Starting phenix.real_space_refine on Tue Jul 29 14:52:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmw_38490/07_2025/8xmw_38490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmw_38490/07_2025/8xmw_38490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2025/8xmw_38490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2025/8xmw_38490.map" model { file = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2025/8xmw_38490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmw_38490/07_2025/8xmw_38490.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2255 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 2 7.16 5 S 70 5.16 5 C 5978 2.51 5 N 1662 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9538 Number of models: 1 Model: "" Number of chains: 13 Chain: "2" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2263 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2442 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 3, 'TRANS': 316} Chain: "G" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2442 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 3, 'TRANS': 316} Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1068 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1091 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 7, 'TRANS': 135} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.77, per 1000 atoms: 0.71 Number of scatterers: 9538 At special positions: 0 Unit cell: (89.88, 130.54, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 Ca 6 19.99 S 70 16.00 O 1820 8.00 N 1662 7.00 C 5978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS 2 52 " - pdb=" SG CYS 2 86 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 90 " - pdb=" SG CYS 2 207 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 250 " - pdb=" SG CYS 2 281 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 292 " - pdb=" SG CYS 2 322 " distance=2.04 Simple disulfide: pdb=" SG CYS D 168 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 197 " - pdb=" SG CYS D 258 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 238 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 355 " distance=2.03 Simple disulfide: pdb=" SG CYS D 304 " - pdb=" SG CYS D 365 " distance=2.03 Simple disulfide: pdb=" SG CYS D 335 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 398 " - pdb=" SG CYS D 462 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 472 " distance=2.03 Simple disulfide: pdb=" SG CYS D 442 " - pdb=" SG CYS D 452 " distance=2.04 Simple disulfide: pdb=" SG CYS G 168 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 184 " - pdb=" SG CYS G 248 " distance=2.02 Simple disulfide: pdb=" SG CYS G 197 " - pdb=" SG CYS G 258 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 238 " distance=2.03 Simple disulfide: pdb=" SG CYS G 275 " - pdb=" SG CYS G 309 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 355 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 365 " distance=2.03 Simple disulfide: pdb=" SG CYS G 335 " - pdb=" SG CYS G 345 " distance=2.03 Simple disulfide: pdb=" SG CYS G 382 " - pdb=" SG CYS G 416 " distance=2.03 Simple disulfide: pdb=" SG CYS G 398 " - pdb=" SG CYS G 462 " distance=2.03 Simple disulfide: pdb=" SG CYS G 411 " - pdb=" SG CYS G 472 " distance=2.03 Simple disulfide: pdb=" SG CYS G 442 " - pdb=" SG CYS G 452 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG 2 401 " - " ASN 2 125 " " NAG 2 402 " - " ASN 2 182 " " NAG C 1 " - " ASN 2 148 " " NAG D1101 " - " ASN D 445 " " NAG E 1 " - " ASN D 320 " " NAG F 1 " - " ASN G 320 " " NAG G1101 " - " ASN G 445 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 15 sheets defined 33.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 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: 3.08 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3617 1.38 - 1.54: 6042 1.54 - 1.71: 15 1.71 - 1.88: 81 1.88 - 2.05: 8 Bond restraints: 9763 Sorted by residual: bond pdb=" C THR A 137 " pdb=" N SER A 138 " ideal model delta sigma weight residual 1.334 1.366 -0.031 1.33e-02 5.65e+03 5.61e+00 bond pdb=" C LYS B 82 " pdb=" O LYS B 82 " ideal model delta sigma weight residual 1.236 1.208 0.028 1.26e-02 6.30e+03 5.00e+00 bond pdb=" C LYS A 139 " pdb=" O LYS A 139 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.47e-02 4.63e+03 2.87e+00 bond pdb=" CA TYR A 140 " pdb=" C TYR A 140 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.30e-02 5.92e+03 2.70e+00 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.314 0.032 2.00e-02 2.50e+03 2.55e+00 ... (remaining 9758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 12646 1.38 - 2.76: 487 2.76 - 4.15: 94 4.15 - 5.53: 26 5.53 - 6.91: 4 Bond angle restraints: 13257 Sorted by residual: angle pdb=" N LYS A 139 " pdb=" CA LYS A 139 " pdb=" C LYS A 139 " ideal model delta sigma weight residual 113.15 108.59 4.56 1.19e+00 7.06e-01 1.47e+01 