Starting phenix.real_space_refine on Wed Mar 4 19:17:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0q_24791/03_2026/7s0q_24791_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0q_24791/03_2026/7s0q_24791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s0q_24791/03_2026/7s0q_24791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0q_24791/03_2026/7s0q_24791.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0q_24791/03_2026/7s0q_24791_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0q_24791/03_2026/7s0q_24791_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 61 5.16 5 C 4970 2.51 5 N 1334 2.21 5 O 1526 1.98 5 H 7466 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15357 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 9039 Classifications: {'peptide': 575} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 549} Chain breaks: 1 Chain: "B" Number of atoms: 5190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 5190 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 13, 'TRANS': 308} Chain breaks: 1 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 913 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 3, 'TRANS': 57} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'BMA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.87, per 1000 atoms: 0.19 Number of scatterers: 15357 At special positions: 0 Unit cell: (85.86, 110.24, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 O 1526 8.00 N 1334 7.00 C 4970 6.00 H 7466 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 458 " distance=2.04 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS B 524 " distance=2.04 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS D 47 " - pdb=" SG CYS D 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1002 " - " ASN A 387 " " NAG A1003 " - " ASN A 408 " " NAG A1004 " - " ASN A 504 " " NAG A1005 " - " ASN A 577 " " NAG B1001 " - " ASN B 337 " " NAG B1002 " - " ASN B 397 " " NAG B1003 " - " ASN B 514 " " NAG C 1 " - " ASN A 105 " " NAG E 1 " - " ASN A 21 " " NAG F 1 " - " ASN A 214 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 565.6 milliseconds 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 19 sheets defined 18.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 13 through 20 removed outlier: 3.541A pdb=" N GLU A 20 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 4.589A pdb=" N ARG A 41 " --> pdb=" O GLU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.604A pdb=" N ASN A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 148 removed outlier: 3.711A pdb=" N GLU A 147 " --> pdb=" O PRO A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 removed outlier: 3.583A pdb=" N ASN A 198 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 199 " --> pdb=" O GLU A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 195 through 199' Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 314 through 319 Processing helix chain 'A' and resid 339 through 348 removed outlier: 3.670A pdb=" N GLU A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 4.250A pdb=" N PHE A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 437 removed outlier: 4.136A pdb=" N ILE A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 330 removed outlier: 3.612A pdb=" N GLU B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 359 Processing helix chain 'B' and resid 435 through 446 removed outlier: 4.059A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 689 through 714 removed outlier: 4.298A pdb=" N LEU B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU B 698 " --> pdb=" O LYS B 694 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B 708 " --> pdb=" O THR B 704 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE B 714 " --> pdb=" O HIS B 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.594A pdb=" N VAL D 11 " --> pdb=" O GLY D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 53 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.508A pdb=" N ILE A 76 " --> pdb=" O ASN A 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.483A pdb=" N LEU A 29 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE A 58 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ARG A 112 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLU A 114 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 90 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 209 removed outlier: 5.641A pdb=" N LEU A 206 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N CYS A 221 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER A 208 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA6, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.898A pdb=" N LEU A 331 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 330 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ARG A 361 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE A 332 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 358 " --> pdb=" O TYR A 391 