Starting phenix.real_space_refine on Fri Mar 14 05:09:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7b_39811/03_2025/8z7b_39811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7b_39811/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7b_39811/03_2025/8z7b_39811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7b_39811/03_2025/8z7b_39811.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7b_39811/03_2025/8z7b_39811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7b_39811/03_2025/8z7b_39811.cif" } resolution = 3.3 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= -0.049 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.43, per 1000 atoms: 0.67 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: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.65 Time building geometry restraints manager: 3.04 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: 4.150 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.000 ------------------------------------------------------------------------------- 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 9837 Z= 0.189 Angle : 0.475 6.178 13375 Z= 0.229 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 : 5.18 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 (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: -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 TRP 0.005 0.001 TRP D 168 HIS 0.003 0.000 HIS D 34 PHE 0.009 0.001 PHE D 369 TYR 0.019 0.001 TYR D 385 ARG 0.002 0.000 ARG D 582 *********************** 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 : 1.060 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: 0.8471 (t) REVERT: D 480 MET cc_start: 0.9093 (mtp) cc_final: 0.8732 (mtp) REVERT: C 129 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8769 (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: 0.2602 time to fit residues: 76.1479 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 : 1.314 ------------------------------------------------------------------------------- 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 95 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN D 101 GLN D 137 ASN D 373 HIS D 397 ASN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.043665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.036118 restraints weight = 33342.032| |-----------------------------------------------------------------------------| r_work (start): 0.2376 rms_B_bonded: 2.48 r_work: 0.2266 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2159 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9837 Z= 0.241 Angle : 0.605 7.222 13375 Z= 0.304 Chirality : 0.046 0.251 1497 Planarity : 0.004 0.035 1698 Dihedral : 12.943 89.380 1754 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.65 % Allowed : 9.57 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1137 helix: 0.82 (0.26), residues: 399 sheet: -0.45 (0.45), residues: 122 loop : -1.87 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 478 HIS 0.006 0.001 HIS C 49 PHE 0.018 0.002 PHE C 133 TYR 0.026 0.002 TYR D 385 ARG 0.006 0.001 ARG C 158 *********************** 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: 37 poor density : 131 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: D 74 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8911 (tttp) REVERT: D 131 LYS cc_start: 0.9246 (mtpp) cc_final: 0.8929 (mtpp) REVERT: D 431 ASP cc_start: 0.8486 (t0) cc_final: 0.7869 (t0) REVERT: D 480 MET cc_start: 0.9234 (mtp) cc_final: 0.9019 (mtp) REVERT: C 183 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8538 (mm110) REVERT: A 468 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8929 (mt) outliers start: 37 outliers final: 15 residues processed: 161 average time/residue: 0.2263 time to fit residues: 50.9159 Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN D 535 HIS ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.040685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2285 r_free = 0.2285 target = 0.033277 restraints weight = 34628.431| |-----------------------------------------------------------------------------| r_work (start): 0.2280 rms_B_bonded: 2.50 r_work: 0.2166 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2057 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9837 Z= 0.323 Angle : 0.654 8.529 13375 Z= 0.328 Chirality : 0.047 0.244 1497 Planarity : 0.004 0.043 1698 Dihedral : 11.539 86.168 1752 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.45 % Allowed : 11.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1137 helix: 1.09 (0.26), residues: 400 sheet: 0.16 (0.43), residues: 144 loop : -1.67 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 478 HIS 0.006 0.002 HIS C 245 PHE 0.018 0.002 PHE D 369 TYR 0.026 0.002 TYR D 385 ARG 0.005 0.001 ARG C 78 *********************** 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 160 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8671 (mp0) cc_final: 0.8398 (pm20) REVERT: D 74 LYS cc_start: 0.9141 (mtpp) cc_final: 0.8933 (tttp) REVERT: D 131 LYS cc_start: 0.9295 (mtpp) cc_final: 0.8841 (mtpp) REVERT: D 431 ASP cc_start: 0.8312 (t0) cc_final: 0.7920 (t0) REVERT: C 145 TYR cc_start: 0.9071 (t80) cc_final: 0.8826 (t80) REVERT: A 324 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7614 (mt-10) REVERT: A 468 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8930 (mt) REVERT: A 571 ASP cc_start: 0.8470 (t0) cc_final: 0.8195 (t0) outliers start: 35 outliers final: 21 residues processed: 153 average time/residue: 0.2434 time to fit residues: 52.4655 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 : 1.228 ------------------------------------------------------------------------------- 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 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 136 CYS Chi-restraints excluded: chain C residue 143 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.040737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2288 r_free = 0.2288 target = 0.033288 restraints weight = 34177.245| |-----------------------------------------------------------------------------| r_work (start): 0.2284 rms_B_bonded: 2.49 r_work: 0.2171 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2062 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9837 Z= 0.249 Angle : 0.646 12.876 13375 Z= 0.324 Chirality : 0.046 0.321 1497 Planarity : 0.004 0.031 1698 Dihedral : 10.926 84.970 1752 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.86 % Allowed : 12.