Starting phenix.real_space_refine on Fri Jul 3 01:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmw_38490/07_2026/8xmw_38490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmw_38490/07_2026/8xmw_38490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2026/8xmw_38490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2026/8xmw_38490.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2026/8xmw_38490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2026/8xmw_38490.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2255 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 2 7.16 5 S 70 5.16 5 C 5978 2.51 5 N 1662 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9538 Number of models: 1 Model: "" Number of chains: 13 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2442 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 3, 'TRANS': 316} Chain: "G" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2442 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 3, 'TRANS': 316} Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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, 14 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 1.89, per 1000 atoms: 0.20 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: 0.95 Conformation dependent library (CDL) restraints added in 340.5 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 33.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain '2' and resid 141 through 146 Processing helix chain '2' and resid 154 through 159 removed outlier: 3.505A pdb=" N ALA 2 159 " --> pdb=" O ALA 2 155 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 255 Processing helix chain '2' and resid 259 through 263 removed outlier: 3.564A pdb=" N LYS 2 263 " --> pdb=" O PRO 2 260 " (cutoff:3.500A) Processing helix chain '2' and resid 333 through 346 removed outlier: 4.788A pdb=" N ASP 2 338 " --> pdb=" O THR 2 334 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N TRP 2 339 " --> pdb=" O SER 2 335 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU 2 346 " --> pdb=" O LYS 2 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.684A pdb=" N CYS D 238 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.658A pdb=" N ASP D 253 " --> pdb=" O HIS D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 Processing helix chain 'D' and resid 341 through 345 removed outlier: 3.600A pdb=" N GLN D 344 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS D 345 " --> pdb=" O ILE D 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 341 through 345' Processing helix chain 'D' and resid 356 through 360 removed outlier: 3.535A pdb=" N ASP D 360 " --> pdb=" O HIS D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 234 through 238 Processing helix chain 'G' and resid 259 through 263 Processing helix chain 'G' and resid 296 through 307 Processing helix chain 'G' and resid 356 through 360 Processing helix chain 'G' and resid 403 through 415 Processing helix chain 'G' and resid 448 through 452 Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.520A pdb=" N THR A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.706A pdb=" N PHE A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.993A pdb=" N LYS B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 35 removed outlier: 4.106A pdb=" N GLY B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLY B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 46 removed outlier: 3.937A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 57 through 77 Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.831A pdb=" N THR B 84 " --> pdb=" O ASN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.940A pdb=" N PHE B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 141 Processing sheet with id=AA1, first strand: chain '2' and resid 56 through 57 Processing sheet with id=AA2, first strand: chain '2' and resid 170 through 172 removed outlier: 4.112A pdb=" N LEU 2 164 " --> pdb=" O VAL 2 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 238 through 243 removed outlier: 7.846A pdb=" N VAL 2 219 " --> pdb=" O HIS 2 303 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N HIS 2 303 " --> pdb=" O VAL 2 219 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER 2 223 " --> pdb=" O ALA 2 299 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA 2 299 " --> pdb=" O SER 2 223 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY 2 314 " --> pdb=" O PHE 2 300 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL 2 302 " --> pdb=" O ALA 2 312 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA 2 312 " --> pdb=" O VAL 2 302 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASP 2 304 " --> pdb=" O TRP 2 310 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N TRP 2 310 " --> pdb=" O ASP 2 304 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL 2 329 " --> pdb=" O SER 2 317 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA5, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA6, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.682A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 