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 393 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A 360 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR A 388 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N TYR A 417 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE A 390 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.713A pdb=" N ILE A 378 " --> pdb=" O THR A 410 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 465 through 470 Processing sheet with id=AB3, first strand: chain 'A' and resid 520 through 525 removed outlier: 4.054A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 554 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 520 through 525 removed outlier: 4.054A pdb=" N SER A 492 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 554 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 311 through 321 removed outlier: 11.004A pdb=" N VAL B 335 " --> pdb=" O HIS B 313 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N LEU B 315 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N ASN B 337 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY B 317 " --> pdb=" O ASN B 337 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 319 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS B 369 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU B 340 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ARG B 371 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE B 342 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 363 through 364 Processing sheet with id=AB7, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.041A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AB9, first strand: chain 'B' and resid 530 through 534 Processing sheet with id=AC1, first strand: chain 'B' and resid 530 through 534 181 hydrogen bonds defined for protein. 453 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: 3.75 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7463 1.03 - 1.23: 156 1.23 - 1.43: 3274 1.43 - 1.63: 4556 1.63 - 1.82: 77 Bond restraints: 15526 Sorted by residual: bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C1 NAG A1004 " pdb=" O5 NAG A1004 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C1 NAG A1005 " pdb=" O5 NAG A1005 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.52e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.48e+00 bond pdb=" C1 NAG B1002 " pdb=" O5 NAG B1002 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.40e+00 ... (remaining 15521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 26946 1.30 - 2.61: 863 2.61 - 3.91: 71 3.91 - 5.22: 14 5.22 - 6.52: 7 Bond angle restraints: 27901 Sorted by residual: angle pdb=" C ILE A 31 " pdb=" N LEU A 32 " pdb=" CA LEU A 32 " ideal model delta sigma weight residual 121.91 116.32 5.59 2.03e+00 2.43e-01 7.57e+00 angle pdb=" N CYS A 152 " pdb=" CA CYS A 152 " pdb=" C CYS A 152 " ideal model delta sigma weight residual 108.07 110.41 -2.34 8.90e-01 1.26e+00 6.94e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.43 6.52 3.00e+00 1.11e-01 4.73e+00 angle pdb=" C TRP A 244 " pdb=" N ARG A 245 " pdb=" CA ARG A 245 " ideal model delta sigma weight residual 122.33 118.68 3.65 1.68e+00 3.54e-01 4.71e+00 angle pdb=" CA VAL B 712 " pdb=" C VAL B 712 " pdb=" N VAL B 713 " ideal model delta sigma weight residual 116.60 119.74 -3.14 1.45e+00 4.76e-01 4.69e+00 ... (remaining 27896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 7093 22.14 - 44.28: 389 44.28 - 66.42: 77 66.42 - 88.56: 25 88.56 - 110.70: 23 Dihedral angle restraints: 7607 sinusoidal: 4295 harmonic: 3312 Sorted by residual: dihedral pdb=" CB CYS D 6 " pdb=" SG CYS D 6 " pdb=" SG CYS D 48 " pdb=" CB CYS D 48 " ideal model delta sinusoidal sigma weight residual 93.00 172.66 -79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " pdb=" SG CYS A 218 " pdb=" CB CYS A 218 " ideal model delta sinusoidal sigma weight residual 93.00 165.84 -72.84 1 1.00e+01 1.00e-02 6.77e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 291 " pdb=" CB CYS A 291 " ideal model delta sinusoidal sigma weight residual 93.00 162.85 -69.85 1 1.00e+01 1.00e-02 6.29e+01 ... (remaining 7604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 1227 0.236 - 0.471: 5 0.471 - 0.707: 0 0.707 - 0.943: 0 0.943 - 1.179: 1 Chirality restraints: 1233 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.22 -1.18 2.00e-02 2.50e+03 3.47e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.65e+02 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 -2.56 0.16 2.00e-02 2.50e+03 6.69e+01 ... (remaining 1230 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 202 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 203 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 203 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 203 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 4 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.12e-01 pdb=" N PRO A 5 