Starting phenix.real_space_refine on Tue Dec 31 13:31:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0q_24791/12_2024/7s0q_24791_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0q_24791/12_2024/7s0q_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_24791/12_2024/7s0q_24791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0q_24791/12_2024/7s0q_24791.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0q_24791/12_2024/7s0q_24791_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0q_24791/12_2024/7s0q_24791_trim.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 9.26, per 1000 atoms: 0.60 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: 4.37 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.60 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: 5.87 Time building geometry restraints manager: 5.08 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: 7.990 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: 0.290 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 37.190 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.220 ------------------------------------------------------------------------------- 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 0.028 8060 Z= 0.236 Angle : 0.606 6.523 10912 Z= 0.319 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 480 PHE 0.011 0.001 PHE A 45 TYR 0.011 0.001 TYR A 85 ARG 0.003 0.000 ARG A 10 *********************** 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 : 1.401 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: 0 outliers final: 0 residues processed: 108 average time/residue: 0.6288 time to fit residues: 86.0741 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 : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 254 ASN A 275 GLN A 287 GLN B 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8060 Z= 0.254 Angle : 0.643 7.025 10912 Z= 0.324 Chirality : 0.048 0.472 1233 Planarity : 0.004 0.051 1387 Dihedral : 13.045 95.514 1386 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.59 % Allowed : 7.85 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.23), residues: 948 helix: -2.46 (0.36), residues: 139 sheet: -2.89 (0.37), residues: 156 loop : -3.14 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 176 HIS 0.007 0.001 HIS A 362 PHE 0.015 0.001 PHE A 45 TYR 0.013 0.001 TYR A 85 ARG 0.009 0.001 ARG D 50 *********************** 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 81 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 1.205 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: B 465 GLN cc_start: 0.7794 (mm110) cc_final: 0.7442 (mm110) outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 0.5825 time to fit residues: 57.8019 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 : 1.309 ------------------------------------------------------------------------------- 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 47 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 86 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** B 417 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8060 Z= 0.219 Angle : 0.596 7.106 10912 Z= 0.301 Chirality : 0.046 0.418 1233 Planarity : 0.004 0.051 1387 Dihedral : 10.070 82.290 1386 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.59 % Allowed : 9.02 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.24), residues: 948 helix: -1.71 (0.43), residues: 132 sheet: -3.05 (0.38), residues: 146 loop : -2.84 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.004 0.001 HIS B 440 PHE 0.015 0.001 PHE A 45 TYR 0.012 0.001 TYR A 224 ARG 0.003 0.000 ARG D 55 *********************** 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 75 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.371 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: A 32 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7384 (pp) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 0.5617 time to fit residues: 55.1354 Evaluate side-chains 73 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 542 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 24 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 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8060 Z= 0.200 Angle : 0.575 5.528 10912 Z= 0.290 Chirality : 0.045 0.414 1233 Planarity : 0.004 0.049 1387 Dihedral : 8.898 66.573 1386 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.59 % Allowed : 10.42 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.25), residues: 948 helix: -1.58 (0.42), residues: 133 sheet: -2.99 (0.38), residues: 146 loop : -2.67 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS B 710 PHE 0.015 0.001 PHE A 45 TYR 0.013 0.001 TYR A 85 ARG 0.004 0.000 ARG A 474 *********************** 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 77 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.235 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: A 32 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7378 (pp) REVERT: D 46 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7137 (mm-30) outliers start: 5 outliers final: 4 residues processed: 76 average time/residue: 0.5652 time to fit residues: 56.5191 Evaluate side-chains 72 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 76 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8060 Z= 0.170 Angle : 0.559 4.771 10912 Z= 0.285 Chirality : 0.044 0.376 1233 Planarity : 0.003 0.046 1387 Dihedral : 8.097 59.512 1386 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.47 % Allowed : 11.94 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.25), residues: 948 helix: -1.37 (0.43), residues: 133 sheet: -3.00 (0.37), residues: 143 loop : -2.54 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 176 HIS 0.003 0.001 HIS A 539 PHE 0.014 0.001 PHE A 45 TYR 0.012 0.001 TYR A 224 ARG 0.005 0.000 ARG A 488 *********************** 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 72 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 1.326 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: A 32 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7338 (pp) REVERT: D 46 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7112 (mm-30) outliers start: 4 outliers final: 3 residues processed: 72 average time/residue: 0.5506 time to fit residues: 52.4088 Evaluate side-chains 71 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8060 Z= 0.193 Angle : 0.564 5.342 10912 Z= 0.286 Chirality : 0.045 0.421 1233 Planarity : 0.003 0.046 1387 Dihedral : 7.029 54.724 1386 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.82 % Allowed : 12.18 