) REVERT: 2 255 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: D 245 LYS cc_start: 0.7565 (tmtt) cc_final: 0.6956 (mppt) REVERT: D 344 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6450 (mt0) REVERT: D 358 ASN cc_start: 0.7798 (m-40) cc_final: 0.7536 (m-40) REVERT: D 381 ARG cc_start: 0.7178 (ttp80) cc_final: 0.5509 (ptt180) REVERT: G 204 SER cc_start: 0.8210 (p) cc_final: 0.7828 (t) REVERT: G 218 SER cc_start: 0.8567 (t) cc_final: 0.8158 (m) REVERT: G 286 GLU cc_start: 0.8317 (pt0) cc_final: 0.8034 (pt0) REVERT: G 381 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7630 (ttp80) REVERT: G 392 ARG cc_start: 0.7418 (tmm160) cc_final: 0.6781 (mtm180) REVERT: A 16 LYS cc_start: 0.8219 (tppt) cc_final: 0.7951 (mmtt) REVERT: A 56 LYS cc_start: 0.7706 (tttt) cc_final: 0.7236 (mttm) REVERT: A 61 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8065 (mtpt) REVERT: A 99 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8470 (mptm) REVERT: A 141 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7566 (ptm-80) REVERT: B 22 GLU cc_start: 0.7444 (mm-30) cc_final: 0.6993 (mt-10) REVERT: B 65 LYS cc_start: 0.8397 (tttp) cc_final: 0.8128 (tttt) REVERT: B 87 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7879 (m) REVERT: B 120 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7920 (pptt) REVERT: B 121 GLU cc_start: 0.8531 (tt0) cc_final: 0.7999 (mt-10) outliers start: 24 outliers final: 14 residues processed: 147 average time/residue: 1.3990 time to fit residues: 219.1728 Evaluate side-chains 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 344 GLN 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 THR 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 28 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.127031 restraints weight = 10421.577| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.57 r_work: 0.3082 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9763 Z= 0.244 Angle : 0.576 6.295 13257 Z= 0.300 Chirality : 0.043 0.178 1440 Planarity : 0.004 0.050 1691 Dihedral : 6.085 73.948 1503 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 2.62 % Allowed : 20.32 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1198 helix: 1.53 (0.29), residues: 329 sheet: -1.32 (0.38), residues: 164 loop : -0.82 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 180 HIS 0.005 0.001 HIS 2 124 PHE 0.020 0.001 PHE D 176 TYR 0.012 0.001 TYR 2 239 ARG 0.011 0.001 ARG 2 202 ********************** 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 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7937 (pt0) cc_final: 0.6762 (mm-30) REVERT: 2 213 TYR cc_start: 0.9213 (m-80) cc_final: 0.8990 (m-80) REVERT: 2 255 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: D 245 LYS cc_start: 0.7618 (tmtt) cc_final: 0.6940 (mppt) REVERT: D 344 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6476 (mt0) REVERT: D 358 ASN cc_start: 0.7800 (m-40) cc_final: 0.7532 (m-40) REVERT: D 381 ARG cc_start: 0.7216 (ttp80) cc_final: 0.5559 (ptt180) REVERT: G 204 SER cc_start: 0.8237 (p) cc_final: 0.7856 (t) REVERT: G 218 SER cc_start: 0.8571 (t) cc_final: 0.8174 (m) REVERT: G 286 GLU cc_start: 0.8353 (pt0) cc_final: 0.8092 (pt0) REVERT: G 344 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7489 (mm-40) REVERT: G 381 ARG cc_start: 0.8182 (tmm-80) cc_final: 0.7662 (ttp80) REVERT: G 392 ARG cc_start: 0.7496 (tmm160) cc_final: 0.6836 (mtm180) REVERT: A 56 LYS cc_start: 0.7772 (tttt) cc_final: 0.7312 (mttm) REVERT: A 61 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: A 99 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8515 (mptm) REVERT: A 141 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7612 (ptm-80) REVERT: B 22 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7059 (mt-10) REVERT: B 65 LYS cc_start: 0.8450 (tttp) cc_final: 0.8190 (tttt) REVERT: B 87 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.7940 (m) REVERT: B 120 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7974 (pptt) REVERT: B 121 GLU cc_start: 0.8571 (tt0) cc_final: 0.8037 (mt-10) outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 1.3990 time to fit residues: 213.0878 Evaluate side-chains 141 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 255 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 344 GLN 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 THR 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 33 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.152856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113917 restraints weight = 10477.130| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.91 r_work: 0.3193 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9763 Z= 0.291 Angle : 0.593 6.242 13257 Z= 0.308 Chirality : 0.044 0.187 1440 Planarity : 0.004 0.050 1691 Dihedral : 6.169 75.263 1503 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.76 % Favored : 94.07 % Rotamer: Outliers : 2.62 % Allowed : 20.52 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1198 helix: 1.45 (0.29), residues: 329 sheet: -1.38 (0.40), residues: 154 loop : -0.80 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 180 HIS 0.005 0.001 HIS 2 124 PHE 0.019 0.002 PHE D 176 TYR 0.013 0.002 TYR 2 239 ARG 0.011 0.001 ARG 2 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7805.60 seconds wall clock time: 140 minutes 55.32 seconds (8455.32 seconds total)