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 308 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.35e-01 pdb=" N PRO B 309 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 309 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 309 " 0.012 5.00e-02 4.00e+02 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 838 2.16 - 2.77: 30577 2.77 - 3.38: 42821 3.38 - 3.99: 55357 3.99 - 4.60: 86060 Nonbonded interactions: 215653 Sorted by model distance: nonbonded pdb="HH11 ARG B 488 " pdb=" O HIS B 548 " model vdw 1.547 2.450 nonbonded pdb=" H THR B 560 " pdb=" OG1 THR B 590 " model vdw 1.553 2.450 nonbonded pdb=" H LYS A 115 " pdb=" O GLY A 141 " model vdw 1.559 2.450 nonbonded pdb=" O LYS A 542 " pdb=" HG1 THR A 576 " model vdw 1.567 2.450 nonbonded pdb="HE21 GLN A 400 " pdb=" O TRP A 402 " model vdw 1.570 2.450 ... (remaining 215648 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 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.000 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8096 Z= 0.198 Angle : 0.903 37.409 10999 Z= 0.390 Chirality : 0.057 1.179 1233 Planarity : 0.003 0.045 1387 Dihedral : 16.050 110.700 3252 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.22), residues: 948 helix: -3.88 (0.27), residues: 129 sheet: -3.07 (0.35), residues: 154 loop : -3.50 (0.20), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 10 TYR 0.011 0.001 TYR A 85 PHE 0.011 0.001 PHE A 45 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8060) covalent geometry : angle 0.60622 (10912) SS BOND : bond 0.00261 ( 21) SS BOND : angle 0.97785 ( 42) hydrogen bonds : bond 0.22694 ( 163) hydrogen bonds : angle 9.39057 ( 453) link_BETA1-4 : bond 0.06533 ( 5) link_BETA1-4 : angle 17.89749 ( 15) link_NAG-ASN : bond 0.00461 ( 10) link_NAG-ASN : angle 2.00540 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3073 time to fit residues: 41.4969 Evaluate side-chains 76 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 275 GLN A 287 GLN B 348 ASN B 417 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.078204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.068979 restraints weight = 121403.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.071359 restraints weight = 56286.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.072831 restraints weight = 32321.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.073774 restraints weight = 21413.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.074442 restraints weight = 15701.789| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8096 Z= 0.155 Angle : 0.639 9.167 10999 Z= 0.316 Chirality : 0.047 0.407 1233 Planarity : 0.004 0.049 1387 Dihedral : 13.221 96.373 1386 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.59 % Allowed : 7.61 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.23), residues: 948 helix: -2.48 (0.37), residues: 139 sheet: -2.89 (0.37), residues: 156 loop : -3.11 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 50 TYR 0.012 0.001 TYR A 85 PHE 0.014 0.001 PHE A 45 TRP 0.011 0.001 TRP A 176 HIS 0.006 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8060) covalent geometry : angle 0.61166 (10912) SS BOND : bond 0.00335 ( 21) SS BOND : angle 1.24918 ( 42) hydrogen bonds : bond 0.05419 ( 163) hydrogen bonds : angle 7.13595 ( 453) link_BETA1-4 : bond 0.00749 ( 5) link_BETA1-4 : angle 3.62977 ( 15) link_NAG-ASN : bond 0.00515 ( 10) link_NAG-ASN : angle 2.23108 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 76 average time/residue: 0.2779 time to fit residues: 26.9819 Evaluate side-chains 69 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** 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 = 0.3991 r_free = 0.3991 target = 0.078363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.069027 restraints weight = 122629.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.071396 restraints weight = 56700.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.072883 restraints weight = 32663.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.073831 restraints weight = 21756.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.074471 restraints weight = 16025.024| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8096 Z= 0.122 Angle : 0.591 7.252 10999 Z= 0.290 Chirality : 0.045 0.351 1233 Planarity : 0.003 0.047 1387 Dihedral : 9.940 82.025 1386 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.47 % Allowed : 8.67 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.24), residues: 948 helix: -1.73 (0.43), residues: 133 sheet: -3.02 (0.38), residues: 146 loop : -2.79 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.011 0.001 TYR A 85 PHE 0.013 0.001 PHE A 45 TRP 0.009 0.001 TRP A 176 HIS 0.004 0.001 HIS B 440 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8060) covalent geometry : angle 0.56296 (10912) SS BOND : bond 0.00348 ( 21) SS BOND : angle 1.20353 ( 42) hydrogen bonds : bond 0.04188 ( 163) hydrogen bonds : angle 6.62005 ( 453) link_BETA1-4 : bond 0.00491 ( 5) link_BETA1-4 : angle 3.46695 ( 15) link_NAG-ASN : bond 0.00460 ( 10) link_NAG-ASN : angle 2.13364 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7332 (pp) outliers start: 4 outliers final: 1 residues processed: 79 average time/residue: 0.2794 time to fit residues: 28.2620 Evaluate side-chains 74 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 205 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.076558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.067216 restraints weight = 122444.