angle pdb=" N GLY 2 224 " pdb=" CA GLY 2 224 " pdb=" C GLY 2 224 " ideal model delta sigma weight residual 110.87 116.36 -5.49 1.54e+00 4.22e-01 1.27e+01 angle pdb=" C VAL D 319 " pdb=" N ASN D 320 " pdb=" CA ASN D 320 " ideal model delta sigma weight residual 121.54 128.18 -6.64 1.91e+00 2.74e-01 1.21e+01 angle pdb=" N GLY G 210 " pdb=" CA GLY G 210 " pdb=" C GLY G 210 " ideal model delta sigma weight residual 113.18 120.09 -6.91 2.37e+00 1.78e-01 8.50e+00 angle pdb=" N LYS 2 94 " pdb=" CA LYS 2 94 " pdb=" C LYS 2 94 " ideal model delta sigma weight residual 111.02 107.47 3.55 1.22e+00 6.72e-01 8.48e+00 ... (remaining 13252 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5244 17.46 - 34.92: 475 34.92 - 52.37: 88 52.37 - 69.83: 24 69.83 - 87.29: 8 Dihedral angle restraints: 5839 sinusoidal: 2426 harmonic: 3413 Sorted by residual: dihedral pdb=" CB CYS D 275 " pdb=" SG CYS D 275 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS G 184 " pdb=" SG CYS G 184 " pdb=" SG CYS G 248 " pdb=" CB CYS G 248 " ideal model delta sinusoidal sigma weight residual 93.00 148.18 -55.18 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS G 275 " pdb=" SG CYS G 275 " pdb=" SG CYS G 309 " pdb=" CB CYS G 309 " ideal model delta sinusoidal sigma weight residual -86.00 -136.02 50.02 1 1.00e+01 1.00e-02 3.43e+01 ... (remaining 5836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1311 0.080 - 0.159: 127 0.159 - 0.239: 1 0.239 - 0.319: 0 0.319 - 0.398: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.75e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN G 320 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CA PRO G 310 " pdb=" N PRO G 310 " pdb=" C PRO G 310 " pdb=" CB PRO G 310 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 1437 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.068 2.00e-02 2.50e+03 5.83e-02 4.25e+01 pdb=" C7 NAG F 1 " 0.011 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.017 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.095 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 138 " 0.025 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C SER A 138 " -0.085 2.00e-02 2.50e+03 pdb=" O SER A 138 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS A 139 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.050 2.00e-02 2.50e+03 4.13e-02 2.14e+01 pdb=" C7 NAG F 2 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.066 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.011 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 137 2.62 - 3.19: 8504 3.19 - 3.76: 15702 3.76 - 4.33: 22701 4.33 - 4.90: 36622 Nonbonded interactions: 83666 Sorted by model distance: nonbonded pdb=" OH TYR 2 254 " pdb=" O TYR 2 327 " model vdw 2.047 3.040 nonbonded pdb=" OG SER G 366 " pdb=" OD1 ASP G 370 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP G 224 " pdb="CA CA G1103 " model vdw 2.227 2.510 nonbonded pdb=" NH2 ARG D 412 " pdb=" O GLY D 444 " model vdw 2.241 3.120 nonbonded pdb=" O PHE A 117 " pdb=" NH2 ARG B 30 " model vdw 2.242 3.120 ... (remaining 83661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.66 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.930 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 9803 Z= 0.211 Angle : 0.667 6.909 13343 Z= 0.354 Chirality : 0.046 0.398 1440 Planarity : 0.005 0.062 1691 Dihedral : 13.866 87.291 3577 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 0.30 % Allowed : 0.10 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1198 helix: 1.12 (0.29), residues: 323 sheet: -0.72 (0.41), residues: 162 loop : -1.04 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 2 310 HIS 0.016 0.001 HIS A 122 PHE 0.022 0.002 PHE A 46 TYR 0.019 0.002 TYR D 424 ARG 0.003 0.000 ARG G 392 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 7) link_NAG-ASN : angle 1.87625 ( 21) link_BETA1-4 : bond 0.00715 ( 3) link_BETA1-4 : angle 1.51673 ( 9) hydrogen bonds : bond 0.16888 ( 377) hydrogen bonds : angle 7.10949 ( 1122) SS BOND : bond 0.00322 ( 28) SS BOND : angle 1.47542 ( 56) covalent geometry : bond 0.00476 ( 9763) covalent geometry : angle 0.65697 (13257) Misc. bond : bond 0.08787 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.1603 (pt0) cc_final: 0.1182 (mm-30) REVERT: 2 95 ASN cc_start: 0.0335 (p0) cc_final: -0.0282 (p0) REVERT: 2 111 LYS cc_start: 0.0737 (mtmt) cc_final: 0.0324 (mtmt) REVERT: 2 128 THR cc_start: 0.1244 (p) cc_final: 0.0651 (p) REVERT: 2 306 GLU cc_start: 0.3789 (mp0) cc_final: 0.3531 (mp0) REVERT: 2 321 SER cc_start: -0.1027 (t) cc_final: -0.1423 (p) REVERT: D 159 MET cc_start: 0.6592 (ttp) cc_final: 0.6359 (ttp) REVERT: D 187 ASN cc_start: 0.7924 (t0) cc_final: 0.7405 (t0) REVERT: D 245 LYS cc_start: 0.7669 (tmtt) cc_final: 0.7253 (mppt) REVERT: D 260 LYS cc_start: 0.8388 (tttp) cc_final: 0.7785 (ttpt) REVERT: G 204 SER cc_start: 0.8549 (p) cc_final: 0.8129 (t) REVERT: G 218 SER cc_start: 0.8716 (t) cc_final: 0.8380 (m) REVERT: G 392 ARG cc_start: 0.7497 (tmm160) cc_final: 0.6988 (mtm180) REVERT: A 42 TYR cc_start: 0.9233 (m-80) cc_final: 0.8995 (m-80) REVERT: A 56 LYS cc_start: 0.7523 (tttt) cc_final: 0.7278 (tptt) REVERT: A 61 LYS cc_start: 0.8426 (mttt) cc_final: 0.8168 (mtpt) REVERT: A 141 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6649 (mtp-110) REVERT: B 22 GLU cc_start: 0.7295 (mm-30) cc_final: 0.6887 (mt-10) REVERT: B 65 LYS cc_start: 0.8416 (tttp) cc_final: 0.8205 (tttt) REVERT: B 121 GLU cc_start: 0.8161 (tt0) cc_final: 0.7737 (mt-10) outliers start: 3 outliers final: 0 residues processed: 215 average time/residue: 1.6378 time to fit residues: 372.2935 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 : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 288 GLN D 327 HIS G 348 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.148881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110981 restraints weight = 10361.063| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.70 r_work: 0.3027 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9803 Z= 0.155 Angle : 0.596 6.116 13343 Z= 0.311 Chirality : 0.043 0.179 1440 Planarity : 0.004 0.043 1691 Dihedral : 7.268 79.802 1507 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 3.22 % Allowed : 11.07 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1198 helix: 1.40 (0.29), residues: 329 sheet: -0.96 (0.38), residues: 170 loop : -0.81 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 402 HIS 0.012 0.001 HIS A 122 PHE 0.011 0.001 PHE A 46 TYR 0.013 0.001 TYR 2 183 ARG 0.003 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00293 ( 7) link_NAG-ASN : angle 1.39081 ( 21) link_BETA1-4 : bond 0.00621 ( 3) link_BETA1-4 : angle 1.28751 ( 9) hydrogen bonds : bond 0.03884 ( 377) hydrogen bonds : angle 5.24355 ( 1122) SS BOND : bond 0.00526 ( 28) SS BOND : angle 1.21485 ( 56) covalent geometry : bond 0.00371 ( 9763) covalent geometry : angle 0.58904 (13257) Misc. bond : bond 0.05878 ( 2) *********************** 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 191 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7799 (pt0) cc_final: 0.6554 (mm-30) REVERT: 2 307 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: D 159 MET cc_start: 0.6876 (ttp) cc_final: 0.6500 (ttp) REVERT: D 167 MET cc_start: 0.7268 (OUTLIER) cc_final: 0.6665 (ttt) REVERT: D 187 ASN cc_start: 0.8083 (t0) cc_final: 0.7363 (t0) REVERT: D 245 LYS cc_start: 0.7678 (tmtt) cc_final: 0.6869 (mppt) REVERT: D 260 LYS cc_start: 0.8403 (tttp) cc_final: 0.7535 (ttpt) REVERT: D 344 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: D 435 THR cc_start: 0.8376 (t) cc_final: 0.8077 (m) REVERT: G 204 SER cc_start: 0.8264 (p) cc_final: 0.7871 (t) REVERT: G 218 SER cc_start: 0.8524 (t) cc_final: 0.8170 (m) REVERT: G 392 ARG cc_start: 0.7457 (tmm160) cc_final: 0.6823 (ttm-80) REVERT: A 56 LYS cc_start: 0.7662 (tttt) cc_final: 0.7379 (tptt) REVERT: A 60 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8542 (tptm) REVERT: A 61 LYS cc_start: 0.8584 (mttt) cc_final: 0.8351 (mtpt) REVERT: B 22 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7006 (mt-10) REVERT: B 65 LYS cc_start: 0.8509 (tttp) cc_final: 0.8259 (tttt) REVERT: B 121 GLU cc_start: 0.8506 (tt0) cc_final: 0.7961 (mt-10) outliers start: 32 outliers final: 8 residues processed: 177 average time/residue: 1.4516 time to fit residues: 272.9283 Evaluate side-chains 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 307 GLU Chi-restraints excluded: chain D residue 167 MET Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain A residue 60 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116215 restraints weight = 10390.216| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.85 r_work: 0.3006 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 9803 Z= 0.209 Angle : 0.625 6.640 13343 Z= 0.323 Chirality : 0.045 0.192 1440 Planarity : 0.004 0.044 1691 Dihedral : 6.944 77.310 1503 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 3.22 % Allowed : 15.29 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.24), residues: 1198 helix: 1.31 (0.29), residues: 329 sheet: -1.29 (0.37), residues: 162 loop : -0.82 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 402 HIS 0.011 0.001 HIS A 122 PHE 0.014 0.002 PHE A 46 TYR 0.015 0.002 TYR 2 239 ARG 0.007 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 7) link_NAG-ASN : angle 1.64046 ( 21) link_BETA1-4 : bond 0.00352 ( 3) link_BETA1-4 : angle 1.41231 ( 9) hydrogen bonds : bond 0.03693 ( 377) hydrogen bonds : angle 5.04517 ( 1122) SS BOND : bond 0.00377 ( 28) SS BOND : angle 1.35115 ( 56) covalent geometry : bond 0.00506 ( 9763) covalent geometry : angle 0.61601 (13257) Misc. bond : bond 0.07642 ( 2) *********************** 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 