Starting phenix.real_space_refine on Wed Sep 17 16:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z64_39791/09_2025/8z64_39791.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z64_39791/09_2025/8z64_39791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z64_39791/09_2025/8z64_39791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z64_39791/09_2025/8z64_39791.map" model { file = "/net/cci-nas-00/data/ceres_data/8z64_39791/09_2025/8z64_39791.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z64_39791/09_2025/8z64_39791.cif" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 47 5.16 5 C 6176 2.51 5 N 1576 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9665 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2145 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2369 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} 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: "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: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 Time building chain proxies: 2.40, per 1000 atoms: 0.25 Number of scatterers: 9665 At special positions: 0 Unit cell: (134.47, 82.11, 155.89, 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 47 16.00 O 1866 8.00 N 1576 7.00 C 6176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 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 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 C 291 " - pdb=" SG CYS C 301 " distance=2.03 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 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-ASN " NAG B 1 " - " ASN A 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 149 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG D 701 " - " ASN D 103 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 53 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN C 17 " " NAG G 1 " - " ASN C 122 " " NAG H 1 " - " ASN D 90 " " NAG I 1 " - " ASN D 546 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 351.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 37.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.727A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.788A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.606A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.715A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 76 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.502A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.535A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 194 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 220 through 250 removed outlier: 3.914A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.747A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 299 removed outlier: 3.555A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.889A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 386 removed outlier: 3.612A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) 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: 3.944A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.687A 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: 4.442A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 503 removed outlier: 3.612A pdb=" N LEU D 503 " --> pdb=" O PRO D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.531A pdb=" N ASN D 508 " --> pdb=" O HIS D 505 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 505 through 509' Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.161A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.523A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.716A 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 599 Proline residue: D 590 - end of helix removed outlier: 3.571A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.517A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.377A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.030A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.512A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.566A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.685A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.169A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 350 362 hydrogen bonds defined for protein. 1041 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3053 1.35 - 1.47: 2589 1.47 - 1.59: 4212 1.59 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 9924 Sorted by residual: bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+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 2.03e+00 ... (remaining 9919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13165 1.43 - 2.87: 296 2.87 - 4.30: 28 4.30 - 5.73: 5 5.73 - 7.16: 1 Bond angle restraints: 13495 Sorted by residual: angle pdb=" CA TYR D 385 " pdb=" CB TYR D 385 " pdb=" CG TYR D 385 " ideal model delta sigma weight residual 113.90 118.01 -4.11 1.80e+00 3.09e-01 5.21e+00 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 123.46 -7.16 3.50e+00 8.16e-02 4.19e+00 angle pdb=" N LYS C 150 " pdb=" CA LYS C 150 " pdb=" C LYS C 150 " ideal model delta sigma weight residual 108.63 111.72 -3.09 1.60e+00 3.91e-01 3.73e+00 angle pdb=" CA ASN C 149 " pdb=" CB ASN C 149 " pdb=" CG ASN C 149 " ideal model delta sigma weight residual 112.60 114.49 -1.89 1.00e+00 1.00e+00 3.59e+00 angle pdb=" N GLN D 139 " pdb=" CA GLN D 139 " pdb=" C GLN D 139 " ideal model delta sigma weight residual 108.34 110.74 -2.40 1.31e+00 5.83e-01 3.35e+00 ... (remaining 13490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 5913 21.68 - 43.37: 195 43.37 - 65.05: 17 65.05 - 86.73: 0 86.73 - 108.42: 8 Dihedral angle restraints: 6133 sinusoidal: 2728 harmonic: 3405 Sorted by residual: dihedral pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sinusoidal sigma weight residual -175.09 -66.67 -108.42 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" C1 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C4 NAG F 1 " ideal model delta sinusoidal sigma weight residual -52.39 55.10 -107.49 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" N2 NAG F 1 " pdb=" C2 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" O3 NAG F 1 " ideal model delta sinusoidal sigma weight residual 62.25 169.68 -107.43 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 6130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1076 0.039 - 0.078: 304 0.078 - 0.117: 118 0.117 - 0.157: 6 0.157 - 0.196: 1 Chirality restraints: 1505 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 149 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA ILE D 468 " pdb=" N ILE D 468 " pdb=" C ILE D 468 " pdb=" CB ILE D 468 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 1502 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 337 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 146 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 582 