269 removed outlier: 3.682A pdb=" N SER D 265 " --> pdb=" O ARG D 282 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 279 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 290 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N TRP D 287 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N LEU D 330 " --> pdb=" O TRP D 287 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N THR D 289 " --> pdb=" O LEU D 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 371 through 377 removed outlier: 3.983A pdb=" N LYS D 421 " --> pdb=" O THR D 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 371 through 377 removed outlier: 6.059A pdb=" N VAL D 386 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU D 437 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS D 396 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N LEU D 439 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AB2, first strand: chain 'G' and resid 159 through 162 Processing sheet with id=AB3, first strand: chain 'G' and resid 265 through 269 removed outlier: 3.621A pdb=" N SER G 265 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 265 through 269 removed outlier: 3.621A pdb=" N SER G 265 " --> pdb=" O ARG G 282 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU G 279 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 290 " --> pdb=" O LEU G 279 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 286 " --> pdb=" O PHE G 283 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N HIS G 327 " --> pdb=" O TRP G 287 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 371 through 380 removed outlier: 3.655A pdb=" N GLY G 378 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA G 383 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 371 through 380 removed outlier: 3.655A pdb=" N GLY G 378 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA G 383 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL G 386 " --> pdb=" O VAL G 397 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL G 397 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N LEU G 437 " --> pdb=" O LEU G 394 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 396 " --> pdb=" O LEU G 437 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.21 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 3.250 nonbonded pdb=" NH2 ARG D 412 " pdb=" O GLY D 444 " model vdw 2.241 3.120 nonbonded pdb=" O PHE A 117 " pdb=" NH2 ARG B 30 " model vdw 2.242 3.120 ... (remaining 83661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.66 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.410 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 9803 Z= 0.211 Angle : 0.667 6.909 13343 Z= 0.354 Chirality : 0.046 0.398 1440 Planarity : 0.005 0.062 1691 Dihedral : 13.866 87.291 3577 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 0.30 % Allowed : 0.10 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1198 helix: 1.12 (0.29), residues: 323 sheet: -0.72 (0.41), residues: 162 loop : -1.04 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 392 TYR 0.019 0.002 TYR D 424 PHE 0.022 0.002 PHE A 46 TRP 0.012 0.002 TRP 2 310 HIS 0.016 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 9763) covalent geometry : angle 0.65697 / 0.35 (13257) SS BOND : bond 0.00322 / 0.21 ( 28) SS BOND : angle 1.47542 / 0.96 ( 56) hydrogen bonds : bond 0.16888 / 11.42 ( 377) hydrogen bonds : angle 7.10949 / 4.99 ( 1122) Misc. bond : bond 0.08787 / 4.26 ( 2) link_BETA1-4 : bond 0.00715 / 0.28 ( 3) link_BETA1-4 : angle 1.51673 / 0.74 ( 9) link_NAG-ASN : bond 0.00425 / 0.19 ( 7) link_NAG-ASN : angle 1.87625 / 1.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.1603 (pt0) cc_final: 0.1182 (mm-30) REVERT: 2 95 ASN cc_start: 0.0335 (p0) cc_final: -0.0285 (p0) REVERT: 2 111 LYS cc_start: 0.0737 (mtmt) cc_final: 0.0314 (mtmt) REVERT: 2 128 THR cc_start: 0.1243 (p) cc_final: 0.0658 (p) REVERT: 2 306 GLU cc_start: 0.3788 (mp0) cc_final: 0.3516 (mp0) REVERT: 2 321 SER cc_start: -0.1028 (t) cc_final: -0.1434 (p) REVERT: D 159 MET cc_start: 0.6592 (ttp) cc_final: 0.6360 (ttp) REVERT: D 187 ASN cc_start: 0.7924 (t0) cc_final: 0.7405 (t0) REVERT: D 245 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7253 (mppt) REVERT: D 260 LYS cc_start: 0.8388 (tttp) cc_final: 0.7786 (ttpt) REVERT: G 204 SER cc_start: 0.8549 (p) cc_final: 0.8129 (t) REVERT: G 218 SER cc_start: 0.8716 (t) cc_final: 0.8380 (m) REVERT: G 392 ARG cc_start: 0.7496 (tmm160) cc_final: 0.6991 (mtm180) REVERT: A 42 TYR cc_start: 0.9233 (m-80) cc_final: 0.8995 (m-80) REVERT: A 56 LYS cc_start: 0.7523 (tttt) cc_final: 0.7278 (tptt) REVERT: A 61 LYS cc_start: 0.8426 (mttt) cc_final: 0.8168 (mtpt) REVERT: A 141 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6648 (mtp-110) REVERT: B 22 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6887 (mt-10) REVERT: B 65 LYS cc_start: 0.8416 (tttp) cc_final: 0.8205 (tttt) REVERT: B 121 GLU