175 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7817 (pt0) cc_final: 0.6584 (mm-30) REVERT: 2 307 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8089 (pt0) REVERT: D 167 MET cc_start: 0.7194 (OUTLIER) cc_final: 0.6677 (ttt) REVERT: D 187 ASN cc_start: 0.8166 (t0) cc_final: 0.7370 (t0) REVERT: D 245 LYS cc_start: 0.7687 (tmtt) cc_final: 0.6825 (mppt) REVERT: D 260 LYS cc_start: 0.8420 (tttp) cc_final: 0.7561 (ttpt) REVERT: D 306 GLN cc_start: 0.7621 (tt0) cc_final: 0.7397 (tt0) REVERT: D 344 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7255 (mt0) REVERT: G 204 SER cc_start: 0.8290 (p) cc_final: 0.7905 (t) REVERT: G 218 SER cc_start: 0.8649 (t) cc_final: 0.8277 (m) REVERT: G 344 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7496 (mm-40) REVERT: G 392 ARG cc_start: 0.7643 (tmm160) cc_final: 0.6830 (ttm-80) REVERT: A 56 LYS cc_start: 0.7801 (tttt) cc_final: 0.7430 (tptt) REVERT: A 61 LYS cc_start: 0.8633 (mttt) cc_final: 0.8428 (mtpt) REVERT: A 78 ASN cc_start: 0.8791 (m-40) cc_final: 0.8446 (m-40) REVERT: B 22 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7058 (mt-10) REVERT: B 65 LYS cc_start: 0.8517 (tttp) cc_final: 0.8269 (tttt) REVERT: B 121 GLU cc_start: 0.8595 (tt0) cc_final: 0.8031 (mt-10) outliers start: 32 outliers final: 13 residues processed: 163 average time/residue: 2.0492 time to fit residues: 357.2053 Evaluate side-chains 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 447 THR Chi-restraints excluded: chain G residue 470 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.160675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125224 restraints weight = 10236.344| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.55 r_work: 0.3058 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9803 Z= 0.191 Angle : 0.601 6.598 13343 Z= 0.311 Chirality : 0.044 0.188 1440 Planarity : 0.004 0.044 1691 Dihedral : 6.652 76.068 1503 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 2.92 % Allowed : 16.70 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1198 helix: 1.36 (0.29), residues: 329 sheet: -1.51 (0.40), residues: 137 loop : -0.81 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 436 HIS 0.008 0.001 HIS A 122 PHE 0.012 0.001 PHE 2 280 TYR 0.015 0.002 TYR 2 183 ARG 0.008 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 7) link_NAG-ASN : angle 1.63804 ( 21) link_BETA1-4 : bond 0.00296 ( 3) link_BETA1-4 : angle 1.36700 ( 9) hydrogen bonds : bond 0.03392 ( 377) hydrogen bonds : angle 4.93735 ( 1122) SS BOND : bond 0.00322 ( 28) SS BOND : angle 1.24500 ( 56) covalent geometry : bond 0.00464 ( 9763) covalent geometry : angle 0.59260 (13257) Misc. bond : bond 0.07065 ( 2) *********************** 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 168 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7767 (pt0) cc_final: 0.6561 (mm-30) REVERT: 2 255 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: 2 307 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8029 (pt0) REVERT: D 245 LYS cc_start: 0.7628 (tmtt) cc_final: 0.6810 (mppt) REVERT: D 260 LYS cc_start: 0.8410 (tttp) cc_final: 0.7558 (ttpt) REVERT: D 306 GLN cc_start: 0.7597 (tt0) cc_final: 0.7382 (tt0) REVERT: D 344 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: D 352 LYS cc_start: 0.8354 (tmtm) cc_final: 0.8093 (tmtm) REVERT: G 204 SER cc_start: 0.8246 (p) cc_final: 0.7864 (t) REVERT: G 218 SER cc_start: 0.8596 (t) cc_final: 0.8228 (m) REVERT: G 249 ASP cc_start: 0.7694 (t0) cc_final: 0.7323 (t70) REVERT: G 344 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7446 (mm-40) REVERT: G 392 ARG cc_start: 0.7479 (tmm160) cc_final: 0.6756 (ttm-80) REVERT: A 56 LYS cc_start: 0.7771 (tttt) cc_final: 0.7293 (mttm) REVERT: A 78 ASN cc_start: 0.8739 (m-40) cc_final: 0.8397 (m-40) REVERT: B 22 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7029 (mt-10) REVERT: B 65 LYS cc_start: 0.8476 (tttp) cc_final: 0.8210 (tttt) REVERT: B 121 GLU cc_start: 0.8610 (tt0) cc_final: 0.8030 (mt-10) outliers start: 29 outliers final: 15 residues processed: 156 average time/residue: 2.0628 time to fit residues: 343.1041 Evaluate side-chains 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.512 ------------------------------------------------------------------------------- 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 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 93 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131540 restraints weight = 10135.248| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.45 r_work: 0.3058 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9803 Z= 0.148 Angle : 0.575 7.154 13343 Z= 0.296 Chirality : 0.043 0.183 1440 Planarity : 0.004 0.044 1691 Dihedral : 6.321 73.570 1503 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.84 % Favored : 94.99 % Rotamer: Outliers : 3.02 % Allowed : 18.11 