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.069582 restraints weight = 56590.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.071058 restraints weight = 32593.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.071995 restraints weight = 21657.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.072627 restraints weight = 16004.058| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8096 Z= 0.191 Angle : 0.658 9.678 10999 Z= 0.322 Chirality : 0.046 0.527 1233 Planarity : 0.004 0.047 1387 Dihedral : 8.840 65.184 1386 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer: Outliers : 0.59 % Allowed : 10.89 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.25), residues: 948 helix: -1.61 (0.42), residues: 132 sheet: -2.89 (0.36), residues: 168 loop : -2.67 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 474 TYR 0.014 0.001 TYR A 85 PHE 0.016 0.001 PHE A 45 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8060) covalent geometry : angle 0.62907 (10912) SS BOND : bond 0.00474 ( 21) SS BOND : angle 1.24705 ( 42) hydrogen bonds : bond 0.03828 ( 163) hydrogen bonds : angle 6.58393 ( 453) link_BETA1-4 : bond 0.00458 ( 5) link_BETA1-4 : angle 3.29145 ( 15) link_NAG-ASN : bond 0.00571 ( 10) link_NAG-ASN : angle 2.72236 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7428 (pp) REVERT: A 381 GLU cc_start: 0.8183 (tt0) cc_final: 0.7931 (tp30) REVERT: D 46 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7231 (mm-30) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.2810 time to fit residues: 28.0632 Evaluate side-chains 74 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 417 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.076982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.067649 restraints weight = 122071.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.070016 restraints weight = 56248.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.071489 restraints weight = 32349.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.072429 restraints weight = 21536.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.073082 restraints weight = 15940.319| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8096 Z= 0.132 Angle : 0.596 6.326 10999 Z= 0.295 Chirality : 0.045 0.405 1233 Planarity : 0.003 0.048 1387 Dihedral : 8.182 59.287 1386 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 1.05 % Allowed : 11.71 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.25), residues: 948 helix: -1.51 (0.43), residues: 133 sheet: -2.77 (0.37), residues: 162 loop : -2.55 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 240 TYR 0.012 0.001 TYR A 85 PHE 0.015 0.001 PHE A 45 TRP 0.010 0.001 TRP A 176 HIS 0.002 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8060) covalent geometry : angle 0.57062 (10912) SS BOND : bond 0.00401 ( 21) SS BOND : angle 0.90268 ( 42) hydrogen bonds : bond 0.03470 ( 163) hydrogen bonds : angle 6.44609 ( 453) link_BETA1-4 : bond 0.00363 ( 5) link_BETA1-4 : angle 3.02553 ( 15) link_NAG-ASN : bond 0.00456 ( 10) link_NAG-ASN : angle 2.43524 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7372 (pp) REVERT: D 46 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7268 (tp30) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.2837 time to fit residues: 26.7913 Evaluate side-chains 72 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.076797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.067440 restraints weight = 121048.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.069837 restraints weight = 55738.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.071306 restraints weight = 32151.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.072244 restraints weight = 21429.