cc_start: 0.8161 (tt0) cc_final: 0.7737 (mt-10) outliers start: 3 outliers final: 0 residues processed: 215 average time/residue: 0.6752 time to fit residues: 153.3017 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 : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3551 r_free = 0.3551 target = 0.146687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108333 restraints weight = 10352.769| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.68 r_work: 0.2996 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 9803 Z= 0.225 Angle : 0.642 6.850 13343 Z= 0.335 Chirality : 0.045 0.185 1440 Planarity : 0.004 0.046 1691 Dihedral : 7.463 80.303 1507 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.76 % Favored : 94.07 % Rotamer: Outliers : 3.42 % Allowed : 11.67 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.24), residues: 1198 helix: 1.20 (0.29), residues: 329 sheet: -1.03 (0.38), residues: 170 loop : -0.88 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 2 252 TYR 0.016 0.002 TYR 2 239 PHE 0.015 0.002 PHE A 46 TRP 0.010 0.002 TRP D 402 HIS 0.015 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 ( 9763) covalent geometry : angle 0.63381 / 0.33 (13257) SS BOND : bond 0.00411 / 0.25 ( 28) SS BOND : angle 1.37515 / 0.88 ( 56) hydrogen bonds : bond 0.04208 / 2.78 ( 377) hydrogen bonds : angle 5.35061 / 3.77 ( 1122) Misc. bond : bond 0.07432 / 3.63 ( 2) link_BETA1-4 : bond 0.00195 / 0.09 ( 3) link_BETA1-4 : angle 1.35118 / 0.65 ( 9) link_NAG-ASN : bond 0.00315 / 0.17 ( 7) link_NAG-ASN : angle 1.56358 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7762 (pt0) cc_final: 0.6537 (mm-30) REVERT: 2 266 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8680 (mtpt) REVERT: 2 307 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: 2 308 ASP cc_start: 0.7648 (t0) cc_final: 0.7434 (t0) REVERT: D 159 MET cc_start: 0.6852 (ttp) cc_final: 0.6415 (ttp) REVERT: D 167 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6696 (ttt) REVERT: D 187 ASN cc_start: 0.8119 (t0) cc_final: 0.7455 (t0) REVERT: D 245 LYS cc_start: 0.7726 (tmtt) cc_final: 0.6886 (mppt) REVERT: D 260 LYS cc_start: 0.8379 (tttp) cc_final: 0.7504 (ttpt) REVERT: D 344 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7380 (mt0) REVERT: G 204 SER cc_start: 0.8283 (p) cc_final: 0.7884 (t) REVERT: G 218 SER cc_start: 0.8556 (t) cc_final: 0.8201 (m) REVERT: G 392 ARG cc_start: 0.7537 (tmm160) cc_final: 0.6827 (ttm-80) REVERT: A 42 TYR cc_start: 0.9297 (m-80) cc_final: 0.9010 (m-80) REVERT: A 56 LYS cc_start: 0.7717 (tttt) cc_final: 0.7426 (tptt) REVERT: A 78 ASN cc_start: 0.8704 (m-40) cc_final: 0.8372 (m-40) REVERT: A 127 LYS cc_start: 0.8680 (mttm) cc_final: 0.8433 (mtmm) REVERT: B 22 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6993 (mt-10) REVERT: B 65 LYS cc_start: 0.8547 (tttp) cc_final: 0.8306 (tttt) REVERT: B 121 GLU cc_start: 0.8539 (tt0) cc_final: 0.7981 (mt-10) outliers start: 34 outliers final: 10 residues processed: 166 average time/residue: 0.6919 time to fit residues: 121.6857 Evaluate side-chains 140 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 266 LYS Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 447 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3642 r_free = 0.3642 target = 0.150967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.112602 restraints weight = 10332.775| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.73 r_work: 0.3248 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 9803 Z= 0.246 Angle : 0.653 7.212 13343 Z= 0.337 Chirality : 0.046 0.196 1440 Planarity : 0.004 0.047 1691 Dihedral : 7.132 78.886 1503 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.84 % Favored : 93.99 % Rotamer: Outliers : 3.82 % Allowed : 15.29 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.24), residues: 1198 helix: 1.16 (0.29), residues: 329 sheet: -1.30 (0.38), residues: 162 loop : -0.90 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 202 TYR 0.016 0.002 TYR 2 239 PHE 0.015 0.002 PHE A 46 TRP 0.012 0.002 TRP D 402 HIS 0.012 0.002 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 ( 9763) covalent geometry : angle 0.64339 / 0.33 (13257) SS BOND : bond 0.00438 / 0.29 ( 28) SS BOND : angle 1.45900 / 0.94 ( 56) hydrogen bonds : bond 0.03853 / 2.52 ( 377) hydrogen bonds : angle 5.15415 / 3.63 ( 1122) Misc. bond : bond 0.08526 / 4.13 ( 2) link_BETA1-4 : bond 0.00263 / 0.11 ( 3) link_BETA1-4 : angle 1.52241 / 0.74 ( 9) link_NAG-ASN : bond 0.00310 / 0.15 ( 7) link_NAG-ASN : angle 1.76599 / 1.09 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7898 (pt0) cc_final: 0.6764 (mm-30) REVERT: 2 307 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: 2 308 ASP cc_start: 0.7918 (t0) cc_final: 0.7662 (t0) REVERT: D 159 MET cc_start: 0.7056 (ttp) cc_final: 0.6467 (ttp) REVERT: D 167 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6715 (ttt) REVERT: D 245 LYS cc_start: 0.7685 (tmtt) cc_final: 0.7012 (mppt) REVERT: D 260 LYS cc_start: 0.8451 (tttp) cc_final: 0.7605 (ttpt) REVERT: D 306 GLN cc_start: 0.7815 (tt0) cc_final: 0.7598 (tt0) REVERT: D 344 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: D 352 LYS cc_start: 0.8415 (tttp) cc_final: 0.8193 (tmtm) REVERT: G 204 SER cc_start: 0.8326 (p) cc_final: 0.7940 (t) REVERT: G 218 SER cc_start: 0.8657 (t) cc_final: 0.8303 (m) REVERT: G 325 PHE cc_start: 0.7683 (t80) cc_final: 0.7451 (m-80) REVERT: G 344 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7587 (mm-40) REVERT: G 392 ARG cc_start: 0.7688 (tmm160) cc_final: 0.6895 (ttm-80) REVERT: A 56 LYS cc_start: 0.7821 (tttt) cc_final: 0.7556 (tptt) REVERT: A 60 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8627 (tptm) REVERT: A 61 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8188 (mtpt) REVERT: A 78 ASN cc_start: 0.8761 (m-40) cc_final: 0.8437 (m-40) REVERT: A 127 LYS cc_start: 0.8698 (mttm) cc_final: 0.8475 (mtmm) REVERT: B 22 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7138 (mt-10) REVERT: B 65 LYS cc_start: 0.8569 (tttp) cc_final: 0.8321 (tttt) REVERT: B 121 GLU cc_start: 0.8606 (tt0) cc_final: 0.8056 (mt-10) outliers start: 38 outliers final: 15 residues processed: 165 average time/residue: 0.6893 time to fit residues: 120.5585 Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain 2 residue 307 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain B residue 126 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS G 241 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123862 restraints weight = 10323.480| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.58 r_work: 0.3091 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9803 Z= 0.138 Angle : 0.572 6.345 13343 Z= 0.296 Chirality : 0.043 0.183 1440 Planarity : 0.004 0.042 1691 Dihedral : 6.616 77.214 1503 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 3.42 % Allowed : 17.20 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1198 helix: 1.48 (0.29), residues: 329 sheet: -1.46 (0.38), residues: 147 loop : -0.83 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 374 TYR 0.014 0.001 TYR 2 183 PHE 0.012 0.001 PHE 2 300 TRP 0.013 0.001 TRP D 402 HIS 0.006 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 9763) covalent geometry : angle 0.56533 / 0.29 (13257) SS BOND : bond 0.00253 / 0.17 ( 28) SS BOND : angle 1.12302 / 0.75 ( 56) hydrogen bonds : bond 0.03234 / 2.13 ( 377) hydrogen bonds : angle 4.89030 / 3.46 ( 1122) Misc. bond : bond 0.06145 / 3.08 ( 2) link_BETA1-4 : bond 0.00375 / 0.15 ( 3) link_BETA1-4 : angle 1.20927 / 0.59 ( 9) link_NAG-ASN : bond 0.00191 / 0.10 ( 7) link_NAG-ASN : angle 1.40076 / 0.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7784 (pt0) cc_final: 0.6621 (mm-30) REVERT: 2 255 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7737 (mt-10) REVERT: 2 307 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8078 (pt0) REVERT: 2 308 ASP cc_start: 0.7924 (t0) cc_final: 0.7714 (t0) REVERT: D 167 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6577 (ttt) REVERT: D 245 LYS cc_start: 0.7648 (tmtt) cc_final: 0.6854 (mppt) REVERT: D 252 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7103 (mm-30) REVERT: D 306 GLN cc_start: 0.7610 (tt0) cc_final: 0.7399 (tt0) REVERT: D 344 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7278 (mt0) REVERT: D 358 ASN cc_start: 0.7938 (m-40) cc_final: 0.7608 (m-40) REVERT: G 204 SER cc_start: 0.8239 (p) cc_final: 0.7850 (t) REVERT: G 218 SER cc_start: 0.8613 (t) cc_final: 0.8238 (m) REVERT: G 249 ASP cc_start: 0.7627 (t70) cc_final: 0.7339 (t70) REVERT: G 392 ARG cc_start: 0.7480 (tmm160) cc_final: 0.6808 (ttm-80) REVERT: A 56 LYS cc_start: 0.7741 (tttt) cc_final: 0.7441 (tptt) REVERT: A 78 ASN cc_start: 0.8732 (m-40) cc_final: 0.8391 (m-40) REVERT: A 84 SER cc_start: 0.9216 (t) cc_final: 0.8926 (m) REVERT: A 127 LYS cc_start: 0.8577 (mttm) cc_final: 0.8369 (mtmm) REVERT: B 22 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7066 (mt-10) REVERT: B 65 LYS cc_start: 0.8494 (tttp) cc_final: 0.8234 (tttt) REVERT: B 121 GLU cc_start: 0.8615 (tt0) cc_final: 0.8073 (mt-10) outliers start: 34 outliers final: 16 residues processed: 167 average time/residue: 0.5372 time to fit residues: 95.6731 Evaluate side-chains 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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 D residue 461 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 241 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 B residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3799 r_free = 0.3799 target = 0.163017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128825 restraints weight = 10289.250| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.47 r_work: 0.3052 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9803 Z= 0.136 Angle : 0.568 6.790 13343 Z= 0.293 Chirality : 0.043 0.176 1440 Planarity : 0.004 0.042 1691 Dihedral : 6.347 74.595 1503 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.32 % Allowed : 18.51 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1198 helix: 1.58 (0.29), residues: 329 sheet: -1.41 (0.39), residues: 147 loop : -0.82 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 202 TYR 0.013 0.001 TYR 2 183 PHE 0.014 0.001 PHE D 176 TRP 0.013 0.001 TRP D 402 HIS 0.005 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9763) covalent geometry : angle 0.55846 / 0.29 (13257) SS BOND : bond 0.00303 / 0.21 ( 28) SS BOND : angle 1.47069 / 1.19 ( 56) hydrogen bonds : bond 0.03114 / 2.05 ( 377) hydrogen bonds : angle 4.80052 / 3.41 ( 1122) Misc. bond : bond 0.05881 / 2.92 ( 2) link_BETA1-4 : bond 0.00336 / 0.14 ( 3) link_BETA1-4 : angle 1.21325 / 0.58 ( 9) link_NAG-ASN : bond 0.00166 / 0.09 ( 7) link_NAG-ASN : angle 1.43150 / 0.