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO D 583 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 583 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 583 " -0.022 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1533 2.76 - 3.30: 9149 3.30 - 3.83: 15807 3.83 - 4.37: 18265 4.37 - 4.90: 32085 Nonbonded interactions: 76839 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.227 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.254 3.040 nonbonded pdb=" ND2 ASN C 125 " pdb=" OG SER C 172 " model vdw 2.256 3.120 nonbonded pdb=" OE2 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR A 500 " pdb=" OH TYR D 41 " model vdw 2.281 3.040 ... (remaining 76834 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.610 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.036 9956 Z= 0.144 Angle : 0.494 7.163 13580 Z= 0.250 Chirality : 0.041 0.196 1505 Planarity : 0.003 0.047 1718 Dihedral : 10.503 108.417 3912 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.20 % Allowed : 4.56 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.69 (0.22), residues: 1156 helix: -0.42 (0.24), residues: 384 sheet: -1.67 (0.38), residues: 172 loop : -2.84 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 219 TYR 0.020 0.001 TYR D 385 PHE 0.005 0.001 PHE D 592 TRP 0.006 0.001 TRP D 610 HIS 0.003 0.000 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9924) covalent geometry : angle 0.48906 (13495) SS BOND : bond 0.00138 ( 11) SS BOND : angle 0.50456 ( 22) hydrogen bonds : bond 0.19602 ( 362) hydrogen bonds : angle 6.85123 ( 1041) link_BETA1-4 : bond 0.00258 ( 6) link_BETA1-4 : angle 0.83026 ( 18) link_NAG-ASN : bond 0.00254 ( 15) link_NAG-ASN : angle 1.22846 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 310 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ILE cc_start: 0.7891 (pt) cc_final: 0.7684 (pt) REVERT: A 350 VAL cc_start: 0.7791 (p) cc_final: 0.7573 (t) REVERT: A 362 VAL cc_start: 0.7618 (OUTLIER) cc_final: 0.6826 (p) REVERT: A 369 TYR cc_start: 0.6740 (t80) cc_final: 0.6388 (t80) REVERT: A 370 ASN cc_start: 0.7390 (t0) cc_final: 0.6935 (t0) REVERT: A 378 LYS cc_start: 0.7570 (mtpp) cc_final: 0.7164 (mtpp) REVERT: A 394 ASN cc_start: 0.7256 (m110) cc_final: 0.7010 (m-40) REVERT: A 396 TYR cc_start: 0.7409 (m-80) cc_final: 0.7128 (m-80) REVERT: A 403 ARG cc_start: 0.7867 (ttp-170) cc_final: 0.7651 (ttp-170) REVERT: A 406 GLU cc_start: 0.7219 (pt0) cc_final: 0.6965 (pt0) REVERT: A 414 GLN cc_start: 0.8402 (mm110) cc_final: 0.7976 (mm110) REVERT: A 473 TYR cc_start: 0.8184 (t80) cc_final: 0.7932 (t80) REVERT: A 512 VAL cc_start: 0.7410 (t) cc_final: 0.6971 (p) REVERT: A 536 ASN cc_start: 0.7375 (t0) cc_final: 0.6337 (p0) REVERT: A 541 PHE cc_start: 0.7754 (p90) cc_final: 0.7550 (p90) REVERT: A 542 ASN cc_start: 0.7001 (t0) cc_final: 0.6777 (t0) REVERT: A 558 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7545 (mtpt) REVERT: A 576 VAL cc_start: 0.8386 (m) cc_final: 0.8067 (p) REVERT: A 584 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7649 (pp) REVERT: C 41 LYS cc_start: 0.8145 (mttp) cc_final: 0.7620 (mttp) REVERT: C 137 ASN cc_start: 0.7199 (m-40) cc_final: 0.6958 (m-40) REVERT: C 191 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7128 (mt-10) REVERT: C 202 LYS cc_start: 0.7997 (mttp) cc_final: 0.7781 (mttt) REVERT: C 206 LYS cc_start: 0.8307 (tptt) cc_final: 0.8097 (tppt) REVERT: C 235 ILE cc_start: 0.8499 (mm) cc_final: 0.8283 (mm) REVERT: C 237 ARG cc_start: 0.7885 (ptm-80) cc_final: 0.7662 (mtm110) REVERT: C 276 LEU cc_start: 0.8274 (tp) cc_final: 0.8038 (tp) REVERT: D 23 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: D 44 SER cc_start: 0.8235 (m) cc_final: 0.7814 (p) REVERT: D 50 TYR cc_start: 0.8061 (t80) cc_final: 0.7725 (t80) REVERT: D 61 ASN cc_start: 0.7473 (m-40) cc_final: 0.7272 (m-40) REVERT: D 70 SER cc_start: 0.8088 (m) cc_final: 0.7636 (t) REVERT: D 82 MET cc_start: 0.6946 (mmt) cc_final: 0.6672 (mmm) REVERT: D 95 LEU cc_start: 0.7444 (mt) cc_final: 0.7241 (mt) REVERT: D 148 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6383 (mp) REVERT: D 194 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: D 198 ASP cc_start: 0.6592 (m-30) cc_final: 0.6365 (m-30) REVERT: D 201 ASP cc_start: 0.8063 (t70) cc_final: 0.7729 (t0) REVERT: D 207 TYR cc_start: 0.8006 (m-80) cc_final: 0.7766 (m-80) REVERT: D 234 LYS cc_start: 0.8082 (mttt) cc_final: 0.7520 (mmtt) REVERT: D 238 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6871 (mt-10) REVERT: D 241 HIS cc_start: 0.6596 (t-90) cc_final: 0.6292 (t-90) REVERT: D 270 MET cc_start: 0.7756 (tpp) cc_final: 0.7428 (tpp) REVERT: D 277 ASN cc_start: 0.8190 (m110) cc_final: 0.7927 (m110) REVERT: D 288 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8135 (mttp) REVERT: D 295 ASP cc_start: 0.7488 (m-30) cc_final: 0.7174 (m-30) REVERT: D 362 THR cc_start: 0.7874 (m) cc_final: 0.7394 (m) REVERT: D 375 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7177 (mm-30) REVERT: D 393 ARG cc_start: 0.8011 (mtm-85) cc_final: 0.7774 (mtt180) REVERT: D 414 THR cc_start: 0.7884 (p) cc_final: 0.7501 (p) REVERT: D 441 LYS cc_start: 0.7535 (tttt) cc_final: 0.7306 (tttp) REVERT: D 458 LYS cc_start: 0.7786 (tttp) cc_final: 0.7547 (ttpp) REVERT: D 500 PRO cc_start: 0.7840 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: D 518 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7729 (ttp80) REVERT: D 544 ILE cc_start: 0.8006 (mt) cc_final: 0.7735 (mt) REVERT: D 549 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6483 (tm-30) REVERT: D 564 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7175 (mt-10) REVERT: D 577 LYS cc_start: 0.7491 (mtpt) cc_final: 0.6806 (mtpt) REVERT: D 596 LYS cc_start: 0.7054 (mtpt) cc_final: 0.6833 (mtpp) outliers start: 33 outliers final: 13 residues processed: 334 average time/residue: 0.1085 time to fit residues: 48.6896 Evaluate side-chains 293 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 364 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 394 ASN A 414 GLN A 437 ASN A 460 ASN A 487 ASN A 493 GLN A 506 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 115 GLN C 125 ASN C 173 GLN D 24 GLN D 81 GLN D 89 GLN D 101 GLN D 134 ASN D 137 ASN D 239 HIS D 397 ASN D 437 ASN D 442 GLN D 524 GLN D 526 GLN D 531 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.108145 restraints weight = 15238.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111547 restraints weight = 7217.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113784 restraints weight = 4468.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115061 restraints weight = 3250.