Starting phenix.real_space_refine on Wed Sep 17 16:01:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7b_39811/09_2025/8z7b_39811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7b_39811/09_2025/8z7b_39811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z7b_39811/09_2025/8z7b_39811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7b_39811/09_2025/8z7b_39811.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z7b_39811/09_2025/8z7b_39811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7b_39811/09_2025/8z7b_39811.map" } resolution = 3.3 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= -0.049 sd= 0.280 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6122 2.51 5 N 1558 2.21 5 O 1854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9580 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "C" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2234 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 14, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2156 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 16, 'TRANS': 256} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: 2.62, per 1000 atoms: 0.27 Number of scatterers: 9580 At special positions: 0 Unit cell: (93.2, 124.888, 145.392, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1854 8.00 N 1558 7.00 C 6122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B 1 " - " ASN D 90 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 103 " " NAG D 703 " - " ASN D 322 " " NAG D 704 " - " ASN D 432 " " NAG E 1 " - " ASN D 546 " " NAG F 1 " - " ASN C 17 " " NAG G 1 " - " ASN C 122 " " NAG H 1 " - " ASN C 149 " " NAG I 1 " - " ASN C 61 " " NAG J 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 331 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 401.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 38.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.753A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 3.792A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 144 through 155 removed outlier: 4.201A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.633A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.677A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 252 removed outlier: 3.863A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.030A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.669A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.551A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 387 through 388 No H-bonds generated for 'chain 'D' and resid 387 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.615A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.397A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.225A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.878A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.898A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.541A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.718A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.253A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.734A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 78 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.734A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.074A pdb=" N PHE C 43 " --> pdb=" O ARG A 567 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.611A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.318A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 11.163A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU C 156 " --> pdb=" O GLY C 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.638A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.604A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 397 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3016 1.34 - 1.46: 2494 1.46 - 1.58: 4258 1.58 - 1.70: 0 1.70 - 1.81: 69 Bond restraints: 9837 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.09e+00 bond pdb=" C1 BMA K 3 " pdb=" C2 BMA K 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 9832 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 12969 1.24 - 2.47: 308 2.47 - 3.71: 81 3.71 - 4.94: 12 4.94 - 6.18: 5 Bond angle restraints: 13375 Sorted by residual: angle pdb=" C CYS D 498 " pdb=" N ASP D 499 " pdb=" CA ASP D 499 " ideal model delta sigma weight residual 120.09 123.81 -3.72 1.25e+00 6.40e-01 8.88e+00 angle pdb=" CA TYR D 385 " pdb=" CB TYR D 385 " pdb=" CG TYR D 385 " ideal model delta sigma weight residual 113.90 117.90 -4.00 1.80e+00 3.09e-01 4.94e+00 angle pdb=" C3 BMA K 3 " pdb=" C2 BMA K 3 " pdb=" O2 BMA K 3 " ideal model delta sigma weight residual 112.95 106.77 6.18 3.00e+00 1.11e-01 4.24e+00 angle pdb=" C ALA D 384 " pdb=" N TYR D 385 " pdb=" CA TYR D 385 " ideal model delta sigma weight