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.072895 restraints weight = 15919.636| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8096 Z= 0.147 Angle : 0.596 6.332 10999 Z= 0.298 Chirality : 0.045 0.436 1233 Planarity : 0.003 0.047 1387 Dihedral : 7.194 56.106 1386 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.82 % Allowed : 12.06 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.25), residues: 948 helix: -1.35 (0.43), residues: 133 sheet: -2.87 (0.37), residues: 155 loop : -2.50 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 474 TYR 0.013 0.001 TYR A 85 PHE 0.015 0.001 PHE A 45 TRP 0.009 0.001 TRP A 176 HIS 0.003 0.001 HIS A 480 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8060) covalent geometry : angle 0.57155 (10912) SS BOND : bond 0.00405 ( 21) SS BOND : angle 0.95125 ( 42) hydrogen bonds : bond 0.03259 ( 163) hydrogen bonds : angle 6.35126 ( 453) link_BETA1-4 : bond 0.00401 ( 5) link_BETA1-4 : angle 2.86040 ( 15) link_NAG-ASN : bond 0.00470 ( 10) link_NAG-ASN : angle 2.49728 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7400 (pp) REVERT: A 474 ARG cc_start: 0.7335 (mtp180) cc_final: 0.7053 (mtp180) REVERT: A 508 TYR cc_start: 0.6160 (t80) cc_final: 0.5578 (t80) REVERT: D 46 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7219 (tp30) outliers start: 7 outliers final: 6 residues processed: 75 average time/residue: 0.2714 time to fit residues: 26.2082 Evaluate side-chains 72 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 417 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.076883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.067529 restraints weight = 120352.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.069902 restraints weight = 55028.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.071372 restraints weight = 31785.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.072325 restraints weight = 21222.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.072981 restraints weight = 15692.927| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8096 Z= 0.120 Angle : 0.563 6.145 10999 Z= 0.282 Chirality : 0.044 0.378 1233 Planarity : 0.003 0.045 1387 Dihedral : 6.288 54.943 1386 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 1.17 % Allowed : 12.30 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.25), residues: 948 helix: -1.20 (0.44), residues: 133 sheet: -2.79 (0.40), residues: 135 loop : -2.35 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.012 0.001 TYR B 562 PHE 0.014 0.001 PHE A 45 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8060) covalent geometry : angle 0.54157 (10912) SS BOND : bond 0.00388 ( 21) SS BOND : angle 0.88593 ( 42) hydrogen bonds : bond 0.02988 ( 163) hydrogen bonds : angle 6.23944 ( 453) link_BETA1-4 : bond 0.00389 ( 5) link_BETA1-4 : angle 2.51868 ( 15) link_NAG-ASN : bond 0.00421 ( 10) link_NAG-ASN : angle 2.31042 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7358 (pp) REVERT: A 508 TYR cc_start: 0.6195 (t80) cc_final: 0.5674 (t80) REVERT: D 46 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7237 (tp30) outliers start: 10 outliers final: 9 residues processed: 76 average time/residue: 0.2794 time to fit residues: 27.1225 Evaluate side-chains 69 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain D residue 43 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** 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 = 0.3944 r_free = 0.3944 target = 0.076560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.067121 restraints weight = 121690.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.069519 restraints weight = 55822.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.070991 restraints weight = 32165.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.071932 restraints weight = 21559.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.072565 restraints weight = 16018.225| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8096 Z= 0.138 Angle : 0.574 6.373 10999 Z= 0.288 Chirality : 0.044 0.439 1233 Planarity : 0.003 0.044 1387 Dihedral : 5.880 47.851 1386 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 1.17 % Allowed : 12.53 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.25), residues: 948 helix: -1.15 (0.45), residues: 133 sheet: -2.84 (0.39), residues: 135 loop : -2.33 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.010 0.001 TYR A 85 PHE 0.015 0.001 PHE A 45 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8060) covalent geometry : angle 0.55165 (10912) SS BOND : bond 0.00382 ( 21) SS BOND : angle 0.96384 ( 42) hydrogen bonds : bond 0.03100 ( 163) hydrogen bonds : angle 6.20161 ( 453) link_BETA1-4 : bond 0.00406 ( 5) link_BETA1-4 : angle 2.47237 ( 15) link_NAG-ASN : bond 0.00452 ( 10) link_NAG-ASN : angle 2.43525 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 TYR cc_start: 0.6285 (t80) cc_final: 0.5853 (t80) REVERT: D 46 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7114 (mm-30) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.2763 time to fit residues: 24.6535 Evaluate side-chains 66 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain B residue 586 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 50 optimal weight: 1.9990 chunk 92 optimal weight: 0.0050 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.077423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.068011 restraints weight = 120141.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.070380 restraints weight = 55325.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.071856 restraints weight = 32014.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.072808 restraints weight = 21438.