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.24), residues: 1137 helix: 1.26 (0.26), residues: 401 sheet: 0.03 (0.46), residues: 110 loop : -1.51 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 478 HIS 0.006 0.001 HIS C 69 PHE 0.014 0.001 PHE D 369 TYR 0.022 0.001 TYR D 497 ARG 0.006 0.000 ARG C 78 *********************** 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 143 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8693 (mp0) cc_final: 0.8397 (pm20) REVERT: D 131 LYS cc_start: 0.9270 (mtpp) cc_final: 0.8896 (mtpp) REVERT: D 166 GLU cc_start: 0.8923 (tp30) cc_final: 0.8720 (tp30) REVERT: D 431 ASP cc_start: 0.8344 (t0) cc_final: 0.8058 (t0) REVERT: D 433 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8542 (mt-10) REVERT: A 468 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 571 ASP cc_start: 0.8332 (t0) cc_final: 0.8092 (t0) outliers start: 29 outliers final: 17 residues processed: 137 average time/residue: 0.2334 time to fit residues: 44.9763 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.408 ------------------------------------------------------------------------------- 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 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 10 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.040288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2273 r_free = 0.2273 target = 0.032908 restraints weight = 34404.289| |-----------------------------------------------------------------------------| r_work (start): 0.2268 rms_B_bonded: 2.48 r_work: 0.2154 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2047 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9837 Z= 0.269 Angle : 0.626 10.478 13375 Z= 0.314 Chirality : 0.047 0.272 1497 Planarity : 0.004 0.039 1698 Dihedral : 10.252 80.356 1751 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.06 % Allowed : 11.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1137 helix: 1.28 (0.26), residues: 402 sheet: 0.08 (0.45), residues: 126 loop : -1.40 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 478 HIS 0.005 0.001 HIS C 245 PHE 0.015 0.002 PHE D 369 TYR 0.021 0.001 TYR D 385 ARG 0.007 0.001 ARG A 346 *********************** 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 148 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 1.219 Fit side-chains REVERT: D 57 GLU cc_start: 0.8677 (mp0) cc_final: 0.8385 (pm20) REVERT: D 131 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8860 (mtpp) REVERT: C 145 TYR cc_start: 0.9104 (t80) cc_final: 0.8901 (t80) REVERT: C 218 GLN cc_start: 0.8675 (tt0) cc_final: 0.8405 (tm-30) REVERT: A 468 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8891 (mt) REVERT: A 571 ASP cc_start: 0.8384 (t0) cc_final: 0.8083 (t0) outliers start: 31 outliers final: 21 residues processed: 140 average time/residue: 0.2200 time to fit residues: 43.3256 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 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 15 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 44 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN ** 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 = 0.2541 r_free = 0.2541 target = 0.040756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2287 r_free = 0.2287 target = 0.033292 restraints weight = 34271.510| |-----------------------------------------------------------------------------| r_work (start): 0.2284 rms_B_bonded: 2.51 r_work: 0.2170 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2062 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9837 Z= 0.215 Angle : 0.613 11.262 13375 Z= 0.305 Chirality : 0.046 0.310 1497 Planarity : 0.004 0.034 1698 Dihedral : 9.793 77.241 1751 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.86 % Allowed : 12.03 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1137 helix: 1.38 (0.26), residues: 402 sheet: 0.16 (0.43), residues: 130 loop : -1.33 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.004 0.001 HIS C 245 PHE 0.013 0.001 PHE D 369 TYR 0.018 0.001 TYR D 385 ARG 0.007 0.001 ARG C 78 *********************** 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 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.038 Fit side-chains REVERT: D 131 LYS cc_start: 0.9193 (mtpp) cc_final: 0.8928 (mtpp) REVERT: A 468 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8922 (mt) REVERT: A 537 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8823 (ttpp) REVERT: A 571 ASP cc_start: 0.8451 (t0) cc_final: 0.8021 (t0) outliers start: 29 outliers final: 20 residues processed: 133 average time/residue: 0.2174 time to fit residues: 41.6995 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 536 GLU 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 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 65 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.038843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.031491 restraints weight = 34796.740| |-----------------------------------------------------------------------------| r_work (start): 0.2220 rms_B_bonded: 2.49 r_work: 0.2104 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.1996 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.1996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9837 Z= 0.344 Angle : 0.686 16.913 13375 Z= 0.343 Chirality : 0.048 0.331 1497 Planarity : 0.004 0.036 1698 Dihedral : 9.672 72.993 1751 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.96 % Allowed : 12.43 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1137 helix: 1.38 (0.26), residues: 396 sheet: 0.29 (0.42), residues: 145 loop : -1.27 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.005 0.001 HIS C 245 PHE 0.016 0.002 PHE D 369 TYR 0.022 0.002 TYR D 385 ARG 0.007 0.001 ARG C 78 *********************** 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 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.130 Fit side-chains REVERT: D 131 LYS cc_start: 0.9185 (mtpp) cc_final: 0.8920 (mtpp) REVERT: D 497 TYR cc_start: 0.7672 (m-10) cc_final: 0.7187 (m-10) REVERT: D 600 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8784 (mmtp) REVERT: C 58 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8043 (m-10) REVERT: C 96 GLU cc_start: 0.8271 (tp30) cc_final: 0.7887 (tp30) REVERT: A 468 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8907 (mt) REVERT: A 571 ASP cc_start: 0.8511 (t0) cc_final: 0.8013 (t0) outliers start: 30 outliers final: 23 residues processed: 137 average time/residue: 0.2293 time to fit residues: 44.1100 