residual 122.38 119.17 3.21 1.81e+00 3.05e-01 3.15e+00 angle pdb=" C4 BMA K 3 " pdb=" C5 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sigma weight residual 113.24 108.12 5.12 3.00e+00 1.11e-01 2.91e+00 ... (remaining 13370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.83: 5882 21.83 - 43.66: 155 43.66 - 65.49: 34 65.49 - 87.32: 15 87.32 - 109.15: 24 Dihedral angle restraints: 6110 sinusoidal: 2755 harmonic: 3355 Sorted by residual: dihedral pdb=" C2 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sinusoidal sigma weight residual 53.78 -55.37 109.15 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C2 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" C4 NAG I 1 " pdb=" O4 NAG I 1 " ideal model delta sinusoidal sigma weight residual 175.11 66.30 108.81 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O4 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C5 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.85 108.56 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 6107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1305 0.059 - 0.118: 184 0.118 - 0.177: 6 0.177 - 0.236: 0 0.236 - 0.295: 2 Chirality restraints: 1497 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 1494 not shown) Planarity restraints: 1713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 388 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO D 389 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 389 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 389 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO D 235 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00 pdb=" N PRO D 583 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.017 5.00e-02 4.00e+02 ... (remaining 1710 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2564 2.80 - 3.33: 8683 3.33 - 3.85: 15804 3.85 - 4.38: 18321 4.38 - 4.90: 31954 Nonbonded interactions: 77326 Sorted by model distance: nonbonded pdb=" O ASN C 99 " pdb=" NH1 ARG C 102 " model vdw 2.279 3.120 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.296 3.040 nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.303 3.040 nonbonded pdb=" O LEU D 29 " pdb=" ND2 ASN D 33 " model vdw 2.317 3.120 nonbonded pdb=" N ASN C 149 " pdb=" OD1 ASN C 149 " model vdw 2.320 3.120 ... (remaining 77321 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 11.090 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 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 : 0.003 0.040 9871 Z= 0.143 Angle : 0.484 6.178 13467 Z= 0.231 Chirality : 0.042 0.295 1497 Planarity : 0.003 0.033 1698 Dihedral : 13.467 109.146 3924 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 4.64 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.22), residues: 1137 helix: -0.11 (0.25), residues: 393 sheet: -1.01 (0.44), residues: 134 loop : -2.37 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 582 TYR 0.019 0.001 TYR D 385 PHE 0.009 0.001 PHE D 369 TRP 0.005 0.001 TRP D 168 HIS 0.003 0.000 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9837) covalent geometry : angle 0.47486 (13375) SS BOND : bond 0.00108 ( 10) SS BOND : angle 0.42723 ( 20) hydrogen bonds : bond 0.17013 ( 392) hydrogen bonds : angle 7.10031 ( 1137) link_BETA1-4 : bond 0.00336 ( 9) link_BETA1-4 : angle 1.47890 ( 27) link_NAG-ASN : bond 0.00220 ( 15) link_NAG-ASN : angle 1.30588 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 SER cc_start: 0.8800 (m) cc_final: 0.8470 (t) REVERT: D 480 MET cc_start: 0.9093 (mtp) cc_final: 0.8751 (mtp) REVERT: C 129 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8768 (mtpp) REVERT: C 190 ARG cc_start: 0.8528 (mtt90) cc_final: 0.8097 (mtm180) REVERT: A 481 ASN cc_start: 0.8232 (t0) cc_final: 0.7991 (t0) REVERT: A 557 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8325 (mtmm) outliers start: 30 outliers final: 8 residues processed: 219 average time/residue: 0.1271 time to fit residues: 37.0915 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN D 137 ASN D 373 HIS D 442 GLN D 522 GLN D 524 GLN C 23 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN A 354 ASN A 414 GLN A 493 GLN A 580 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.044035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2391 r_free = 0.2391 target = 0.036496 restraints weight = 33685.125| |-----------------------------------------------------------------------------| r_work (start): 0.2388 rms_B_bonded: 2.50 r_work: 0.2278 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2170 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9871 Z= 0.155 Angle : 0.621 7.346 13467 Z= 0.308 Chirality : 0.045 0.230 1497 Planarity : 0.004 0.032 1698 Dihedral : 13.190 90.617 1754 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.55 % Allowed : 9.57 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.24), residues: 1137 helix: 0.81 (0.27), residues: 399 sheet: -0.46 (0.45), residues: 122 loop : -1.89 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 78 TYR 0.026 0.002 TYR D 385 PHE 0.021 0.002 PHE C 133 TRP 0.012 0.001 TRP D 478 HIS 0.006 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9837) covalent geometry : angle 0.59780 (13375) SS BOND : bond 0.00612 ( 10) SS BOND : angle 3.02619 ( 20) hydrogen bonds : bond 0.04578 ( 392) hydrogen bonds : angle 5.28717 ( 1137) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 2.08564 ( 27) link_NAG-ASN : bond 0.00194 ( 15) link_NAG-ASN : angle 1.60890 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 74 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8906 (tttp) REVERT: D 131 LYS cc_start: 0.9247 (mtpp) cc_final: 0.8934 (mtpp) REVERT: D 160 GLU cc_start: 0.8548 (tt0) cc_final: 0.8175 (tt0) REVERT: D 431 ASP cc_start: 0.8489 (t0) cc_final: 0.8027 (t0) REVERT: D 480 MET cc_start: 0.9267 (mtp) cc_final: 0.9047 (mtp) REVERT: C 53 ASP cc_start: 0.9035 (t0) cc_final: 0.8629 (t0) REVERT: C 183 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8522 (mm110) REVERT: A 468 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8952 (mt) outliers start: 36 outliers final: 16 residues processed: 161 average time/residue: 0.1063 time to fit residues: 23.8857 Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 0.0670 chunk 95 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 239 HIS D 397 ASN D 535 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.042356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2341 r_free = 0.2341 target = 0.034933 restraints weight = 34263.104| |-----------------------------------------------------------------------------| r_work (start): 0.2337 rms_B_bonded: 2.50 r_work: 0.2224 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2116 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9871 Z= 0.161 Angle : 0.635 8.795 13467 Z= 0.312 Chirality : 0.046 0.233 1497 Planarity : 0.004 0.045 1698 Dihedral : 11.622 87.297 1752 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.45 % Allowed : 10.16 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.24), residues: 1137 helix: 1.15 (0.27), residues: 400 sheet: -0.10 (0.47), residues: 110 loop : -1.66 (0.22), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 78 TYR 0.023 0.002 TYR D 385 PHE 0.015 0.002 PHE C 133 TRP 0.010 0.001 TRP D 478 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9837) covalent geometry : angle 0.60814 (13375) SS BOND : bond 0.00727 ( 10) SS BOND : angle 3.32504 ( 20) hydrogen bonds : bond 0.04554 ( 392) hydrogen bonds : angle 5.08263 ( 1137) link_BETA1-4 : bond 0.00187 ( 9) link_BETA1-4 : angle 2.19915 ( 27) link_NAG-ASN : bond 0.00171 ( 15) link_NAG-ASN : angle 1.72518 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8619 (mp0) cc_final: 0.8349 (pm20) REVERT: D 74 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8921 (tttp) REVERT: D 131 LYS cc_start: 0.9245 (mtpp) cc_final: 0.8798 (mtpp) REVERT: C 99 ASN cc_start: 0.8379 (m110) cc_final: 0.7933 (m-40) REVERT: C 183 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8525 (mm-40) REVERT: A 468 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8939 (mt) REVERT: A 571 ASP cc_start: 0.8282 (t0) cc_final: 0.8001 (t0) outliers start: 35 outliers final: 20 residues processed: 154 average time/residue: 0.1063 time to fit residues: 22.7515 Evaluate side-chains 137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.041431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2308 r_free = 0.2308 target = 0.033894 restraints weight = 34651.349| |-----------------------------------------------------------------------------| r_work (start): 0.2306 rms_B_bonded: 2.52 r_work: 0.2193 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2085 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9871 Z= 0.161 Angle : 0.650 9.624 13467 Z= 0.321 Chirality : 0.046 0.312 1497 Planarity : 0.004 0.030 1698 Dihedral : 10.800 85.553 1752 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.86 % Allowed : 11.24 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.46 (0.24), residues: 1137 helix: 1.28 (0.26), residues: 401 sheet: 0.01 (0.47), residues: 110 loop : -1.50 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 78 TYR 0.022 0.001 TYR D 385 PHE 0.014 0.001 PHE D 369 TRP 0.010 0.001 TRP D 478 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9837) covalent geometry : angle 0.62297 (13375) SS BOND : bond 0.00690 ( 10) SS BOND : angle 3.17391 ( 20) hydrogen bonds : bond 0.04521 ( 392) hydrogen bonds : angle 5.08855 ( 1137) link_BETA1-4 : bond 0.00297 ( 9) link_BETA1-4 : angle 2.19994 ( 27) link_NAG-ASN : bond 0.00209 ( 15) link_NAG-ASN : angle 1.96849 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8678 (mp0) cc_final: 0.8411 (pm20) REVERT: D 131 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8819 (mtpp) REVERT: D 160 GLU cc_start: 0.8641 (tt0) cc_final: 0.8436 (pt0) REVERT: D 497 TYR cc_start: 0.7846 (m-80) cc_final: 0.7554 (m-10) REVERT: C 183 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8535 (mm-40) REVERT: A 468 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8925 (mt) REVERT: A 571 ASP cc_start: 0.8269 (t0) cc_final: 0.8036 (t0) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.1040 time to fit residues: 20.3805 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.0570 chunk 43 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.040333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2272 r_free = 0.2272 target = 0.032860 restraints weight = 34493.477| |-----------------------------------------------------------------------------| r_work (start): 0.2269 rms_B_bonded: 2.51 r_work: 0.2154 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2045 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9871 Z= 0.182 Angle : 0.656 10.632 13467 Z= 0.323 Chirality : 0.046 0.281 1497 Planarity : 0.004 0.034 1698 Dihedral : 10.201 80.440 1751 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.16 % Allowed : 11.34 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.24), residues: 1137 helix: 1.41 (0.26), residues: 395 sheet: 0.03 (0.45), residues: 126 loop : -1.41 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 78 TYR 0.022 0.002 TYR D 385 PHE 0.016 0.002 PHE D 369 TRP 0.011 0.001 TRP D 478 HIS 0.005 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9837) covalent geometry : angle 0.62944 (13375) SS BOND : bond 0.00844 ( 10) SS BOND : angle 3.00792 ( 20) hydrogen bonds : bond 0.04804 ( 392) hydrogen bonds : angle 4.96377 ( 1137) link_BETA1-4 : bond 0.00239 ( 9) link_BETA1-4 : angle 2.21814 ( 27) link_NAG-ASN : bond 0.00206 ( 15) link_NAG-ASN : angle 2.02507 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: D 131 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8917 (mtpp) REVERT: C 183 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8544 (mm110) REVERT: C 218 GLN cc_start: 0.8678 (tt0) cc_final: 0.8424 (tm-30) REVERT: A 468 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8932 (mt) REVERT: A 571 ASP cc_start: 0.8403 (t0) cc_final: 0.8102 (t0) outliers start: 32 outliers final: 21 residues processed: 145 average time/residue: 0.0931 time to fit residues: 19.0544 Evaluate side-chains 137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 27 optimal weight: 0.0980 chunk 99 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN ** C 146 HIS ** 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 = 0.2538 r_free = 0.2538 target = 0.040646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.033198 restraints weight = 34536.837| |-----------------------------------------------------------------------------| r_work (start): 0.2277 rms_B_bonded: 2.51 r_work: 0.2165 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2057 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9871 Z= 0.141 Angle : 0.642 11.221 13467 Z= 0.312 Chirality : 0.046 0.298 1497 Planarity : 0.004 0.034 1698 Dihedral : 9.721 77.399 1751 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 11.44 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.24), residues: 1137 helix: 1.44 (0.26), residues: 402 sheet: 0.02 (0.44), residues: 125 loop : -1.32 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 78 TYR 0.021 0.001 TYR D 497 PHE 0.013 0.001 PHE D 369 TRP 0.009 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9837) covalent geometry : angle 0.61164 (13375) SS BOND : bond 0.00893 ( 10) SS BOND : angle 2.77528 ( 20) hydrogen bonds : bond 0.04409 ( 392) hydrogen bonds : angle 4.87527 ( 1137) link_BETA1-4 : bond 0.00243 ( 9) link_BETA1-4 : angle 2.32148 ( 27) link_NAG-ASN : bond 0.00217 ( 15) link_NAG-ASN : angle 2.35494 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: D 131 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8835 (mtpp) REVERT: C 183 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8520 (mm110) REVERT: A 468 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8901 (mt) REVERT: A 537 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.9026 (ttpp) REVERT: A 571 ASP cc_start: 0.8387 (t0) cc_final: 0.7937 (t0) outliers start: 33 outliers final: 24 residues processed: 140 average time/residue: 0.1031 time to fit residues: 20.1536 Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 27 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.040183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.032742 