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1198 helix: 1.54 (0.29), residues: 329 sheet: -1.47 (0.38), residues: 147 loop : -0.79 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 180 HIS 0.005 0.001 HIS A 122 PHE 0.012 0.001 PHE 2 300 TYR 0.014 0.001 TYR 2 183 ARG 0.008 0.000 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 7) link_NAG-ASN : angle 1.52564 ( 21) link_BETA1-4 : bond 0.00320 ( 3) link_BETA1-4 : angle 1.29081 ( 9) hydrogen bonds : bond 0.03215 ( 377) hydrogen bonds : angle 4.81410 ( 1122) SS BOND : bond 0.00254 ( 28) SS BOND : angle 1.57400 ( 56) covalent geometry : bond 0.00362 ( 9763) covalent geometry : angle 0.56342 (13257) Misc. bond : bond 0.06233 ( 2) *********************** 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 178 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7725 (pt0) cc_final: 0.6485 (mm-30) REVERT: 2 213 TYR cc_start: 0.9168 (m-80) cc_final: 0.8948 (m-80) REVERT: 2 255 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: 2 307 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7911 (pt0) REVERT: D 167 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6446 (ttt) REVERT: D 245 LYS cc_start: 0.7597 (tmtt) cc_final: 0.6764 (mppt) REVERT: D 344 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7103 (mt0) REVERT: D 358 ASN cc_start: 0.7833 (m-40) cc_final: 0.7477 (m-40) REVERT: D 381 ARG cc_start: 0.7135 (ttp80) cc_final: 0.5493 (ptt180) REVERT: G 204 SER cc_start: 0.8186 (p) cc_final: 0.7793 (t) REVERT: G 218 SER cc_start: 0.8604 (t) cc_final: 0.8215 (m) REVERT: G 269 VAL cc_start: 0.8798 (t) cc_final: 0.8595 (m) REVERT: G 392 ARG cc_start: 0.7354 (tmm160) cc_final: 0.6662 (ttm-80) REVERT: G 466 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 6 ASP cc_start: 0.8381 (m-30) cc_final: 0.8171 (m-30) REVERT: A 56 LYS cc_start: 0.7688 (tttt) cc_final: 0.7209 (mttm) REVERT: A 78 ASN cc_start: 0.8687 (m-40) cc_final: 0.8328 (m-40) REVERT: B 22 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6919 (mt-10) REVERT: B 65 LYS cc_start: 0.8406 (tttp) cc_final: 0.8128 (tttt) REVERT: B 120 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7805 (pptt) REVERT: B 121 GLU cc_start: 0.8552 (tt0) cc_final: 0.7958 (mt-10) outliers start: 30 outliers final: 13 residues processed: 166 average time/residue: 1.4202 time to fit residues: 250.7579 Evaluate side-chains 152 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 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 G residue 179 ARG Chi-restraints excluded: chain G residue 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 1 VAL Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 199 GLN ** 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 = 0.3824 r_free = 0.3824 target = 0.164646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130924 restraints weight = 10170.134| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.44 r_work: 0.3282 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2952 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9803 Z= 0.162 Angle : 0.583 6.013 13343 Z= 0.300 Chirality : 0.043 0.186 1440 Planarity : 0.004 0.048 1691 Dihedral : 6.226 72.364 1503 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.51 % Favored : 94.32 % Rotamer: Outliers : 2.92 % Allowed : 18.51 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1198 helix: 1.52 (0.29), residues: 329 sheet: -1.54 (0.41), residues: 135 loop : -0.79 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 402 HIS 0.005 0.001 HIS D 464 PHE 0.011 0.001 PHE 2 280 TYR 0.014 0.002 TYR D 354 ARG 0.011 0.000 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 7) link_NAG-ASN : angle 1.55639 ( 21) link_BETA1-4 : bond 0.00297 ( 3) link_BETA1-4 : angle 1.37003 ( 9) hydrogen bonds : bond 0.03225 ( 377) hydrogen bonds : angle 4.80441 ( 1122) SS BOND : bond 0.00292 ( 28) SS BOND : angle 1.27076 ( 56) covalent geometry : bond 0.00396 ( 9763) covalent geometry : angle 0.57436 (13257) Misc. bond : bond 0.06508 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7924 (pt0) cc_final: 0.6918 (mm-30) REVERT: 2 213 TYR cc_start: 0.9145 (m-80) cc_final: 0.8901 (m-80) REVERT: 2 255 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: 2 307 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: D 167 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6589 (ttt) REVERT: D 245 LYS cc_start: 0.7654 (tmtt) cc_final: 0.7038 (mppt) REVERT: D 344 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6564 (mt0) REVERT: D 358 ASN cc_start: 0.7839 (m-40) cc_final: 0.7558 (m-40) REVERT: D 381 ARG cc_start: 0.7203 (ttp80) cc_final: 0.5651 (ptt180) REVERT: G 204 SER cc_start: 0.8314 (p) cc_final: 0.7922 (t) REVERT: G 218 SER cc_start: 0.8584 (t) cc_final: 0.8253 (m) REVERT: G 344 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7597 (mm-40) REVERT: G 392 ARG cc_start: 0.7539 (tmm160) cc_final: 0.6945 (ttm-80) REVERT: G 466 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7618 (mm-30) REVERT: A 56 LYS cc_start: 0.7914 (tttt) cc_final: 0.7560 (mttm) REVERT: A 141 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7760 (ptm-80) REVERT: B 22 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7208 (mt-10) REVERT: B 65 LYS cc_start: 0.8600 (tttp) cc_final: 0.8348 (tttt) REVERT: B 120 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7928 (pptt) REVERT: B 121 GLU cc_start: 0.8647 (tt0) cc_final: 0.8125 (mt-10) outliers start: 29 outliers final: 15 residues processed: 149 average time/residue: 1.6006 time to fit residues: 253.1801 Evaluate side-chains 144 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 37 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN D 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.152547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113394 restraints weight = 10577.622| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.92 r_work: 0.3225 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 9803 Z= 0.191 Angle : 0.601 6.371 13343 Z= 0.309 Chirality : 0.044 0.185 1440 Planarity : 0.004 0.048 1691 Dihedral : 6.242 73.396 1503 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 3.12 % Allowed : 18.91 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1198 helix: 1.47 (0.29), residues: 329 sheet: -1.46 (0.41), residues: 139 loop : -0.79 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 180 HIS 0.006 0.001 HIS A 122 PHE 0.012 0.001 PHE 2 280 TYR 0.014 0.002 TYR 2 239 ARG 0.011 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 7) link_NAG-ASN : angle 1.66604 ( 21) link_BETA1-4 : bond 0.00304 ( 3) link_BETA1-4 : angle 1.51633 ( 9) hydrogen bonds : bond 0.03334 ( 377) hydrogen bonds : angle 4.83028 ( 1122) SS BOND : bond 0.00342 ( 28) SS BOND : angle 1.24343 ( 56) covalent geometry : bond 0.00468 ( 9763) covalent geometry : angle 0.59202 (13257) Misc. bond : bond 0.07473 ( 2) *********************** 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 157 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7928 (pt0) cc_final: 0.6792 (mm-30) REVERT: 2 255 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7778 (mt-10) REVERT: 2 307 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (pt0) REVERT: D 245 LYS cc_start: 0.7626 (tmtt) cc_final: 0.7031 (mppt) REVERT: D 252 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6705 (mt-10) REVERT: D 344 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6532 (mt0) REVERT: D 358 ASN cc_start: 0.7898 (m-40) cc_final: 0.7615 (m-40) REVERT: D 381 ARG cc_start: 0.7214 (ttp80) cc_final: 0.5598 (ptt180) REVERT: G 204 SER cc_start: 0.8308 (p) cc_final: 0.7902 (t) REVERT: G 218 SER cc_start: 0.8625 (t) cc_final: 0.8246 (m) REVERT: G 344 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7607 (mm-40) REVERT: G 392 ARG cc_start: 0.7622 (tmm160) cc_final: 0.6869 (mtm180) REVERT: A 56 LYS cc_start: 0.7863 (tttt) cc_final: 0.7371 (mttm) REVERT: A 141 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7688 (ptm-80) REVERT: B 22 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7114 (mt-10) REVERT: B 65 LYS cc_start: 0.8504 (tttp) cc_final: 0.8240 (tttt) REVERT: B 120 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7946 (pptt) REVERT: B 121 GLU cc_start: 0.8675 (tt0) cc_final: 0.8097 (mt-10) outliers start: 31 outliers final: 15 residues processed: 148 average time/residue: 1.3521 time to fit residues: 212.7155 Evaluate side-chains 138 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 141 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.154065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115422 restraints weight = 10620.330| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.89 r_work: 0.3290 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2405 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= 0.152 Angle : 0.573 6.085 13343 Z= 0.296 Chirality : 0.043 0.178 1440 Planarity : 0.004 0.047 1691 Dihedral : 6.091 73.114 1503 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 2.72 % Allowed : 19.92 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1198 helix: 1.55 (0.29), residues: 329 sheet: -1.29 (0.39), residues: 159 loop : -0.79 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 180 HIS 0.005 0.001 HIS A 122 PHE 0.024 0.001 PHE D 176 TYR 0.013 0.002 TYR 2 183 ARG 0.010 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 7) link_NAG-ASN : angle 1.55710 ( 21) link_BETA1-4 : bond 0.00338 ( 3) link_BETA1-4 : angle 1.35985 ( 9) hydrogen bonds : bond 0.03160 ( 377) hydrogen bonds : angle 4.77169 ( 1122) SS BOND : bond 0.00294 ( 28) SS BOND : angle 1.08129 ( 56) covalent geometry : bond 0.00372 ( 9763) covalent geometry : angle 0.56557 (13257) Misc. bond : bond 0.06218 ( 2) *********************** 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 