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7738 (pt0) cc_final: 0.6495 (mm-30) REVERT: 2 213 TYR cc_start: 0.9162 (m-80) cc_final: 0.8947 (m-80) REVERT: 2 255 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7688 (mt-10) REVERT: 2 307 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: 2 308 ASP cc_start: 0.7888 (t0) cc_final: 0.7657 (t0) REVERT: D 245 LYS cc_start: 0.7613 (tmtt) cc_final: 0.6802 (mppt) REVERT: D 344 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: D 358 ASN cc_start: 0.7819 (m-40) cc_final: 0.7493 (m-40) REVERT: G 204 SER cc_start: 0.8201 (p) cc_final: 0.7803 (t) REVERT: G 218 SER cc_start: 0.8602 (t) cc_final: 0.8201 (m) REVERT: G 249 ASP cc_start: 0.7600 (t70) cc_final: 0.7280 (t70) REVERT: G 392 ARG cc_start: 0.7389 (tmm160) cc_final: 0.6789 (ttm-80) REVERT: G 466 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 56 LYS cc_start: 0.7641 (tttt) cc_final: 0.7199 (mmtm) REVERT: A 78 ASN cc_start: 0.8689 (m-40) cc_final: 0.8341 (m-40) REVERT: B 22 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6956 (mt-10) REVERT: B 65 LYS cc_start: 0.8425 (tttp) cc_final: 0.8143 (tttt) REVERT: B 121 GLU cc_start: 0.8545 (tt0) cc_final: 0.7948 (mt-10) outliers start: 33 outliers final: 13 residues processed: 162 average time/residue: 0.6034 time to fit residues: 104.0489 Evaluate side-chains 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 307 GLU Chi-restraints excluded: chain 2 residue 331 VAL 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 167 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 5.9990 chunk 68 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 4 optimal weight: 0.2980 chunk 102 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN D 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.168872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135460 restraints weight = 10157.813| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.48 r_work: 0.3056 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9803 Z= 0.134 Angle : 0.561 5.767 13343 Z= 0.289 Chirality : 0.043 0.183 1440 Planarity : 0.004 0.048 1691 Dihedral : 6.158 73.490 1503 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 3.22 % Allowed : 18.71 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.25), residues: 1198 helix: 1.60 (0.29), residues: 329 sheet: -1.36 (0.40), residues: 147 loop : -0.78 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 202 TYR 0.012 0.001 TYR 2 183 PHE 0.023 0.001 PHE D 176 TRP 0.013 0.001 TRP D 402 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 ( 9763) covalent geometry : angle 0.55326 / 0.29 (13257) SS BOND : bond 0.00252 / 0.17 ( 28) SS BOND : angle 1.19720 / 0.93 ( 56) hydrogen bonds : bond 0.03058 / 2.03 ( 377) hydrogen bonds : angle 4.72538 / 3.35 ( 1122) Misc. bond : bond 0.05657 / 2.80 ( 2) link_BETA1-4 : bond 0.00325 / 0.14 ( 3) link_BETA1-4 : angle 1.25858 / 0.61 ( 9) link_NAG-ASN : bond 0.00164 / 0.09 ( 7) link_NAG-ASN : angle 1.42180 / 0.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7898 (pt0) cc_final: 0.6662 (mm-30) REVERT: 2 241 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8321 (mtp) REVERT: 2 255 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: 2 307 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8045 (pt0) REVERT: 2 308 ASP cc_start: 0.7880 (t0) cc_final: 0.7639 (t0) REVERT: D 167 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6464 (ttt) REVERT: D 245 LYS cc_start: 0.7606 (tmtt) cc_final: 0.6934 (mppt) REVERT: D 252 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6623 (tp30) REVERT: D 344 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6542 (mt0) REVERT: D 358 ASN cc_start: 0.7820 (m-40) cc_final: 0.7492 (m-40) REVERT: G 204 SER cc_start: 0.8219 (p) cc_final: 0.7819 (t) REVERT: G 218 SER cc_start: 0.8611 (t) cc_final: 0.8225 (m) REVERT: G 344 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7524 (mm-40) REVERT: G 392 ARG cc_start: 0.7428 (tmm160) cc_final: 0.6834 (ttm-80) REVERT: A 56 LYS cc_start: 0.7761 (tttt) cc_final: 0.7296 (mmtm) REVERT: A 78 ASN cc_start: 0.8691 (m-40) cc_final: 0.8367 (m-40) REVERT: B 22 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7020 (mt-10) REVERT: B 65 LYS cc_start: 0.8466 (tttp) cc_final: 0.8192 (tttt) REVERT: B 121 GLU cc_start: 0.8576 (tt0) cc_final: 