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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 58 PHE 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 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 82 optimal weight: 0.0370 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 99 ASN ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.039520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.032276 restraints weight = 35259.215| |-----------------------------------------------------------------------------| r_work (start): 0.2242 rms_B_bonded: 2.49 r_work: 0.2127 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2019 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9837 Z= 0.240 Angle : 0.656 14.531 13375 Z= 0.323 Chirality : 0.047 0.343 1497 Planarity : 0.004 0.035 1698 Dihedral : 9.191 71.357 1751 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.76 % Allowed : 12.72 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1137 helix: 1.42 (0.26), residues: 396 sheet: 0.30 (0.42), residues: 145 loop : -1.23 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.004 0.001 HIS D 374 PHE 0.014 0.001 PHE D 369 TYR 0.019 0.001 TYR D 385 ARG 0.007 0.001 ARG C 78 *********************** 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 139 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 1.026 Fit side-chains REVERT: C 58 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.7964 (m-10) REVERT: C 96 GLU cc_start: 0.8162 (tp30) cc_final: 0.7759 (tp30) REVERT: A 468 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8878 (mt) REVERT: A 571 ASP cc_start: 0.8488 (t0) cc_final: 0.7993 (t0) outliers start: 28 outliers final: 22 residues processed: 130 average time/residue: 0.2116 time to fit residues: 39.2154 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 58 PHE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 0.0870 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.0570 chunk 77 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 HIS C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.040167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2268 r_free = 0.2268 target = 0.032773 restraints weight = 34526.581| |-----------------------------------------------------------------------------| r_work (start): 0.2266 rms_B_bonded: 2.50 r_work: 0.2153 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2044 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9837 Z= 0.211 Angle : 0.647 16.957 13375 Z= 0.318 Chirality : 0.046 0.305 1497 Planarity : 0.004 0.034 1698 Dihedral : 8.856 70.046 1751 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.76 % Allowed : 12.72 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1137 helix: 1.43 (0.26), residues: 402 sheet: 0.39 (0.42), residues: 143 loop : -1.21 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.018 0.001 TYR D 385 ARG 0.008 0.000 ARG C 78 *********************** 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 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.221 Fit side-chains revert: symmetry clash REVERT: C 58 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: A 468 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8898 (mt) REVERT: A 571 ASP cc_start: 0.8539 (t0) cc_final: 0.8073 (t0) outliers start: 28 outliers final: 21 residues processed: 133 average time/residue: 0.2204 time to fit residues: 42.0827 Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 136 CYS Chi-restraints excluded: chain C residue 146 HIS 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 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 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** A 321 GLN ** 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 = 0.2494 r_free = 0.2494 target = 0.039237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2238 r_free = 0.2238 target = 0.031915 restraints weight = 34859.581| |-----------------------------------------------------------------------------| r_work (start): 0.2235 rms_B_bonded: 2.49 r_work: 0.2121 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2012 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9837 Z= 0.275 Angle : 0.672 18.015 13375 Z= 0.335 Chirality : 0.048 0.308 1497 Planarity : 0.004 0.034 1698 Dihedral : 8.540 66.118 1747 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.37 % Allowed : 13.02 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1137 helix: 1.40 (0.26), residues: 402 sheet: 0.31 (0.42), residues: 145 loop : -1.21 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 478 HIS 0.007 0.001 HIS C 146 PHE 0.015 0.001 PHE D 369 TYR 0.020 0.001 TYR D 385 ARG 0.007 0.001 ARG C 78 ********************** 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 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 1.018 Fit side-chains REVERT: C 58 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.7956 (m-10) REVERT: A 468 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8883 (mt) REVERT: A 571 ASP cc_start: 0.8574 (t0) cc_final: 0.8110 (t0) outliers start: 24 outliers final: 19 residues processed: 130 average time/residue: 0.2038 time to fit residues: 37.9668 Evaluate side-chains 130 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 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 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 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 33 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 69 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.039056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2237 r_free = 0.2237 target = 0.031895 restraints weight = 34926.312| |-----------------------------------------------------------------------------| r_work (start): 0.2229 rms_B_bonded: 2.45 r_work: 0.2114 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2006 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9837 Z= 0.276 Angle : 0.689 17.904 13375 Z= 0.340 Chirality : 0.048 0.309 1497 Planarity : 0.004 0.044 1698 Dihedral : 8.389 64.997 1747 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.17 % Allowed : 13.12 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1137 helix: 1.46 (0.26), residues: 395 sheet: 0.31 (0.42), residues: 145 loop : -1.19 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 478 HIS 0.004 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.020 0.001 TYR D 385 ARG 0.007 0.001 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4807.26 seconds wall clock time: 85 minutes 24.88 seconds (5124.88 seconds total)