154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.8063 (pt0) cc_final: 0.6911 (mm-30) REVERT: 2 255 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7794 (mt-10) REVERT: 2 342 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8179 (pttt) REVERT: D 245 LYS cc_start: 0.7630 (tmtt) cc_final: 0.7054 (mppt) REVERT: D 252 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6781 (mt-10) REVERT: D 344 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6630 (mt0) REVERT: D 358 ASN cc_start: 0.7874 (m-40) cc_final: 0.7605 (m-40) REVERT: D 381 ARG cc_start: 0.7220 (ttp80) cc_final: 0.5610 (ptt180) REVERT: G 204 SER cc_start: 0.8278 (p) cc_final: 0.7900 (t) REVERT: G 218 SER cc_start: 0.8631 (t) cc_final: 0.8245 (m) REVERT: G 344 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7663 (mm-40) REVERT: G 381 ARG cc_start: 0.8170 (tmm-80) cc_final: 0.7625 (ttp80) REVERT: G 392 ARG cc_start: 0.7594 (tmm160) cc_final: 0.6895 (mtm180) REVERT: G 466 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 56 LYS cc_start: 0.7864 (tttt) cc_final: 0.7409 (mttm) REVERT: A 141 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7675 (ptm-80) REVERT: B 22 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7144 (mt-10) REVERT: B 65 LYS cc_start: 0.8522 (tttp) cc_final: 0.8259 (tttt) REVERT: B 120 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7961 (pptt) REVERT: B 121 GLU cc_start: 0.8684 (tt0) cc_final: 0.8124 (mt-10) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 1.6805 time to fit residues: 259.8257 Evaluate side-chains 139 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain 2 residue 342 LYS 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 141 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.150092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111700 restraints weight = 10519.875| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.79 r_work: 0.3253 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9803 Z= 0.194 Angle : 0.610 6.444 13343 Z= 0.314 Chirality : 0.044 0.186 1440 Planarity : 0.004 0.048 1691 Dihedral : 6.246 75.009 1503 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.76 % Favored : 94.07 % Rotamer: Outliers : 2.52 % Allowed : 20.12 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1198 helix: 1.45 (0.29), residues: 329 sheet: -1.40 (0.40), residues: 154 loop : -0.78 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 180 HIS 0.006 0.001 HIS 2 124 PHE 0.025 0.002 PHE D 176 TYR 0.014 0.002 TYR 2 213 ARG 0.011 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 7) link_NAG-ASN : angle 1.67616 ( 21) link_BETA1-4 : bond 0.00282 ( 3) link_BETA1-4 : angle 1.54732 ( 9) hydrogen bonds : bond 0.03349 ( 377) hydrogen bonds : angle 4.84349 ( 1122) SS BOND : bond 0.00404 ( 28) SS BOND : angle 1.33335 ( 56) covalent geometry : bond 0.00475 ( 9763) covalent geometry : angle 0.60048 (13257) Misc. bond : bond 0.07712 ( 2) *********************** 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 145 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7941 (pt0) cc_final: 0.6894 (mm-30) REVERT: 2 255 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7808 (mt-10) REVERT: D 245 LYS cc_start: 0.7660 (tmtt) cc_final: 0.7090 (mppt) REVERT: D 252 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6825 (mt-10) REVERT: D 344 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6636 (mt0) REVERT: D 358 ASN cc_start: 0.7917 (m-40) cc_final: 0.7659 (m-40) REVERT: D 381 ARG cc_start: 0.7262 (ttp80) cc_final: 0.5672 (ptt180) REVERT: G 204 SER cc_start: 0.8316 (p) cc_final: 0.7905 (t) REVERT: G 218 SER cc_start: 0.8645 (t) cc_final: 0.8279 (m) REVERT: G 249 ASP cc_start: 0.7817 (t0) cc_final: 0.7614 (t70) REVERT: G 344 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7715 (mm-40) REVERT: G 381 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.7696 (ttp80) REVERT: G 392 ARG cc_start: 0.7669 (tmm160) cc_final: 0.6967 (ttm-80) REVERT: A 56 LYS cc_start: 0.7877 (tttt) cc_final: 0.7464 (mttm) REVERT: A 61 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8204 (mtpt) REVERT: A 141 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7726 (ptm-80) REVERT: B 22 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7187 (mt-10) REVERT: B 65 LYS cc_start: 0.8553 (tttp) cc_final: 0.8298 (tttt) REVERT: B 120 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8013 (pptt) REVERT: B 121 GLU cc_start: 0.8668 (tt0) cc_final: 0.8127 (mt-10) outliers start: 25 outliers final: 15 residues processed: 138 average time/residue: 1.5833 time to fit residues: 233.3074 Evaluate side-chains 137 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASN Chi-restraints excluded: chain 2 residue 161 THR Chi-restraints excluded: chain 2 residue 178 VAL Chi-restraints excluded: chain 2 residue 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain 2 