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.116084 restraints weight = 2670.851| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 9956 Z= 0.328 Angle : 0.713 8.937 13580 Z= 0.362 Chirality : 0.051 0.288 1505 Planarity : 0.005 0.049 1718 Dihedral : 9.648 91.349 1735 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.17 % Allowed : 10.39 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.23), residues: 1156 helix: -0.28 (0.25), residues: 405 sheet: -1.37 (0.37), residues: 185 loop : -2.50 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 328 TYR 0.030 0.003 TYR D 385 PHE 0.024 0.003 PHE D 285 TRP 0.018 0.002 TRP D 477 HIS 0.009 0.002 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 9924) covalent geometry : angle 0.70238 (13495) SS BOND : bond 0.00449 ( 11) SS BOND : angle 1.15909 ( 22) hydrogen bonds : bond 0.05252 ( 362) hydrogen bonds : angle 5.17124 ( 1041) link_BETA1-4 : bond 0.00252 ( 6) link_BETA1-4 : angle 1.67327 ( 18) link_NAG-ASN : bond 0.00460 ( 15) link_NAG-ASN : angle 1.93376 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 272 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6759 (pp30) REVERT: A 326 ILE cc_start: 0.8136 (pt) cc_final: 0.7930 (pt) REVERT: A 345 THR cc_start: 0.8063 (p) cc_final: 0.6359 (t) REVERT: A 346 ARG cc_start: 0.7065 (mmm160) cc_final: 0.6693 (mmm160) REVERT: A 351 TYR cc_start: 0.8191 (p90) cc_final: 0.7851 (p90) REVERT: A 362 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7094 (p) REVERT: A 369 TYR cc_start: 0.6785 (t80) cc_final: 0.6555 (t80) REVERT: A 370 ASN cc_start: 0.7672 (t0) cc_final: 0.7288 (t0) REVERT: A 378 LYS cc_start: 0.7378 (mtpp) cc_final: 0.6884 (mtpp) REVERT: A 408 ARG cc_start: 0.8022 (ptm-80) cc_final: 0.7741 (ptt90) REVERT: A 414 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8160 (mm-40) REVERT: A 422 ASN cc_start: 0.8342 (m-40) cc_final: 0.8054 (m-40) REVERT: A 448 ASN cc_start: 0.8361 (t0) cc_final: 0.8066 (t0) REVERT: A 450 ASN cc_start: 0.8269 (m-40) cc_final: 0.7735 (m110) REVERT: A 466 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7880 (ttp-170) REVERT: A 492 LEU cc_start: 0.8317 (mt) cc_final: 0.8087 (mm) REVERT: A 512 VAL cc_start: 0.7548 (t) cc_final: 0.7251 (m) REVERT: A 536 ASN cc_start: 0.7911 (t0) cc_final: 0.6939 (p0) REVERT: A 542 ASN cc_start: 0.7256 (t0) cc_final: 0.6999 (t0) REVERT: A 546 LEU cc_start: 0.7451 (mp) cc_final: 0.7204 (mt) REVERT: A 558 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7574 (mtpt) REVERT: A 576 VAL cc_start: 0.8368 (m) cc_final: 0.8135 (p) REVERT: C 125 ASN cc_start: 0.6616 (OUTLIER) cc_final: 0.6358 (t0) REVERT: C 133 PHE cc_start: 0.7551 (m-80) cc_final: 0.6720 (m-80) REVERT: C 235 ILE cc_start: 0.8577 (mm) cc_final: 0.8237 (mt) REVERT: C 237 ARG cc_start: 0.7958 (ptm-80) cc_final: 0.7652 (mtp-110) REVERT: D 44 SER cc_start: 0.8558 (m) cc_final: 0.8207 (t) REVERT: D 58 ASN cc_start: 0.7733 (m110) cc_final: 0.7278 (m110) REVERT: D 70 SER cc_start: 0.8278 (m) cc_final: 0.7906 (t) REVERT: D 91 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7562 (mm) REVERT: D 127 TYR cc_start: 0.8322 (t80) cc_final: 0.7923 (t80) REVERT: D 148 LEU cc_start: 0.7743 (mm) cc_final: 0.7286 (mt) REVERT: D 151 ILE cc_start: 0.8494 (tt) cc_final: 0.8266 (tt) REVERT: D 152 MET cc_start: 0.8002 (tpp) cc_final: 0.7312 (mmp) REVERT: D 219 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7924 (ttp-170) REVERT: D 221 GLN cc_start: 0.7121 (tt0) cc_final: 0.6905 (tt0) REVERT: D 241 HIS cc_start: 0.7069 (t-90) cc_final: 0.6757 (t-90) REVERT: D 277 ASN cc_start: 0.8217 (m110) cc_final: 0.7994 (m-40) REVERT: D 312 GLU cc_start: 0.7657 (tt0) cc_final: 0.7428 (tt0) REVERT: D 320 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (mt) REVERT: D 360 MET cc_start: 0.8261 (ttm) cc_final: 0.7981 (ttm) REVERT: D 398 GLU cc_start: 0.7920 (pt0) cc_final: 0.7490 (pt0) REVERT: D 441 LYS cc_start: 0.7702 (tttt) cc_final: 0.7455 (tttp) REVERT: D 458 LYS cc_start: 0.7920 (tttp) cc_final: 0.7713 (ttpp) REVERT: D 503 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7692 (tt) REVERT: D 518 ARG cc_start: 0.8310 (ttp80) cc_final: 0.8080 (ttp80) REVERT: D 534 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7366 (mmmm) REVERT: D 549 GLU cc_start: 0.7005 (tm-30) cc_final: 0.6749 (tm-30) REVERT: D 557 MET cc_start: 0.8319 (tmm) cc_final: 0.7966 (tmm) REVERT: D 577 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7935 (mtmm) REVERT: D 589 GLU cc_start: 0.7327 (tt0) cc_final: 0.7044 (tt0) outliers start: 43 outliers final: 25 residues processed: 298 average time/residue: 0.1108 time to fit residues: 44.5619 Evaluate side-chains 272 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.2980 chunk 61 optimal weight: 0.0970 chunk 13 optimal weight: 0.1980 chunk 76 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 85 optimal weight: 0.1980 chunk 29 optimal weight: 0.1980 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 overall best weight: 0.1978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 409 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 245 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 58 ASN D 250 ASN D 397 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.128673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.109825 restraints weight = 15011.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113252 restraints weight = 7361.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115488 restraints weight = 4650.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116758 restraints weight = 3423.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117787 restraints weight = 2827.805| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9956 Z= 0.127 Angle : 0.572 11.083 13580 Z= 0.286 Chirality : 0.044 0.256 1505 Planarity : 0.004 0.053 1718 Dihedral : 8.606 87.273 1720 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.82 % Allowed : 14.37 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.24), residues: 1156 helix: 0.32 (0.26), residues: 404 sheet: -1.19 (0.37), residues: 188 loop : -2.16 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.023 0.002 TYR A 473 PHE 0.011 0.001 PHE A 565 TRP 0.014 0.001 TRP D 610 HIS 0.011 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9924) covalent geometry : angle 0.56451 (13495) SS BOND : bond 0.00178 ( 11) SS BOND : angle 0.57107 ( 22) hydrogen bonds : bond 0.03991 ( 362) hydrogen bonds : angle 4.87250 ( 1041) link_BETA1-4 : bond 0.00261 ( 6) link_BETA1-4 : angle 1.36009 ( 18) link_NAG-ASN : bond 0.00243 ( 15) link_NAG-ASN : angle 1.45871 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 247 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6510 (pp30) REVERT: A 326 ILE cc_start: 0.7959 (pt) cc_final: 0.7742 (pt) REVERT: A 345 THR cc_start: 0.8072 (p) cc_final: 0.5926 (m) REVERT: A 362 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7152 (p) REVERT: A 370 ASN cc_start: 0.7483 (t0) cc_final: 0.7128 (t0) REVERT: A 378 LYS cc_start: 0.7253 (mtpp) cc_final: 0.6766 (mtpp) REVERT: A 414 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8135 (mm-40) REVERT: A 466 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7925 (ttp80) REVERT: A 512 VAL cc_start: 0.7610 (t) cc_final: 0.7237 (p) REVERT: A 536 ASN cc_start: 0.7737 (t0) cc_final: 0.6852 (p0) REVERT: A 542 ASN cc_start: 0.7246 (t0) cc_final: 0.7011 (t0) REVERT: A 558 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7548 (mtpt) REVERT: A 586 ASP cc_start: 0.7259 (t0) cc_final: 0.7049 (t70) REVERT: C 235 ILE cc_start: 0.8691 (mm) cc_final: 0.8341 (mt) REVERT: D 44 SER cc_start: 0.8574 (m) cc_final: 0.8215 (t) REVERT: D 58 ASN cc_start: 0.7535 (m-40) cc_final: 0.7031 (m110) REVERT: D 70 SER cc_start: 0.8340 (m) cc_final: 0.7984 (t) REVERT: D 76 GLN cc_start: 0.7912 (mm-40) cc_final: 0.6987 (mm-40) REVERT: D 98 GLN cc_start: 0.7946 (tt0) cc_final: 0.7622 (tt0) REVERT: D 101 GLN cc_start: 0.8411 (mt0) cc_final: 0.8118 (mt0) REVERT: D 126 ILE cc_start: 0.8248 (tt) cc_final: 0.8024 (pt) REVERT: D 148 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6838 (mt) REVERT: D 151 ILE cc_start: 0.8376 (tt) cc_final: 0.7983 (tp) REVERT: D 152 MET cc_start: 0.7907 (tpp) cc_final: 0.7106 (mmp) REVERT: D 219 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7742 (ttp-170) REVERT: D 241 HIS cc_start: 0.7048 (t-90) cc_final: 0.6816 (t-170) REVERT: D 277 ASN cc_start: 0.8097 (m110) cc_final: 0.7838 (m110) REVERT: D 503 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7976 (tt) REVERT: D 518 ARG cc_start: 0.8294 (ttp80) cc_final: 0.8017 (ttp80) REVERT: D 534 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7373 (mmmm) REVERT: D 557 MET cc_start: 0.8182 (tmm) cc_final: 0.7957 (tmm) REVERT: D 577 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7405 (mtpp) outliers start: 29 outliers final: 20 residues processed: 265 average time/residue: 0.1196 time to fit residues: 42.4374 Evaluate side-chains 254 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 230 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 29 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.128771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109998 restraints weight = 15137.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113491 restraints weight = 7421.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115784 restraints weight = 4666.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116949 restraints weight = 3410.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118120 restraints weight = 2850.304| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9956 Z= 0.190 Angle : 0.596 9.722 13580 Z= 0.298 Chirality : 0.046 0.262 1505 Planarity : 0.005 0.059 1718 Dihedral : 7.991 79.868 1720 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.47 % Allowed : 13.50 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.24), residues: 1156 helix: 0.44 (0.26), residues: 405 sheet: -1.08 (0.38), residues: 188 loop : -2.06 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.033 0.002 TYR A 473 PHE 0.020 0.002 PHE C 133 TRP 0.018 0.001 TRP D 610 HIS 0.008 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9924) covalent geometry : angle 0.58743 (13495) SS BOND : bond 0.00221 ( 11) SS BOND : angle 0.66984 ( 22) hydrogen bonds : bond 0.04117 ( 362) hydrogen bonds : angle 4.79004 ( 1041) link_BETA1-4 : bond 0.00184 ( 6) link_BETA1-4 : angle 1.44755 ( 18) link_NAG-ASN : bond 0.00285 ( 15) link_NAG-ASN : angle 1.58150 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6679 (pp30) REVERT: A 324 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6807 (tp30) REVERT: A 326 ILE cc_start: 0.7976 (pt) cc_final: 0.7729 (pt) REVERT: A 328 ARG cc_start: 0.8482 (mtp180) cc_final: 0.8250 (mtp180) REVERT: A 345 THR cc_start: 0.7917 (p) cc_final: 0.7166 (t) REVERT: A 346 ARG cc_start: 0.6507 (mmm160) cc_final: 0.6110 (mmm160) REVERT: A 362 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7187 (p) REVERT: A 370 ASN cc_start: 0.7440 (t0) cc_final: 0.7101 (t0) REVERT: A 403 ARG cc_start: 0.8162 (ttp-170) cc_final: 0.7907 (ttp80) REVERT: A 414 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8151 (mm-40) REVERT: A 424 LYS cc_start: 0.8149 (tttp) cc_final: 0.7845 (tptt) REVERT: A 450 ASN cc_start: 0.8062 (m-40) cc_final: 0.7419 (m-40) REVERT: A 466 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7988 (ttp80) REVERT: A 512 VAL cc_start: 0.7634 (t) cc_final: 0.7296 (p) REVERT: A 536 ASN cc_start: 0.7903 (t0) cc_final: 0.7025 (p0) REVERT: A 542 ASN cc_start: 0.7259 (t0) cc_final: 0.6991 (t0) REVERT: A 558 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7526 (mtpt) REVERT: C 156 GLU cc_start: 0.6547 (tp30) cc_final: 0.6211 (tp30) REVERT: C 210 ILE cc_start: 0.8066 (tt) cc_final: 0.7817 (pt) REVERT: C 235 ILE cc_start: 0.8718 (mm) cc_final: 0.8350 (mt) REVERT: D 44 SER cc_start: 0.8617 (m) cc_final: 0.8263 (t) REVERT: D 58 ASN cc_start: 0.7579 (m-40) cc_final: 0.7042 (m110) REVERT: D 70 SER cc_start: 0.8376 (m) cc_final: 0.8019 (t) REVERT: D 76 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7120 (mm-40) REVERT: D 91 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7619 (mm) REVERT: D 98 GLN cc_start: 0.7988 (tt0) cc_final: 0.7688 (tt0) REVERT: D 126 ILE cc_start: 0.8299 (tt) cc_final: 0.8027 (pt) REVERT: D 148 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6925 (mt) REVERT: D 151 ILE cc_start: 0.8451 (tt) cc_final: 0.8222 (tt) REVERT: D 152 MET cc_start: 0.7925 (tpp) cc_final: 0.7157 (mmp) REVERT: D 241 HIS cc_start: 0.7120 (t-90) cc_final: 0.6906 (t-170) REVERT: D 310 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6631 (mm-30) REVERT: D 349 TRP cc_start: 0.8569 (m100) cc_final: 0.8356 (m100) REVERT: D 376 MET cc_start: 0.7493 (ttm) cc_final: 0.7292 (mtt) REVERT: D 460 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6720 (mtt90) REVERT: D 503 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7989 (tt) REVERT: D 518 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8025 (ttp80) REVERT: D 534 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7433 (mmmm) REVERT: D 557 MET cc_start: 0.8224 (tmm) cc_final: 0.7994 (tmm) REVERT: D 574 VAL cc_start: 0.8632 (t) cc_final: 0.8374 (p) outliers start: 46 outliers final: 31 residues processed: 283 average time/residue: 0.1245 time to fit residues: 46.8606 Evaluate side-chains 282 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 78 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109234 restraints weight = 15012.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112672 restraints weight = 7382.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114905 restraints weight = 4641.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116303 restraints weight = 3423.