0.7982 (mt-10) outliers start: 32 outliers final: 17 residues processed: 157 average time/residue: 0.5560 time to fit residues: 93.3711 Evaluate side-chains 149 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 241 MET 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 167 MET Chi-restraints excluded: chain D residue 257 ILE 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 167 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 0.3980 chunk 87 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.157365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.119817 restraints weight = 10456.196| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.81 r_work: 0.3270 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9803 Z= 0.149 Angle : 0.566 5.684 13343 Z= 0.292 Chirality : 0.043 0.178 1440 Planarity : 0.004 0.042 1691 Dihedral : 6.061 72.337 1503 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.59 % Favored : 95.24 % Rotamer: Outliers : 3.12 % Allowed : 19.42 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.25), residues: 1198 helix: 1.58 (0.29), residues: 329 sheet: -1.23 (0.39), residues: 159 loop : -0.77 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 2 202 TYR 0.012 0.001 TYR 2 183 PHE 0.022 0.001 PHE D 176 TRP 0.016 0.001 TRP D 180 HIS 0.005 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 9763) covalent geometry : angle 0.55882 / 0.29 (13257) SS BOND : bond 0.00279 / 0.19 ( 28) SS BOND : angle 1.10088 / 0.81 ( 56) hydrogen bonds : bond 0.03112 / 2.05 ( 377) hydrogen bonds : angle 4.70485 / 3.34 ( 1122) Misc. bond : bond 0.06173 / 3.00 ( 2) link_BETA1-4 : bond 0.00329 / 0.13 ( 3) link_BETA1-4 : angle 1.36978 / 0.67 ( 9) link_NAG-ASN : bond 0.00171 / 0.09 ( 7) link_NAG-ASN : angle 1.46963 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.8042 (pt0) cc_final: 0.6948 (mm-30) REVERT: 2 255 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: 2 307 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: 2 308 ASP cc_start: 0.8022 (t0) cc_final: 0.7768 (t0) REVERT: D 245 LYS cc_start: 0.7662 (tmtt) cc_final: 0.7055 (mppt) REVERT: D 252 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6800 (tp30) REVERT: D 344 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: D 357 HIS cc_start: 0.8460 (m-70) cc_final: 0.8199 (m-70) REVERT: D 358 ASN cc_start: 0.7896 (m-40) cc_final: 0.7602 (m-40) REVERT: G 204 SER cc_start: 0.8246 (p) cc_final: 0.7865 (t) REVERT: G 218 SER cc_start: 0.8647 (t) cc_final: 0.8271 (m) REVERT: G 344 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7634 (mm-40) REVERT: G 381 ARG cc_start: 0.8185 (tmm-80) cc_final: 0.7597 (ttp80) REVERT: G 392 ARG cc_start: 0.7593 (tmm160) cc_final: 0.6919 (mtm180) REVERT: A 56 LYS cc_start: 0.7869 (tttt) cc_final: 0.7460 (mttm) REVERT: B 22 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7134 (mt-10) REVERT: B 65 LYS cc_start: 0.8551 (tttp) cc_final: 0.8288 (tttt) REVERT: B 120 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7959 (pptt) REVERT: B 121 GLU cc_start: 0.8634 (tt0) cc_final: 0.8078 (mt-10) outliers start: 31 outliers final: 17 residues processed: 151 average time/residue: 0.6175 time to fit residues: 99.3764 Evaluate side-chains 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 399 ASP Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 167 MET Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 0.0040 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 0.3980 chunk 96 optimal weight: 0.0770 chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.0370 chunk 117 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.2228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3901 r_free = 0.3901 target = 0.171678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.138767 restraints weight = 10167.996| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.46 r_work: 0.3172 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9803 Z= 0.106 Angle : 0.537 5.861 13343 Z= 0.277 Chirality : 0.042 0.167 1440 Planarity : 0.004 0.043 1691 Dihedral : 5.807 71.566 1503 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.33 % Rotamer: Outliers : 2.82 % Allowed : 19.72 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1198 helix: 1.75 (0.30), residues: 329 sheet: -0.89 (0.41), residues: 142 loop : -0.76 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 202 TYR 0.012 0.001 TYR 2 183 PHE 0.021 0.001 PHE D 176 TRP 0.020 0.001 TRP D 180 HIS 0.005 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9763) covalent geometry : angle 0.53122 / 0.28 (13257) SS BOND : bond 0.00199 / 0.15 ( 28) SS BOND : angle 1.03949 / 0.77 ( 56) hydrogen bonds : bond 0.02907 / 1.96 ( 377) hydrogen bonds : angle 4.57718 / 3.24 ( 1122) Misc. bond : bond 0.04082 / 2.06 ( 2) link_BETA1-4 : bond 0.00339 / 0.14 ( 3) link_BETA1-4 : angle 1.18312 / 0.57 ( 9) link_NAG-ASN : bond 0.00140 / 0.07 ( 7) link_NAG-ASN : angle 1.27414 / 0.80 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7869 (pt0) cc_final: 0.6626 (mm-30) REVERT: 