restraints weight = 34827.397| |-----------------------------------------------------------------------------| r_work (start): 0.2264 rms_B_bonded: 2.53 r_work: 0.2149 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2041 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9871 Z= 0.155 Angle : 0.660 15.738 13467 Z= 0.321 Chirality : 0.047 0.318 1497 Planarity : 0.004 0.035 1698 Dihedral : 9.518 75.192 1751 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.25 % Allowed : 11.83 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.25), residues: 1137 helix: 1.42 (0.26), residues: 402 sheet: 0.27 (0.42), residues: 143 loop : -1.30 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 78 TYR 0.020 0.001 TYR D 385 PHE 0.014 0.001 PHE D 369 TRP 0.007 0.001 TRP D 477 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9837) covalent geometry : angle 0.63205 (13375) SS BOND : bond 0.00873 ( 10) SS BOND : angle 2.72656 ( 20) hydrogen bonds : bond 0.04545 ( 392) hydrogen bonds : angle 4.84944 ( 1137) link_BETA1-4 : bond 0.00211 ( 9) link_BETA1-4 : angle 2.29140 ( 27) link_NAG-ASN : bond 0.00220 ( 15) link_NAG-ASN : angle 2.23160 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8686 (mp0) cc_final: 0.8470 (pm20) REVERT: D 131 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8813 (mtpp) REVERT: D 474 MET cc_start: 0.8682 (mmp) cc_final: 0.8472 (mmp) REVERT: D 600 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8750 (mmtp) REVERT: C 96 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8240 (tp30) REVERT: A 408 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8905 (ppt170) REVERT: A 468 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8913 (mt) REVERT: A 537 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.9033 (ttpp) REVERT: A 571 ASP cc_start: 0.8437 (t0) cc_final: 0.8071 (t0) outliers start: 33 outliers final: 25 residues processed: 139 average time/residue: 0.1050 time to fit residues: 20.2058 Evaluate side-chains 142 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.039579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2248 r_free = 0.2248 target = 0.032188 restraints weight = 34505.362| |-----------------------------------------------------------------------------| r_work (start): 0.2245 rms_B_bonded: 2.50 r_work: 0.2130 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2021 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9871 Z= 0.173 Angle : 0.687 13.878 13467 Z= 0.334 Chirality : 0.047 0.303 1497 Planarity : 0.004 0.035 1698 Dihedral : 9.208 71.381 1751 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.25 % Allowed : 11.64 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.10 (0.24), residues: 1137 helix: 1.45 (0.26), residues: 396 sheet: 0.35 (0.42), residues: 143 loop : -1.27 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 78 TYR 0.021 0.001 TYR D 385 PHE 0.015 0.002 PHE D 369 TRP 0.011 0.001 TRP D 478 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9837) covalent geometry : angle 0.65518 (13375) SS BOND : bond 0.00818 ( 10) SS BOND : angle 2.70995 ( 20) hydrogen bonds : bond 0.04721 ( 392) hydrogen bonds : angle 4.88042 ( 1137) link_BETA1-4 : bond 0.00205 ( 9) link_BETA1-4 : angle 2.43974 ( 27) link_NAG-ASN : bond 0.00226 ( 15) link_NAG-ASN : angle 2.61335 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8711 (mp0) cc_final: 0.8497 (pm20) REVERT: C 58 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7929 (m-10) REVERT: C 96 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8057 (tp30) REVERT: A 408 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8916 (ppt170) REVERT: A 468 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8877 (mt) REVERT: A 537 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9050 (ttpp) REVERT: A 571 ASP cc_start: 0.8489 (t0) cc_final: 0.7998 (t0) outliers start: 33 outliers final: 26 residues processed: 138 average time/residue: 0.1119 time to fit residues: 21.3968 Evaluate side-chains 141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.039648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.032283 restraints weight = 34851.827| |-----------------------------------------------------------------------------| r_work (start): 0.2248 rms_B_bonded: 2.51 r_work: 0.2134 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2025 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9871 Z= 0.158 Angle : 0.683 16.606 13467 Z= 0.330 Chirality : 0.047 0.308 1497 Planarity : 0.004 0.035 1698 Dihedral : 8.899 70.958 1751 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.16 % Allowed : 11.64 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.04 (0.24), residues: 1137 helix: 1.49 (0.26), residues: 396 