Starting phenix.real_space_refine on Fri Feb 14 01:14:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7b_39811/02_2025/8z7b_39811.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7b_39811/02_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_39811/02_2025/8z7b_39811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7b_39811/02_2025/8z7b_39811.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7b_39811/02_2025/8z7b_39811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7b_39811/02_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-5592/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: 6.42, 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: 2.80 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 2.95 Time building geometry restraints manager: 3.17 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: 4.190 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.430 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.110 ------------------------------------------------------------------------------- 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 : 1.140 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: 0.2615 time to fit residues: 75.7160 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 : 1.149 ------------------------------------------------------------------------------- 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 = 0.2628 r_free = 0.2628 target = 0.043714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.036251 restraints weight = 33499.468| |-----------------------------------------------------------------------------| r_work (start): 0.2377 rms_B_bonded: 2.48 r_work: 0.2266 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2160 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 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 89.379 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 : 0.926 Fit side-chains revert: symmetry clash REVERT: D 74 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8912 (tttp) REVERT: D 131 LYS cc_start: 0.9245 (mtpp) cc_final: 0.8928 (mtpp) REVERT: D 431 ASP cc_start: 0.8486 (t0) cc_final: 0.7867 (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: 0.2460 time to fit residues: 54.4381 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 : 1.126 ------------------------------------------------------------------------------- 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: 0.8980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.2563 r_free = 0.2563 target = 0.041427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.034031 restraints weight = 34570.395| |-----------------------------------------------------------------------------| r_work (start): 0.2307 rms_B_bonded: 2.50 r_work: 0.2193 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2084 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9837 Z= 0.289 Angle : 0.635 8.749 13375 Z= 0.317 Chirality : 0.046 0.230 1497 Planarity : 0.004 0.037 1698 Dihedral : 11.612 87.376 1752 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.45 % Allowed : 10.65 % Favored : 85.90 % 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: -0.66 (0.24), residues: 1137 helix: 1.14 (0.26), residues: 400 sheet: -0.06 (0.47), residues: 110 loop : -1.63 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 478 HIS 0.005 0.001 HIS D 417 PHE 0.016 0.002 PHE D 369 TYR 0.025 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 155 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8642 (mp0) cc_final: 0.8394 (pm20) REVERT: D 131 LYS cc_start: 0.9255 (mtpp) cc_final: 0.8819 (mtpp) REVERT: D 431 ASP cc_start: 0.8319 (t0) cc_final: 0.7945 (t0) REVERT: A 324 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: A 468 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 571 ASP cc_start: 0.8320 (t0) cc_final: 0.8046 (t0) outliers start: 35 outliers final: 19 residues processed: 148 average time/residue: 0.2288 time to fit residues: 47.4242 Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 324 GLU 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 24 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 88 optimal weight: 0.0870 chunk 94 optimal weight: 0.6980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 = 0.2574 r_free = 0.2574 target = 0.041802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.034296 restraints weight = 34035.702| |-----------------------------------------------------------------------------| r_work (start): 0.2319 rms_B_bonded: 2.49 r_work: 0.2207 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2098 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9837 Z= 0.213 Angle : 0.618 11.304 13375 Z= 0.308 Chirality : 0.046 0.314 1497 Planarity : 0.004 0.037 1698 Dihedral : 10.771 85.824 1752 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.76 % Allowed : 11.44 % Favored : 85.80 % 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: -0.44 (0.24), residues: 1137 helix: 1.31 (0.26), residues: 402 sheet: -0.17 (0.46), residues: 116 loop : -1.47 (0.23), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 478 HIS 0.003 0.001 HIS D 374 PHE 0.012 0.001 PHE C 157 TYR 0.020 0.001 TYR D 385 ARG 0.007 0.001 ARG A 346 *********************** 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 141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8656 (mp0) cc_final: 0.8356 (pm20) REVERT: D 79 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8842 (tp) REVERT: D 131 LYS cc_start: 0.9210 (mtpp) cc_final: 0.8759 (mtpp) REVERT: D 166 GLU cc_start: 0.8892 (tp30) cc_final: 0.8681 (tp30) REVERT: D 431 ASP cc_start: 0.8346 (t0) cc_final: 0.8047 (t0) REVERT: D 480 MET cc_start: 0.9272 (mtp) cc_final: 0.8997 (mtp) REVERT: D 497 TYR cc_start: 0.7724 (m-10) cc_final: 0.7434 (m-10) REVERT: A 468 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8942 (mt) REVERT: A 571 ASP cc_start: 0.8295 (t0) cc_final: 0.8074 (t0) outliers start: 28 outliers final: 18 residues processed: 134 average time/residue: 0.2435 time to fit residues: 46.1993 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 LEU 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 10 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 540 HIS ** C 69 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 = 0.2530 r_free = 0.2530 target = 0.040408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2276 r_free = 0.2276 target = 0.032964 restraints weight = 34286.562| |-----------------------------------------------------------------------------| r_work (start): 0.2273 rms_B_bonded: 2.50 r_work: 0.2158 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2050 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9837 Z= 0.285 Angle : 0.631 10.367 13375 Z= 0.317 Chirality : 0.047 0.271 1497 Planarity : 0.004 0.040 1698 Dihedral : 10.232 81.221 1751 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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 : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1137 helix: 1.31 (0.26), residues: 401 sheet: 0.02 (0.44), residues: 126 loop : -1.42 (0.23), residues: 610 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 0.016 0.002 PHE D 369 TYR 0.022 0.002 TYR D 385 ARG 0.007 0.001 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 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 153 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: D 57 GLU cc_start: 0.8676 (mp0) cc_final: 0.8357 (pm20) REVERT: D 79 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8880 (tp) REVERT: D 131 LYS cc_start: 0.9136 (mtpp) cc_final: 0.8829 (mtpp) REVERT: C 218 GLN cc_start: 0.8646 (tt0) cc_final: 0.8415 (tm-30) REVERT: A 468 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8924 (mt) REVERT: A 571 ASP cc_start: 0.8431 (t0) cc_final: 0.8133 (t0) outliers start: 33 outliers final: 22 residues processed: 145 average time/residue: 0.2198 time to fit residues: 44.9305 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 : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 LEU 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 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: 0.7980 chunk 63 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.2552 r_free = 0.2552 target = 0.041145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2300 r_free = 0.2300 target = 0.033694 restraints weight = 34317.676| |-----------------------------------------------------------------------------| r_work (start): 0.2294 rms_B_bonded: 2.49 r_work: 0.2181 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2074 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9837 Z= 0.217 Angle : 0.612 11.336 13375 Z= 0.304 Chirality : 0.046 0.341 1497 Planarity : 0.004 0.033 1698 Dihedral : 9.759 78.177 1751 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.35 % Allowed : 11.74 % 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 (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: 1.40 (0.26), residues: 402 sheet: 0.09 (0.43), residues: 130 loop : -1.32 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 165 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 0.000 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 146 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.125 Fit side-chains REVERT: D 131 LYS cc_start: 0.9123 (mtpp) cc_final: 0.8895 (mtpp) REVERT: D 497 TYR cc_start: 0.7673 (m-10) cc_final: 0.7133 (m-10) REVERT: A 468 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8892 (mt) REVERT: A 571 ASP cc_start: 0.8370 (t0) cc_final: 0.8049 (t0) outliers start: 34 outliers final: 22 residues processed: 139 average time/residue: 0.2252 time to fit residues: 43.7843 Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 62 optimal weight: 0.0670 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN 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 = 0.041459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.034007 restraints weight = 34122.772| |-----------------------------------------------------------------------------| r_work (start): 0.2310 rms_B_bonded: 2.49 r_work: 0.2196 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2088 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9837 Z= 0.205 Angle : 0.616 14.256 13375 Z= 0.305 Chirality : 0.046 0.302 1497 Planarity : 0.004 0.036 1698 Dihedral : 9.315 72.406 1751 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.76 % Allowed : 12.52 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1137 helix: 1.44 (0.26), residues: 402 sheet: 0.06 (0.43), residues: 130 loop : -1.24 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 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: 28 poor density : 116 time to evaluate : 1.243 Fit side-chains REVERT: D 57 GLU cc_start: 0.8691 (mp0) cc_final: 0.8485 (pm20) REVERT: D 497 TYR cc_start: 0.7593 (m-10) cc_final: 0.6992 (m-10) REVERT: C 96 GLU cc_start: 0.8147 (tp30) cc_final: 0.7716 (tp30) REVERT: C 145 TYR cc_start: 0.9085 (t80) cc_final: 0.8883 (t80) REVERT: A 468 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8896 (mt) REVERT: A 571 ASP cc_start: 0.8370 (t0) cc_final: 0.7905 (t0) outliers start: 28 outliers final: 23 residues processed: 137 average time/residue: 0.2224 time to fit residues: 43.0986 Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 335 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 12 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN 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 = 0.040736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.033333 restraints weight = 34971.075| |-----------------------------------------------------------------------------| r_work (start): 0.2284 rms_B_bonded: 2.51 r_work: 0.2170 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2062 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9837 Z= 0.232 Angle : 0.637 16.856 13375 Z= 0.316 Chirality : 0.047 0.315 1497 Planarity : 0.004 0.036 1698 Dihedral : 8.953 70.089 1750 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.76 % Allowed : 13.21 % Favored : 84.02 % 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: -0.09 (0.25), residues: 1137 helix: 1.43 (0.26), residues: 402 sheet: 0.28 (0.42), residues: 143 loop : -1.24 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 477 HIS 0.004 0.001 HIS C 245 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 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.115 Fit side-chains REVERT: D 57 GLU cc_start: 0.8700 (mp0) cc_final: 0.8475 (pm20) REVERT: D 131 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8760 (mtpp) REVERT: C 187 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8692 (mmtm) REVERT: A 408 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8929 (ppt170) REVERT: A 468 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8912 (mt) REVERT: A 571 ASP cc_start: 0.8468 (t0) cc_final: 0.8002 (t0) outliers start: 28 outliers final: 22 residues processed: 138 average time/residue: 0.2302 time to fit residues: 44.4555 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 335 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 77 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.040469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2279 r_free = 0.2279 target = 0.033069 restraints weight = 34606.222| |-----------------------------------------------------------------------------| r_work (start): 0.2275 rms_B_bonded: 2.50 r_work: 0.2162 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2055 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9837 Z= 0.225 Angle : 0.645 16.137 13375 Z= 0.318 Chirality : 0.047 0.348 1497 Planarity : 0.004 0.035 1698 Dihedral : 8.625 69.949 1750 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % 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: 1.46 (0.26), residues: 402 sheet: 0.29 (0.41), residues: 143 loop : -1.20 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 478 HIS 0.004 0.001 HIS D 374 PHE 0.013 0.001 PHE D 369 TYR 0.019 0.001 TYR D 385 ARG 0.007 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 : 1.024 Fit side-chains REVERT: D 57 GLU cc_start: 0.8693 (mp0) cc_final: 0.8476 (pm20) REVERT: A 408 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8936 (ppt170) REVERT: A 468 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8869 (mt) REVERT: A 571 ASP cc_start: 0.8479 (t0) cc_final: 0.7988 (t0) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.2159 time to fit residues: 40.1664 Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 86 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.039475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2246 r_free = 0.2246 target = 0.032106 restraints weight = 34929.374| |-----------------------------------------------------------------------------| r_work (start): 0.2242 rms_B_bonded: 2.51 r_work: 0.2131 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2024 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.3458 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= 0.269 Angle : 0.671 16.204 13375 Z= 0.331 Chirality : 0.047 0.306 1497 Planarity : 0.004 0.035 1698 Dihedral : 8.458 70.584 1750 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.47 % Allowed : 12.92 % 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: -0.05 (0.25), residues: 1137 helix: 1.41 (0.26), residues: 402 sheet: 0.25 (0.41), residues: 145 loop : -1.17 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 478 HIS 0.004 0.001 HIS D 374 PHE 0.015 0.001 PHE D 369 TYR 0.019 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 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.107 Fit side-chains REVERT: D 131 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8788 (mtpp) REVERT: C 187 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8614 (mmtm) REVERT: A 468 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8872 (mt) REVERT: A 571 ASP cc_start: 0.8552 (t0) cc_final: 0.8077 (t0) outliers start: 25 outliers final: 23 residues processed: 132 average time/residue: 0.2285 time to fit residues: 42.4796 Evaluate side-chains 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 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: 0.3980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 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 378 HIS C 69 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.039401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.032069 restraints weight = 34800.970| |-----------------------------------------------------------------------------| r_work (start): 0.2242 rms_B_bonded: 2.49 r_work: 0.2128 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2019 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9837 Z= 0.261 Angle : 0.674 15.896 13375 Z= 0.332 Chirality : 0.047 0.307 1497 Planarity : 0.004 0.035 1698 Dihedral : 8.267 70.302 1750 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.56 % Allowed : 12.92 % 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: 401 sheet: 0.29 (0.41), residues: 145 loop : -1.18 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4736.66 seconds wall clock time: 85 minutes 10.42 seconds (5110.42 seconds total)