2 196 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8625 (mtpp) REVERT: 2 255 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7661 (mt-10) REVERT: 2 308 ASP cc_start: 0.7870 (t0) cc_final: 0.7643 (t0) REVERT: D 159 MET cc_start: 0.7123 (ttp) cc_final: 0.6899 (ttp) REVERT: D 224 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6966 (t0) REVERT: D 245 LYS cc_start: 0.7578 (tmtt) cc_final: 0.6927 (mppt) REVERT: D 252 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6788 (tp30) REVERT: D 344 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6519 (mt0) REVERT: D 358 ASN cc_start: 0.7760 (m-40) cc_final: 0.7438 (m-40) REVERT: D 381 ARG cc_start: 0.7337 (ttp80) cc_final: 0.5685 (ptt180) REVERT: G 204 SER cc_start: 0.8217 (p) cc_final: 0.7822 (t) REVERT: G 218 SER cc_start: 0.8587 (t) cc_final: 0.8189 (m) REVERT: G 344 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7400 (mm-40) REVERT: G 381 ARG cc_start: 0.8147 (tmm-80) cc_final: 0.7584 (ttp80) REVERT: G 392 ARG cc_start: 0.7318 (tmm160) cc_final: 0.6755 (mtm180) REVERT: A 47 ASP cc_start: 0.7923 (t0) cc_final: 0.7690 (t0) REVERT: A 56 LYS cc_start: 0.7704 (tttt) cc_final: 0.7260 (mttm) REVERT: A 99 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8471 (mptm) REVERT: A 141 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7566 (ptm-80) REVERT: B 22 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7004 (mt-10) REVERT: B 65 LYS cc_start: 0.8420 (tttp) cc_final: 0.8139 (tttt) REVERT: B 120 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7894 (pptt) REVERT: B 121 GLU cc_start: 0.8552 (tt0) cc_final: 0.7972 (mt-10) outliers start: 28 outliers final: 15 residues processed: 160 average time/residue: 0.5918 time to fit residues: 100.9619 Evaluate side-chains 146 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 196 LYS Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 324 VAL Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 399 ASP 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 216 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 106 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 247 GLN G 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133175 restraints weight = 10256.333| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.46 r_work: 0.3069 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9803 Z= 0.146 Angle : 0.565 5.567 13343 Z= 0.293 Chirality : 0.043 0.181 1440 Planarity : 0.004 0.048 1691 Dihedral : 5.912 73.633 1503 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 2.72 % Allowed : 20.52 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1198 helix: 1.70 (0.30), residues: 329 sheet: -1.10 (0.40), residues: 146 loop : -0.77 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 202 TYR 0.012 0.002 TYR 2 213 PHE 0.019 0.001 PHE D 176 TRP 0.026 0.001 TRP D 180 HIS 0.005 0.001 HIS 2 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 9763) covalent geometry : angle 0.55827 / 0.29 (13257) SS BOND : bond 0.00283 / 0.20 ( 28) SS BOND : angle 1.17127 / 0.85 ( 56) hydrogen bonds : bond 0.03064 / 2.04 ( 377) hydrogen bonds : angle 4.63847 / 3.28 ( 1122) Misc. bond : bond 0.05838 / 2.81 ( 2) link_BETA1-4 : bond 0.00339 / 0.14 ( 3) link_BETA1-4 : angle 1.32712 / 0.64 ( 9) link_NAG-ASN : bond 0.00159 / 0.08 ( 7) link_NAG-ASN : angle 1.37510 / 0.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7844 (pt0) cc_final: 0.6582 (mm-30) REVERT: 2 308 ASP cc_start: 0.7902 (t0) cc_final: 0.7649 (t0) REVERT: D 159 MET cc_start: 0.7190 (ttp) cc_final: 0.6804 (ttp) REVERT: D 224 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7099 (t0) REVERT: D 245 LYS cc_start: 0.7586 (tmtt) cc_final: 0.6913 (mppt) REVERT: D 252 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6782 (tp30) REVERT: D 344 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6475 (mt0) REVERT: D 358 ASN cc_start: 0.7798 (m-40) cc_final: 0.7461 (m-40) REVERT: D 381 ARG cc_start: 0.7320 (ttp80) cc_final: 0.5581 (ptt180) REVERT: G 204 SER cc_start: 0.8256 (p) cc_final: 0.7852 (t) REVERT: G 218 SER cc_start: 0.8591 (t) cc_final: 0.8184 (m) REVERT: G 249 ASP cc_start: 0.7516 (t70) cc_final: 0.6773 (p0) REVERT: G 344 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7403 (mm-40) REVERT: G 381 ARG cc_start: 0.8153 (tmm-80) cc_final: 0.7617 (ttp80) REVERT: G 392 ARG cc_start: 0.7374 (tmm160) cc_final: 0.6757 (mtm180) REVERT: A 47 ASP cc_start: 0.7958 (t0) cc_final: 0.7735 (t0) REVERT: A 56 LYS cc_start: 0.7693 (tttt) cc_final: 0.7240 (mttm) REVERT: A 99 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8445 (mptm) REVERT: A 141 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7566 (ptm-80) REVERT: B 22 GLU cc_start: 0.7424 (mm-30) cc_final: 0.6966 (mt-10) REVERT: B 65 LYS cc_start: 0.8422 (tttp) cc_final: 0.8151 (tttt) REVERT: B 120 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7903 (pptt) REVERT: B 121 GLU cc_start: 0.8540 (tt0) cc_final: 0.7928 (mt-10) outliers start: 27 outliers final: 16 residues processed: 141 