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.073477 restraints weight = 15895.227| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8096 Z= 0.099 Angle : 0.541 6.097 10999 Z= 0.273 Chirality : 0.044 0.347 1233 Planarity : 0.003 0.042 1387 Dihedral : 5.469 44.719 1386 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.94 % Allowed : 13.23 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.26), residues: 948 helix: -0.98 (0.45), residues: 133 sheet: -2.69 (0.40), residues: 135 loop : -2.23 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.011 0.001 TYR A 85 PHE 0.012 0.001 PHE A 45 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8060) covalent geometry : angle 0.52304 (10912) SS BOND : bond 0.00303 ( 21) SS BOND : angle 0.75259 ( 42) hydrogen bonds : bond 0.02786 ( 163) hydrogen bonds : angle 6.01357 ( 453) link_BETA1-4 : bond 0.00386 ( 5) link_BETA1-4 : angle 2.24530 ( 15) link_NAG-ASN : bond 0.00397 ( 10) link_NAG-ASN : angle 2.14536 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7356 (mtm-85) REVERT: A 508 TYR cc_start: 0.6199 (t80) cc_final: 0.5769 (t80) REVERT: D 46 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7223 (tp30) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.2496 time to fit residues: 22.4969 Evaluate side-chains 67 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 ASN Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 34 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.077549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.068119 restraints weight = 121683.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.070519 restraints weight = 56068.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.071989 restraints weight = 32362.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.072924 restraints weight = 21707.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.073493 restraints weight = 16110.683| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8096 Z= 0.106 Angle : 0.562 6.119 10999 Z= 0.282 Chirality : 0.044 0.365 1233 Planarity : 0.003 0.041 1387 Dihedral : 5.383 39.800 1386 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.82 % Allowed : 13.35 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.26), residues: 948 helix: -0.94 (0.45), residues: 133 sheet: -2.63 (0.40), residues: 135 loop : -2.23 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.010 0.001 TYR A 85 PHE 0.012 0.001 PHE A 45 TRP 0.014 0.001 TRP B 551 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8060) covalent geometry : angle 0.54268 (10912) SS BOND : bond 0.00600 ( 21) SS BOND : angle 1.00101 ( 42) hydrogen bonds : bond 0.02911 ( 163) hydrogen bonds : angle 6.02739 ( 453) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 2.25784 ( 15) link_NAG-ASN : bond 0.00401 ( 10) link_NAG-ASN : angle 2.15193 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1896 Ramachandran restraints generated. 948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ARG cc_start: 0.7598 (mtm-85) cc_final: 0.7344 (mtm-85) REVERT: D 46 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7241 (tp30) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.2759 time to fit residues: 23.3680 Evaluate side-chains 66 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 468 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** 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 = 0.3958 r_free = 0.3958 target = 0.077582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.068064 restraints weight = 121063.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.070415 restraints weight = 55972.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.071883 restraints weight = 32765.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.072821 restraints weight = 22177.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.073495 restraints weight = 16580.884| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8096 Z= 0.114 Angle : 0.553 6.309 10999 Z= 0.278 Chirality : 0.044 0.413 1233 Planarity : 0.003 0.047 1387 Dihedral : 5.245 33.284 1386 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.82 % Allowed : 13.35 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.26), residues: 948 helix: -0.94 (0.45), residues: 133 sheet: -2.64 (0.40), residues: 135 loop : -2.21 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.010 0.001 TYR A 85 PHE 0.012 0.001 PHE A 45 TRP 0.010 0.001 TRP B 551 HIS 0.004 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8060) covalent geometry : angle 0.53324 (10912) SS BOND : bond 0.00394 ( 21) SS BOND : angle 0.85989 ( 42) hydrogen bonds : bond 0.02715 ( 163) hydrogen bonds : angle 5.99771 ( 453) link_BETA1-4 : bond 0.00347 ( 5) link_BETA1-4 : angle 2.28503 ( 15) link_NAG-ASN : bond 0.00439 ( 10) link_NAG-ASN : angle 2.26603 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3071.48 seconds wall clock time: 53 minutes 7.48 seconds (3187.48 seconds total)