residue 331 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 352 LYS Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 95 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 78 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.168874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135456 restraints weight = 10330.386| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.49 r_work: 0.3071 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9803 Z= 0.125 Angle : 0.562 5.969 13343 Z= 0.292 Chirality : 0.042 0.177 1440 Planarity : 0.004 0.050 1691 Dihedral : 5.991 73.348 1503 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer: Outliers : 2.11 % Allowed : 20.82 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1198 helix: 1.65 (0.29), residues: 329 sheet: -1.38 (0.41), residues: 152 loop : -0.78 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 180 HIS 0.006 0.001 HIS D 464 PHE 0.022 0.001 PHE D 176 TYR 0.013 0.001 TYR 2 183 ARG 0.011 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 7) link_NAG-ASN : angle 1.44511 ( 21) link_BETA1-4 : bond 0.00331 ( 3) link_BETA1-4 : angle 1.26970 ( 9) hydrogen bonds : bond 0.03058 ( 377) hydrogen bonds : angle 4.71610 ( 1122) SS BOND : bond 0.00256 ( 28) SS BOND : angle 1.15540 ( 56) covalent geometry : bond 0.00305 ( 9763) covalent geometry : angle 0.55510 (13257) Misc. bond : bond 0.05202 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 87 GLU cc_start: 0.7863 (pt0) cc_final: 0.6615 (mm-30) REVERT: 2 255 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: D 245 LYS cc_start: 0.7619 (tmtt) cc_final: 0.6903 (mppt) REVERT: D 252 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6654 (mt-10) REVERT: D 344 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7113 (mt0) REVERT: D 346 LYS cc_start: 0.7033 (mtmt) cc_final: 0.6699 (ptpt) REVERT: D 358 ASN cc_start: 0.7756 (m-40) cc_final: 0.7465 (m-40) REVERT: D 381 ARG cc_start: 0.7128 (ttp80) cc_final: 0.5485 (ptt180) REVERT: G 204 SER cc_start: 0.8201 (p) cc_final: 0.7820 (t) REVERT: G 218 SER cc_start: 0.8554 (t) cc_final: 0.8146 (m) REVERT: G 286 GLU cc_start: 0.8459 (pt0) cc_final: 0.8241 (pt0) REVERT: G 392 ARG cc_start: 0.7385 (tmm160) cc_final: 0.6767 (mtm180) REVERT: G 466 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7380 (mm-30) REVERT: A 56 LYS cc_start: 0.7692 (tttt) cc_final: 0.7239 (mttm) REVERT: A 99 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8539 (mptm) REVERT: B 22 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6977 (mt-10) REVERT: B 47 ASP cc_start: 0.8076 (t0) cc_final: 0.7861 (t0) REVERT: B 65 LYS cc_start: 0.8408 (tttp) cc_final: 0.8133 (tttt) REVERT: B 87 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.7880 (m) REVERT: B 120 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7976 (pptt) REVERT: B 121 GLU cc_start: 0.8524 (tt0) cc_final: 0.8010 (mt-10) outliers start: 21 outliers final: 11 residues processed: 144 average time/residue: 1.4023 time to fit residues: 214.9487 Evaluate side-chains 136 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain 2 residue 255 GLU Chi-restraints excluded: chain 2 residue 305 LEU Chi-restraints excluded: chain D residue 344 GLN Chi-restraints excluded: chain D residue 416 CYS Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain G residue 179 ARG Chi-restraints excluded: chain G residue 447 THR Chi-restraints excluded: chain G residue 470 ILE Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 120 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 0.0020 chunk 62 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.164388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130880 restraints weight = 10242.151| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.44 r_work: 0.3041 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9803 Z= 0.162 Angle : 0.578 5.897 13343 Z= 0.300 Chirality : 0.043 0.180 1440 Planarity : 0.004 0.050 1691 Dihedral : 6.070 74.867 1503 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 2.11 % Allowed : 21.43 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1198 helix: 1.55 (0.29), residues: 329 sheet: -1.39 (0.41), residues: 152 loop : -0.76 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 180 HIS 0.006 0.001 HIS D 464 PHE 0.017 0.001 PHE D 176 TYR 0.013 0.002 TYR 2 213 ARG 0.011 0.001 ARG 2 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 7) link_NAG-ASN : angle 1.54862 ( 21) link_BETA1-4 : bond 0.00342 ( 3) link_BETA1-4 : angle 1.44161 ( 9) hydrogen bonds : bond 0.03185 ( 377) hydrogen bonds : angle 4.74093 ( 1122) SS BOND : bond 0.00323 ( 28) SS BOND : angle 1.17567 ( 56) covalent geometry : bond 0.00398 ( 9763) covalent geometry : angle 0.57037 (13257) Misc. bond : bond 0.06545 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8817.39 seconds wall clock time: 157 minutes 27.80 seconds (9447.80 seconds total)