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117046 restraints weight = 2789.383| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9956 Z= 0.240 Angle : 0.635 10.301 13580 Z= 0.318 Chirality : 0.048 0.271 1505 Planarity : 0.005 0.068 1718 Dihedral : 7.628 72.830 1720 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 5.15 % Allowed : 14.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.24), residues: 1156 helix: 0.43 (0.26), residues: 401 sheet: -1.06 (0.38), residues: 188 loop : -2.01 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 158 TYR 0.037 0.002 TYR A 473 PHE 0.017 0.002 PHE C 79 TRP 0.023 0.002 TRP D 610 HIS 0.007 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 9924) covalent geometry : angle 0.62562 (13495) SS BOND : bond 0.00216 ( 11) SS BOND : angle 0.65443 ( 22) hydrogen bonds : bond 0.04386 ( 362) hydrogen bonds : angle 4.83868 ( 1041) link_BETA1-4 : bond 0.00245 ( 6) link_BETA1-4 : angle 1.55549 ( 18) link_NAG-ASN : bond 0.00335 ( 15) link_NAG-ASN : angle 1.73213 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 266 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6710 (pp30) REVERT: A 324 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6952 (tp30) REVERT: A 326 ILE cc_start: 0.7901 (pt) cc_final: 0.7669 (pt) REVERT: A 346 ARG cc_start: 0.6783 (mmm160) cc_final: 0.6529 (mmm160) REVERT: A 362 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7200 (p) REVERT: A 370 ASN cc_start: 0.7495 (t0) cc_final: 0.7186 (t0) REVERT: A 414 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8192 (mm-40) REVERT: A 424 LYS cc_start: 0.8171 (tttp) cc_final: 0.7862 (tptt) REVERT: A 450 ASN cc_start: 0.8015 (m-40) cc_final: 0.7419 (m-40) REVERT: A 512 VAL cc_start: 0.7562 (t) cc_final: 0.7230 (p) REVERT: A 536 ASN cc_start: 0.8025 (t0) cc_final: 0.7038 (p0) REVERT: A 542 ASN cc_start: 0.7273 (t0) cc_final: 0.6999 (t0) REVERT: A 574 ASP cc_start: 0.7445 (p0) cc_final: 0.7221 (p0) REVERT: C 102 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7646 (ttm170) REVERT: C 116 SER cc_start: 0.7821 (m) cc_final: 0.7401 (t) REVERT: C 156 GLU cc_start: 0.6668 (tp30) cc_final: 0.6441 (tp30) REVERT: C 158 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7806 (mtt90) REVERT: C 182 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7757 (mmmt) REVERT: C 235 ILE cc_start: 0.8666 (mm) cc_final: 0.8369 (mt) REVERT: D 44 SER cc_start: 0.8634 (m) cc_final: 0.8275 (t) REVERT: D 58 ASN cc_start: 0.7630 (m-40) cc_final: 0.7139 (m110) REVERT: D 70 SER cc_start: 0.8392 (m) cc_final: 0.8038 (t) REVERT: D 76 GLN cc_start: 0.7863 (mm-40) cc_final: 0.7070 (mm-40) REVERT: D 91 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7695 (mm) REVERT: D 98 GLN cc_start: 0.8037 (tt0) cc_final: 0.7688 (tt0) REVERT: D 127 TYR cc_start: 0.8346 (t80) cc_final: 0.8014 (t80) REVERT: D 148 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7217 (mt) REVERT: D 151 ILE cc_start: 0.8494 (tt) cc_final: 0.8247 (tt) REVERT: D 310 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6651 (mm-30) REVERT: D 320 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7981 (mt) REVERT: D 349 TRP cc_start: 0.8598 (m100) cc_final: 0.8375 (m100) REVERT: D 376 MET cc_start: 0.7589 (ttm) cc_final: 0.7270 (ttm) REVERT: D 397 ASN cc_start: 0.7620 (m-40) cc_final: 0.7399 (t0) REVERT: D 460 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6818 (mtt90) REVERT: D 503 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7769 (tt) REVERT: D 518 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8034 (ttp80) REVERT: D 534 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7477 (mmmm) REVERT: D 557 MET cc_start: 0.8210 (tmm) cc_final: 0.7960 (tmm) REVERT: D 574 VAL cc_start: 0.8658 (t) cc_final: 0.8365 (p) outliers start: 53 outliers final: 41 residues processed: 299 average time/residue: 0.1192 time to fit residues: 47.2774 Evaluate side-chains 303 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 42 optimal weight: 0.0040 chunk 110 optimal weight: 0.0970 chunk 107 optimal weight: 0.0070 chunk 15 optimal weight: 0.0470 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.0706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN A 580 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 101 GLN D 175 GLN D 250 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109473 restraints weight = 15042.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112886 restraints weight = 7305.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115157 restraints weight = 4582.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116439 restraints weight = 3348.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117416 restraints weight = 2748.653| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9956 Z= 0.110 Angle : 0.574 9.979 13580 Z= 0.286 Chirality : 0.044 0.256 1505 Planarity : 0.004 0.047 1718 Dihedral : 7.036 66.546 1720 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.85 % Allowed : 15.15 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.25), residues: 1156 helix: 0.76 (0.27), residues: 404 sheet: -0.80 (0.39), residues: 178 loop : -1.87 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 158 TYR 0.033 0.001 TYR A 473 PHE 0.027 0.001 PHE D 285 TRP 0.020 0.001 TRP D 610 HIS 0.011 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9924) covalent geometry : angle 0.56775 (13495) SS BOND : bond 0.00242 ( 11) SS BOND : angle 0.50330 ( 22) hydrogen bonds : bond 0.03497 ( 362) hydrogen bonds : angle 4.69420 ( 1041) link_BETA1-4 : bond 0.00366 ( 6) link_BETA1-4 : angle 1.38018 ( 18) link_NAG-ASN : bond 0.00271 ( 15) link_NAG-ASN : angle 1.41177 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6570 (pp30) REVERT: A 324 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6721 (tp30) REVERT: A 326 ILE cc_start: 0.7771 (pt) cc_final: 0.7537 (pt) REVERT: A 345 THR cc_start: 0.7879 (p) cc_final: 0.6801 (t) REVERT: A 346 ARG cc_start: 0.6888 (mmm160) cc_final: 0.6455 (mmm160) REVERT: A 362 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7217 (p) REVERT: A 370 ASN cc_start: 0.7432 (t0) cc_final: 0.7092 (t0) REVERT: A 414 GLN cc_start: 0.8376 (mm-40) cc_final: 0.8134 (mm-40) REVERT: A 424 LYS cc_start: 0.8122 (tttp) cc_final: 0.7791 (tptt) REVERT: A 450 ASN cc_start: 0.7947 (m-40) cc_final: 0.7351 (m-40) REVERT: A 512 VAL cc_start: 0.7556 (t) cc_final: 0.7155 (p) REVERT: A 536 ASN cc_start: 0.7886 (t0) cc_final: 0.6966 (p0) REVERT: A 542 ASN cc_start: 0.7160 (t0) cc_final: 0.6908 (t0) REVERT: C 158 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7616 (mtt90) REVERT: C 182 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7711 (mmmt) REVERT: C 235 ILE cc_start: 0.8683 (mm) cc_final: 0.8351 (mt) REVERT: D 44 SER cc_start: 0.8579 (m) cc_final: 0.8207 (t) REVERT: D 58 ASN cc_start: 0.7584 (m-40) cc_final: 0.7018 (m110) REVERT: D 70 SER cc_start: 0.8377 (m) cc_final: 0.8023 (t) REVERT: D 76 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7042 (mm-40) REVERT: D 91 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7649 (mm) REVERT: D 98 GLN cc_start: 0.8003 (tt0) cc_final: 0.7695 (tt0) REVERT: D 126 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7822 (pt) REVERT: D 148 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7071 (mt) REVERT: D 151 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.7976 (tp) REVERT: D 152 MET cc_start: 0.7958 (tpp) cc_final: 0.7139 (mmp) REVERT: D 207 TYR cc_start: 0.8000 (m-80) cc_final: 0.7205 (m-80) REVERT: D 216 ASP cc_start: 0.7238 (p0) cc_final: 0.6877 (p0) REVERT: D 219 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7755 (ttp-170) REVERT: D 349 TRP cc_start: 0.8585 (m100) cc_final: 0.8323 (m100) REVERT: D 397 ASN cc_start: 0.7498 (m-40) cc_final: 0.7256 (t0) REVERT: D 484 ILE cc_start: 0.8028 (mt) cc_final: 0.7575 (mm) REVERT: D 503 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7954 (tt) REVERT: D 518 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8042 (ttp80) REVERT: D 534 LYS cc_start: 0.7713 (mtpt) cc_final: 0.7359 (mmmm) REVERT: D 557 MET cc_start: 0.8206 (tmm) cc_final: 0.7976 (tmm) REVERT: D 574 VAL cc_start: 0.8651 (t) cc_final: 0.8327 (p) outliers start: 50 outliers final: 36 residues processed: 271 average time/residue: 0.1200 time to fit residues: 43.4202 Evaluate side-chains 276 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 232 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 22 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 42 GLN D 81 GLN D 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.108102 restraints weight = 14957.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111728 restraints weight = 7010.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114038 restraints weight = 4288.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115244 restraints weight = 3103.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116244 restraints weight = 2577.562| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9956 Z= 0.231 Angle : 0.640 9.971 13580 Z= 0.321 Chirality : 0.048 0.268 1505 Planarity : 0.005 0.063 1718 Dihedral : 6.845 58.111 1720 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.76 % Allowed : 16.12 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.25), residues: 1156 helix: 0.63 (0.26), residues: 403 sheet: -0.96 (0.38), residues: 190 loop : -1.77 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 158 TYR 0.033 0.002 TYR A 473 PHE 0.022 0.002 PHE D 285 TRP 0.026 0.002 TRP D 610 HIS 0.012 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9924) covalent geometry : angle 0.63132 (13495) SS BOND : bond 0.00218 ( 11) SS BOND : angle 0.60862 ( 22) hydrogen bonds : bond 0.04260 ( 362) hydrogen bonds : angle 4.74814 ( 1041) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 1.61927 ( 18) link_NAG-ASN : bond 0.00285 ( 15) link_NAG-ASN : angle 1.65250 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.6733 (pp30) REVERT: A 324 GLU cc_start: 0.7444 (tp30) cc_final: 0.6930 (tp30) REVERT: A 326 ILE cc_start: 0.7970 (pt) cc_final: 0.7731 (pt) REVERT: A 328 ARG cc_start: 0.8504 (mtp180) cc_final: 0.8296 (mtt-85) REVERT: A 346 ARG cc_start: 0.6873 (mmm160) cc_final: 0.6482 (mmm160) REVERT: A 362 VAL cc_start: 0.7700 (OUTLIER) cc_final: 0.7147 (p) REVERT: A 370 ASN cc_start: 0.7568 (t0) cc_final: 0.7249 (t0) REVERT: A 408 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.7807 (ptt90) REVERT: A 414 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8184 (mm-40) REVERT: A 450 ASN cc_start: 0.7991 (m-40) cc_final: 0.7368 (m-40) REVERT: A 536 ASN cc_start: 0.8108 (t0) cc_final: 0.7082 (p0) REVERT: A 542 ASN cc_start: 0.7258 (t0) cc_final: 0.6992 (t0) REVERT: C 131 CYS cc_start: 0.3909 (OUTLIER) cc_final: 0.3601 (m) REVERT: C 156 GLU cc_start: 0.6791 (tp30) cc_final: 0.6456 (tp30) REVERT: C 158 ARG cc_start: 0.8112 (mtt90) cc_final: 0.7795 (mtt180) REVERT: C 182 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7784 (mmmt) REVERT: C 235 ILE cc_start: 0.8597 (mm) cc_final: 0.8331 (mt) REVERT: D 44 SER cc_start: 0.8579 (m) cc_final: 0.8202 (t) REVERT: D 58 ASN cc_start: 0.7694 (m-40) cc_final: 0.7097 (m110) REVERT: D 70 SER cc_start: 0.8380 (m) cc_final: 0.8022 (t) REVERT: D 76 GLN cc_start: 0.7818 (mm-40) cc_final: 0.6965 (mm-40) REVERT: D 91 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7661 (mm) REVERT: D 98 GLN cc_start: 0.8111 (tt0) cc_final: 0.7768 (tt0) REVERT: D 101 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: D 126 ILE cc_start: 0.7971 (tt) cc_final: 0.7725 (pt) REVERT: D 127 TYR cc_start: 0.8171 (t80) cc_final: 0.7841 (t80) REVERT: D 148 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7177 (mt) REVERT: D 151 ILE cc_start: 0.8491 (tt) cc_final: 0.8056 (tp) REVERT: D 152 MET cc_start: 0.8138 (tpp) cc_final: 0.7343 (mmp) REVERT: D 166 GLU cc_start: 0.7604 (tp30) cc_final: 0.7276 (mm-30) REVERT: D 349 TRP cc_start: 0.8589 (m100) cc_final: 0.8332 (m100) REVERT: D 376 MET cc_start: 0.7588 (ttm) cc_final: 0.7172 (mtt) REVERT: D 460 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: D 470 LYS cc_start: 0.7854 (tppt) cc_final: 0.7337 (tppt) REVERT: D 503 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7693 (tt) REVERT: D 518 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8008 (ttp80) REVERT: D 534 LYS cc_start: 0.7814 (mtpt) cc_final: 0.7428 (mmmm) REVERT: D 557 MET cc_start: 0.8233 (tmm) cc_final: 0.7947 (tmm) outliers start: 49 outliers final: 38 residues processed: 288 average time/residue: 0.1245 time to fit residues: 47.6550 Evaluate side-chains 297 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 251 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 101 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 92 optimal weight: 0.1980 chunk 41 optimal weight: 0.0170 chunk 63 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 99 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 overall best weight: 0.2418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN D 42 GLN ** D 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.107862 restraints weight = 15046.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111305 restraints weight = 7303.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113523 restraints weight = 4569.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114830 restraints weight = 3359.