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.25), residues: 948 helix: -1.20 (0.44), residues: 133 sheet: -2.91 (0.38), residues: 145 loop : -2.44 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 176 HIS 0.003 0.001 HIS A 539 PHE 0.014 0.001 PHE A 45 TYR 0.013 0.001 TYR A 85 ARG 0.003 0.000 ARG A 488 *********************** 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 75 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 1.290 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: A 32 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7386 (pp) REVERT: D 46 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7136 (mm-30) outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 0.5598 time to fit residues: 54.2684 Evaluate side-chains 69 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 1.493 ------------------------------------------------------------------------------- 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 B residue 542 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** A 563 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8060 Z= 0.306 Angle : 0.634 6.942 10912 Z= 0.327 Chirality : 0.047 0.569 1233 Planarity : 0.004 0.048 1387 Dihedral : 6.673 41.979 1386 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.87 % Favored : 87.13 % Rotamer: Outliers : 1.41 % Allowed : 12.65 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.25), residues: 948 helix: -1.34 (0.44), residues: 133 sheet: -3.01 (0.38), residues: 140 loop : -2.59 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 176 HIS 0.006 0.001 HIS A 539 PHE 0.019 0.001 PHE A 45 TYR 0.013 0.002 TYR B 708 ARG 0.004 0.000 ARG B 389 *********************** 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 73 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 1.112 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: A 32 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7410 (pp) REVERT: D 46 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7192 (mm-30) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.5508 time to fit residues: 52.0314 Evaluate side-chains 69 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 537 LEU Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain D residue 17 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.0030 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8060 Z= 0.160 Angle : 0.553 5.924 10912 Z= 0.284 Chirality : 0.044 0.375 1233 Planarity : 0.003 0.045 1387 Dihedral : 6.003 45.646 1386 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.59 % Allowed : 13.35 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.25), residues: 948 helix: -1.13 (0.45), residues: 133 sheet: -2.80 (0.39), residues: 135 loop : -2.38 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 176 HIS 0.004 0.001 HIS A 539 PHE 0.015 0.001 PHE A 45 TYR 0.012 0.001 TYR A 224 ARG 0.003 0.000 ARG B 389 *********************** 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: 5 poor density : 65 time to evaluate : 1.319 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: D 46 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7016 (mm-30) outliers start: 5 outliers final: 4 residues processed: 70 average time/residue: 0.5685 time to fit residues: 52.1912 Evaluate side-chains 62 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8060 Z= 0.275 Angle : 0.610 6.381 10912 Z= 0.315 Chirality : 0.046 0.561 1233 Planarity : 0.004 0.044 1387 Dihedral : 6.103 42.413 1386 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.45 % Favored : 87.55 % Rotamer: Outliers : 0.82 % Allowed : 14.17 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.25), residues: 948 helix: -1.19 (0.45), residues: 133 sheet: -2.93 (0.39), residues: 135 loop : -2.51 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 551 HIS 0.005 0.001 HIS A 539 PHE 0.017 0.001 PHE A 45 TYR 0.012 0.001 TYR B 708 ARG 0.003 0.000 ARG A 108 *********************** 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 67 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 1.284 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: D 46 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7121 (mm-30) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.5704 time to fit residues: 49.4476 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 : 1.303 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 468 CYS Chi-restraints excluded: chain B residue 586 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8060 Z= 0.171 Angle : 0.554 5.980 10912 Z= 0.286 Chirality : 0.044 0.403 1233 Planarity : 0.003 0.043 1387 Dihedral : 5.674 32.927 1386 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 0.70 % Allowed : 14.40 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.25), residues: 948 helix: -1.07 (0.45), residues: 133 sheet: -2.83 (0.39), residues: 135 loop : -2.34 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 551 HIS 0.004 0.001 HIS A 539 PHE 0.014 0.001 PHE A 45 TYR 0.011 0.001 TYR A 85 ARG 0.002 0.000 ARG A 240 ********************** 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 69 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 1.364 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: D 46 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7165 (tp30) outliers start: 6 outliers final: 6 residues processed: 68 average time/residue: 0.7027 time to fit residues: 62.1644 Evaluate side-chains 66 residues out of total 854 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain B residue 308 CYS 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 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.076686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.067207 restraints weight = 120584.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.069586 restraints weight = 55106.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.071089 restraints weight = 32043.163| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8060 Z= 0.172 Angle : 0.560 6.436 10912 Z= 0.288 Chirality : 0.044 0.424 1233 Planarity : 0.003 0.042 1387 Dihedral : 5.549 33.327 1386 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 0.82 % Allowed : 14.29 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.26), residues: 948 helix: -1.03 (0.45), residues: 133 sheet: -2.79 (0.39), residues: 135 loop : -2.29 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 551 HIS 0.004 0.001 HIS A 539 PHE 0.014 0.001 PHE A 45 TYR 0.011 0.001 TYR B 579 ARG 0.002 0.000 ARG B 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3855.24 seconds wall clock time: 70 minutes 18.28 seconds (4218.28 seconds total)