sheet: 0.37 (0.41), residues: 143 loop : -1.22 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 78 TYR 0.020 0.001 TYR D 385 PHE 0.014 0.001 PHE D 369 TRP 0.009 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 9837) covalent geometry : angle 0.65368 (13375) SS BOND : bond 0.00953 ( 10) SS BOND : angle 2.59260 ( 20) hydrogen bonds : bond 0.04556 ( 392) hydrogen bonds : angle 4.85640 ( 1137) link_BETA1-4 : bond 0.00232 ( 9) link_BETA1-4 : angle 2.39198 ( 27) link_NAG-ASN : bond 0.00220 ( 15) link_NAG-ASN : angle 2.49203 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8721 (mp0) cc_final: 0.8521 (pm20) REVERT: D 131 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8922 (mtpp) REVERT: D 497 TYR cc_start: 0.7577 (m-10) cc_final: 0.7331 (m-10) REVERT: C 58 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7870 (m-10) REVERT: C 96 GLU cc_start: 0.8208 (mm-30) cc_final: 0.8003 (tp30) REVERT: A 408 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8910 (ppt170) REVERT: A 468 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8883 (mt) REVERT: A 571 ASP cc_start: 0.8528 (t0) cc_final: 0.8062 (t0) outliers start: 32 outliers final: 26 residues processed: 135 average time/residue: 0.1086 time to fit residues: 20.2227 Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 378 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.039062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2232 r_free = 0.2232 target = 0.031713 restraints weight = 34692.109| |-----------------------------------------------------------------------------| r_work (start): 0.2230 rms_B_bonded: 2.50 r_work: 0.2114 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2006 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9871 Z= 0.178 Angle : 0.703 17.041 13467 Z= 0.341 Chirality : 0.048 0.315 1497 Planarity : 0.004 0.035 1698 Dihedral : 8.737 71.324 1750 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.76 % Allowed : 12.23 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 aren not related in a simple way. whole: -0.07 (0.24), residues: 1137 helix: 1.43 (0.26), residues: 396 sheet: 0.30 (0.41), residues: 145 loop : -1.20 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 78 TYR 0.021 0.001 TYR D 385 PHE 0.015 0.002 PHE D 369 TRP 0.010 0.001 TRP D 478 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9837) covalent geometry : angle 0.67262 (13375) SS BOND : bond 0.00914 ( 10) SS BOND : angle 2.80830 ( 20) hydrogen bonds : bond 0.04797 ( 392) hydrogen bonds : angle 4.85647 ( 1137) link_BETA1-4 : bond 0.00192 ( 9) link_BETA1-4 : angle 2.45770 ( 27) link_NAG-ASN : bond 0.00201 ( 15) link_NAG-ASN : angle 2.47689 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.388 Fit side-chains REVERT: D 57 GLU cc_start: 0.8728 (mp0) cc_final: 0.8525 (pm20) REVERT: D 131 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8849 (mtpp) REVERT: C 58 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: A 408 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8931 (ppt170) REVERT: A 468 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 571 ASP cc_start: 0.8593 (t0) cc_final: 0.8135 (t0) outliers start: 28 outliers final: 24 residues processed: 133 average time/residue: 0.1102 time to fit residues: 20.4198 Evaluate side-chains 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN C 69 HIS A 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.039197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.031835 restraints weight = 34719.823| |-----------------------------------------------------------------------------| r_work (start): 0.2234 rms_B_bonded: 2.51 r_work: 0.2120 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2011 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9871 Z= 0.168 Angle : 0.701 17.234 13467 Z= 0.339 Chirality : 0.047 0.309 1497 Planarity : 0.004 0.035 1698 Dihedral : 8.585 70.315 1750 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.86 % Allowed : 12.13 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.24), residues: 1137 helix: 1.47 (0.26), residues: 396 sheet: 0.28 (0.41), residues: 145 loop : -1.20 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 78 TYR 0.020 0.001 TYR D 385 PHE 0.014 0.001 PHE D 369 TRP 0.009 0.001 TRP D 477 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9837) covalent geometry : angle 0.67217 (13375) SS BOND : bond 0.00920 ( 10) SS BOND : angle 2.72937 ( 20) hydrogen bonds : bond 0.04664 ( 392) hydrogen bonds : angle 4.85038 ( 1137) link_BETA1-4 : bond 0.00212 ( 9) link_BETA1-4 : angle 2.47098 ( 27) link_NAG-ASN : bond 0.00207 ( 15) link_NAG-ASN : angle 2.40122 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.31 seconds wall clock time: 45 minutes 24.24 seconds (2724.24 seconds total)