average time/residue: 0.6097 time to fit residues: 91.4228 Evaluate side-chains 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 196 LYS Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 399 ASP 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 216 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 29 optimal weight: 0.0980 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3871 r_free = 0.3871 target = 0.168943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135649 restraints weight = 10119.522| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.46 r_work: 0.3056 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9803 Z= 0.145 Angle : 0.568 5.659 13343 Z= 0.294 Chirality : 0.043 0.178 1440 Planarity : 0.004 0.050 1691 Dihedral : 5.911 73.980 1503 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 2.52 % Allowed : 20.93 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1198 helix: 1.66 (0.30), residues: 329 sheet: -1.12 (0.40), residues: 146 loop : -0.77 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 202 TYR 0.012 0.002 TYR 2 213 PHE 0.018 0.001 PHE D 176 TRP 0.031 0.001 TRP D 180 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.14 ( 9763) covalent geometry : angle 0.56094 / 0.29 (13257) SS BOND : bond 0.00264 / 0.18 ( 28) SS BOND : angle 1.17200 / 0.85 ( 56) hydrogen bonds : bond 0.03056 / 2.04 ( 377) hydrogen bonds : angle 4.64821 / 3.28 ( 1122) Misc. bond : bond 0.05744 / 2.76 ( 2) link_BETA1-4 : bond 0.00307 / 0.13 ( 3) link_BETA1-4 : angle 1.33623 / 0.64 ( 9) link_NAG-ASN : bond 0.00153 / 0.08 ( 7) link_NAG-ASN : angle 1.40149 / 0.89 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7870 (pt0) cc_final: 0.6662 (mm-30) REVERT: 2 308 ASP cc_start: 0.7906 (t0) cc_final: 0.7665 (t0) REVERT: D 159 MET cc_start: 0.7249 (ttp) cc_final: 0.6856 (ttp) REVERT: D 224 ASP cc_start: 0.7449 (OUTLIER) cc_final: 0.7120 (t0) REVERT: D 245 LYS cc_start: 0.7603 (tmtt) cc_final: 0.6928 (mppt) REVERT: D 252 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6681 (tp30) REVERT: D 344 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6401 (mt0) REVERT: D 358 ASN cc_start: 0.7790 (m-40) cc_final: 0.7503 (m-40) REVERT: D 381 ARG cc_start: 0.7422 (ttp80) cc_final: 0.5704 (ptt180) REVERT: G 204 SER cc_start: 0.8279 (p) cc_final: 0.7879 (t) REVERT: G 218 SER cc_start: 0.8592 (t) cc_final: 0.8205 (m) REVERT: G 249 ASP cc_start: 0.7613 (t70) cc_final: 0.7405 (t70) REVERT: G 344 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7428 (mm-40) REVERT: G 381 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7648 (ttp80) REVERT: G 392 ARG cc_start: 0.7374 (tmm160) cc_final: 0.6769 (mtm180) REVERT: A 56 LYS cc_start: 0.7707 (tttt) cc_final: 0.7281 (mttm) REVERT: A 99 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8458 (mptm) REVERT: A 141 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7602 (ptm-80) REVERT: B 22 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7001 (mt-10) REVERT: B 65 LYS cc_start: 0.8448 (tttp) cc_final: 0.8180 (tttt) REVERT: B 120 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7969 (pptt) REVERT: B 121 GLU cc_start: 0.8547 (tt0) cc_final: 0.7953 (mt-10) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.6166 time to fit residues: 90.7521 Evaluate side-chains 143 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 196 LYS Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 399 ASP 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 216 GLU Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 98 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 0.0370 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3889 r_free = 0.3889 target = 0.170703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137730 restraints weight = 10149.551| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.46 r_work: 0.3090 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9803 Z= 0.118 Angle : 0.544 5.391 13343 Z= 0.282 Chirality : 0.042 0.166 1440 Planarity : 0.004 0.048 1691 Dihedral : 5.794 73.198 1503 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 2.62 % Allowed : 21.33 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1198 helix: 1.71 (0.30), residues: 331 sheet: -1.04 (0.41), residues: 146 loop : -0.75 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 2 202 TYR 0.012 0.001 TYR 2 183 PHE 0.019 0.001 PHE D 176 TRP 0.031 0.001 TRP D 180 HIS 0.006 0.001 HIS D 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9763) covalent geometry : angle 0.53840 / 0.28 (13257) SS BOND : bond 0.00219 / 0.16 ( 28) SS BOND : angle 1.03573 / 0.76 ( 56) hydrogen bonds : bond 0.02928 / 1.96 ( 377) hydrogen bonds : angle 4.60085 / 3.25 ( 1122) Misc. bond : bond 0.04408 / 2.14 ( 2) link_BETA1-4 : bond 0.00328 / 0.14 ( 3) link_BETA1-4 : angle 1.22392 / 0.59 ( 9) link_NAG-ASN : bond 0.00136 / 0.07 ( 7) link_NAG-ASN : angle 1.31013 / 0.82 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3782.99 seconds wall clock time: 65 minutes 10.79 seconds (3910.79 seconds total)