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115397 restraints weight = 2761.746| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9956 Z= 0.139 Angle : 0.610 10.037 13580 Z= 0.303 Chirality : 0.045 0.261 1505 Planarity : 0.005 0.052 1718 Dihedral : 6.431 51.632 1720 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.85 % Allowed : 17.18 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.25), residues: 1156 helix: 0.78 (0.27), residues: 403 sheet: -0.82 (0.38), residues: 186 loop : -1.68 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 237 TYR 0.034 0.002 TYR A 473 PHE 0.033 0.002 PHE D 285 TRP 0.028 0.001 TRP D 610 HIS 0.010 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9924) covalent geometry : angle 0.60214 (13495) SS BOND : bond 0.00241 ( 11) SS BOND : angle 0.69116 ( 22) hydrogen bonds : bond 0.03766 ( 362) hydrogen bonds : angle 4.68854 ( 1041) link_BETA1-4 : bond 0.00293 ( 6) link_BETA1-4 : angle 1.50918 ( 18) link_NAG-ASN : bond 0.00239 ( 15) link_NAG-ASN : angle 1.51135 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6639 (pp30) REVERT: A 324 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: A 326 ILE cc_start: 0.7816 (pt) cc_final: 0.7578 (pt) REVERT: A 345 THR cc_start: 0.7960 (p) cc_final: 0.6614 (t) REVERT: A 346 ARG cc_start: 0.6912 (mmm160) cc_final: 0.6617 (mmm160) REVERT: A 362 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7263 (p) REVERT: A 370 ASN cc_start: 0.7455 (t0) cc_final: 0.7143 (t0) REVERT: A 374 PHE cc_start: 0.8644 (m-10) cc_final: 0.8376 (m-80) REVERT: A 378 LYS cc_start: 0.7196 (mtpp) cc_final: 0.6825 (mtpp) REVERT: A 408 ARG cc_start: 0.7952 (ptm-80) cc_final: 0.7703 (ptt90) REVERT: A 414 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8099 (mm-40) REVERT: A 450 ASN cc_start: 0.7931 (m-40) cc_final: 0.7349 (m-40) REVERT: A 536 ASN cc_start: 0.8013 (t0) cc_final: 0.7097 (p0) REVERT: A 542 ASN cc_start: 0.7198 (t0) cc_final: 0.6994 (t0) REVERT: C 131 CYS cc_start: 0.3770 (OUTLIER) cc_final: 0.3518 (m) REVERT: C 158 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7850 (mtt90) REVERT: C 182 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7795 (mmmt) REVERT: C 235 ILE cc_start: 0.8694 (mm) cc_final: 0.8375 (mt) REVERT: D 44 SER cc_start: 0.8586 (m) cc_final: 0.8198 (t) REVERT: D 70 SER cc_start: 0.8385 (m) cc_final: 0.8029 (t) REVERT: D 76 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7036 (mm-40) REVERT: D 91 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7720 (mm) REVERT: D 98 GLN cc_start: 0.8014 (tt0) cc_final: 0.7586 (tt0) REVERT: D 126 ILE cc_start: 0.8023 (tt) cc_final: 0.7795 (pt) REVERT: D 127 TYR cc_start: 0.8169 (t80) cc_final: 0.7854 (t80) REVERT: D 148 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7221 (mt) REVERT: D 151 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.7996 (tp) REVERT: D 152 MET cc_start: 0.8037 (tpp) cc_final: 0.7282 (mmp) REVERT: D 166 GLU cc_start: 0.7506 (tp30) cc_final: 0.7278 (mm-30) REVERT: D 349 TRP cc_start: 0.8584 (m100) cc_final: 0.8364 (m100) REVERT: D 376 MET cc_start: 0.7523 (ttm) cc_final: 0.7166 (mtt) REVERT: D 460 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7353 (mtm-85) REVERT: D 470 LYS cc_start: 0.7772 (tppt) cc_final: 0.7296 (tppt) REVERT: D 479 GLU cc_start: 0.6175 (tm-30) cc_final: 0.5765 (tp30) REVERT: D 500 PRO cc_start: 0.7912 (Cg_exo) cc_final: 0.7667 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7765 (tt) REVERT: D 518 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8054 (ttp80) REVERT: D 534 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7414 (mmmm) REVERT: D 557 MET cc_start: 0.8213 (tmm) cc_final: 0.8004 (tmm) REVERT: D 571 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6653 (mm-30) outliers start: 50 outliers final: 38 residues processed: 264 average time/residue: 0.1283 time to fit residues: 44.8047 Evaluate side-chains 287 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 0.0270 chunk 97 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 105 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN D 42 GLN D 58 ASN D 250 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.109009 restraints weight = 15084.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112323 restraints weight = 7311.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114502 restraints weight = 4564.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115661 restraints weight = 3331.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116527 restraints weight = 2762.096| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9956 Z= 0.161 Angle : 0.619 9.861 13580 Z= 0.309 Chirality : 0.045 0.259 1505 Planarity : 0.005 0.055 1718 Dihedral : 6.175 52.086 1719 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.95 % Allowed : 16.99 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.25), residues: 1156 helix: 0.77 (0.26), residues: 405 sheet: -0.91 (0.37), residues: 193 loop : -1.61 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.031 0.002 TYR A 473 PHE 0.031 0.002 PHE D 285 TRP 0.030 0.001 TRP D 610 HIS 0.005 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9924) covalent geometry : angle 0.61116 (13495) SS BOND : bond 0.00202 ( 11) SS BOND : angle 0.73668 ( 22) hydrogen bonds : bond 0.03858 ( 362) hydrogen bonds : angle 4.69813 ( 1041) link_BETA1-4 : bond 0.00293 ( 6) link_BETA1-4 : angle 1.53287 ( 18) link_NAG-ASN : bond 0.00219 ( 15) link_NAG-ASN : angle 1.54270 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6663 (pp30) REVERT: A 324 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6822 (tp30) REVERT: A 328 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8330 (mtp180) REVERT: A 345 THR cc_start: 0.8014 (p) cc_final: 0.6642 (t) REVERT: A 346 ARG cc_start: 0.6946 (mmm160) cc_final: 0.6611 (mmm160) REVERT: A 362 VAL cc_start: 0.7837 (OUTLIER) cc_final: 0.7339 (p) REVERT: A 370 ASN cc_start: 0.7449 (t0) cc_final: 0.7150 (t0) REVERT: A 374 PHE cc_start: 0.8635 (m-10) cc_final: 0.8375 (m-80) REVERT: A 378 LYS cc_start: 0.7180 (mtpp) cc_final: 0.6825 (mtpp) REVERT: A 403 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7753 (ttp-170) REVERT: A 408 ARG cc_start: 0.7949 (ptm-80) cc_final: 0.7686 (ptt90) REVERT: A 414 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8067 (mm-40) REVERT: A 450 ASN cc_start: 0.7908 (m-40) cc_final: 0.7315 (m-40) REVERT: A 466 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7915 (ttp80) REVERT: A 536 ASN cc_start: 0.8038 (t0) cc_final: 0.7116 (p0) REVERT: C 131 CYS cc_start: 0.3746 (OUTLIER) cc_final: 0.3432 (m) REVERT: C 158 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7825 (mtt90) REVERT: C 182 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7801 (mmmt) REVERT: C 235 ILE cc_start: 0.8704 (mm) cc_final: 0.8380 (mt) REVERT: D 44 SER cc_start: 0.8602 (m) cc_final: 0.8207 (t) REVERT: D 70 SER cc_start: 0.8374 (m) cc_final: 0.8033 (t) REVERT: D 76 GLN cc_start: 0.7772 (mm-40) cc_final: 0.6981 (mm-40) REVERT: D 91 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7687 (mm) REVERT: D 98 GLN cc_start: 0.8010 (tt0) cc_final: 0.7584 (tt0) REVERT: D 126 ILE cc_start: 0.8026 (tt) cc_final: 0.7820 (pt) REVERT: D 127 TYR cc_start: 0.8187 (t80) cc_final: 0.7860 (t80) REVERT: D 148 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7188 (mt) REVERT: D 151 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8014 (tp) REVERT: D 152 MET cc_start: 0.8049 (tpp) cc_final: 0.7319 (mmp) REVERT: D 166 GLU cc_start: 0.7472 (tp30) cc_final: 0.7265 (mm-30) REVERT: D 203 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.8142 (m-10) REVERT: D 219 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7763 (mtm-85) REVERT: D 349 TRP cc_start: 0.8582 (m100) cc_final: 0.8370 (m100) REVERT: D 368 ASP cc_start: 0.6962 (m-30) cc_final: 0.6761 (m-30) REVERT: D 376 MET cc_start: 0.7543 (ttm) cc_final: 0.7156 (mtt) REVERT: D 435 GLU cc_start: 0.5418 (mp0) cc_final: 0.5067 (mp0) REVERT: D 460 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6769 (mtt90) REVERT: D 470 LYS cc_start: 0.7736 (tppt) cc_final: 0.7315 (tppt) REVERT: D 479 GLU cc_start: 0.6189 (tm-30) cc_final: 0.5790 (tp30) REVERT: D 500 PRO cc_start: 0.7925 (Cg_exo) cc_final: 0.7658 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7759 (tt) REVERT: D 518 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8036 (ttp80) REVERT: D 534 LYS cc_start: 0.7754 (mtpt) cc_final: 0.7429 (mmmm) REVERT: D 557 MET cc_start: 0.8222 (tmm) cc_final: 0.7993 (tmm) REVERT: D 571 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6673 (mm-30) outliers start: 51 outliers final: 38 residues processed: 297 average time/residue: 0.1263 time to fit residues: 50.1013 Evaluate side-chains 298 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 0.0870 chunk 16 optimal weight: 0.0470 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 101 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 556 ASN D 42 GLN D 250 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109966 restraints weight = 14848.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113642 restraints weight = 6916.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115947 restraints weight = 4217.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117469 restraints weight = 3061.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.118524 restraints weight = 2468.599| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9956 Z= 0.142 Angle : 0.628 9.884 13580 Z= 0.316 Chirality : 0.045 0.258 1505 Planarity : 0.005 0.051 1718 Dihedral : 5.981 51.958 1719 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.66 % Allowed : 18.06 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.25), residues: 1156 helix: 0.87 (0.27), residues: 405 sheet: -0.93 (0.37), residues: 190 loop : -1.51 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.032 0.002 TYR A 473 PHE 0.029 0.002 PHE D 285 TRP 0.032 0.002 TRP D 610 HIS 0.004 0.001 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9924) covalent geometry : angle 0.62084 (13495) SS BOND : bond 0.00210 ( 11) SS BOND : angle 0.66053 ( 22) hydrogen bonds : bond 0.03691 ( 362) hydrogen bonds : angle 4.68124 ( 1041) link_BETA1-4 : bond 0.00285 ( 6) link_BETA1-4 : angle 1.49840 ( 18) link_NAG-ASN : bond 0.00250 ( 15) link_NAG-ASN : angle 1.52066 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 321 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6628 (pp30) REVERT: A 324 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: A 328 ARG cc_start: 0.8508 (mtt-85) cc_final: 0.8304 (mtp180) REVERT: A 345 THR cc_start: 0.8039 (p) cc_final: 0.6569 (t) REVERT: A 346 ARG cc_start: 0.7010 (mmm160) cc_final: 0.6625 (mmm160) REVERT: A 362 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7291 (p) REVERT: A 370 ASN cc_start: 0.7497 (t0) cc_final: 0.7193 (t0) REVERT: A 374 PHE cc_start: 0.8631 (m-10) cc_final: 0.8367 (m-80) REVERT: A 378 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6778 (mtpp) REVERT: A 403 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7713 (ttp-170) REVERT: A 408 ARG cc_start: 0.7991 (ptm-80) cc_final: 0.7740 (ptt90) REVERT: A 414 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8086 (mm-40) REVERT: A 450 ASN cc_start: 0.7798 (m-40) cc_final: 0.7182 (m-40) REVERT: A 451 TYR cc_start: 0.8070 (m-80) cc_final: 0.7843 (m-10) REVERT: A 466 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7916 (ttp80) REVERT: A 536 ASN cc_start: 0.8027 (t0) cc_final: 0.7075 (p0) REVERT: C 41 LYS cc_start: 0.8039 (mttp) cc_final: 0.7798 (mttp) REVERT: C 131 CYS cc_start: 0.3771 (OUTLIER) cc_final: 0.3478 (m) REVERT: C 158 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7758 (mtt90) REVERT: C 182 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7776 (mmmt) REVERT: C 235 ILE cc_start: 0.8646 (mm) cc_final: 0.8342 (mt) REVERT: D 44 SER cc_start: 0.8545 (m) cc_final: 0.8137 (t) REVERT: D 70 SER cc_start: 0.8360 (m) cc_final: 0.7997 (t) REVERT: D 76 GLN cc_start: 0.7750 (mm-40) cc_final: 0.6935 (mm-40) REVERT: D 91 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7653 (mm) REVERT: D 98 GLN cc_start: 0.8028 (tt0) cc_final: 0.7574 (tt0) REVERT: D 126 ILE cc_start: 0.7967 (tt) cc_final: 0.7742 (pt) REVERT: D 127 TYR cc_start: 0.8132 (t80) cc_final: 0.7762 (t80) REVERT: D 148 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7188 (mt) REVERT: D 151 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7969 (tp) REVERT: D 152 MET cc_start: 0.8042 (tpp) cc_final: 0.7265 (mmp) REVERT: D 166 GLU cc_start: 0.7495 (tp30) cc_final: 0.7276 (mm-30) REVERT: D 203 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7983 (m-10) REVERT: D 208 GLU cc_start: 0.7252 (tt0) cc_final: 0.6714 (mt-10) REVERT: D 349 TRP cc_start: 0.8592 (m100) cc_final: 0.8374 (m100) REVERT: D 376 MET cc_start: 0.7506 (ttm) cc_final: 0.7125 (mtt) REVERT: D 460 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6675 (mtt90) REVERT: D 470 LYS cc_start: 0.7755 (tppt) cc_final: 0.7339 (tppt) REVERT: D 479 GLU cc_start: 0.6282 (tm-30) cc_final: 0.5855 (tp30) REVERT: D 483 GLU cc_start: 0.6959 (tp30) cc_final: 0.6641 (tp30) REVERT: D 500 PRO cc_start: 0.7947 (Cg_exo) cc_final: 0.7718 (Cg_endo) REVERT: D 503 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7698 (tt) REVERT: D 518 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8086 (tmm160) REVERT: D 534 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7424 (mmmm) REVERT: D 557 MET cc_start: 0.8220 (tmm) cc_final: 0.7962 (tmm) REVERT: D 564 GLU cc_start: 0.7266 (mp0) cc_final: 0.7056 (mp0) REVERT: D 571 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6712 (mm-30) outliers start: 48 outliers final: 38 residues processed: 280 average time/residue: 0.1216 time to fit residues: 45.3429 Evaluate side-chains 298 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 271 TRP Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 477 TRP Chi-restraints excluded: chain D residue 485 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 512 PHE Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 608 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 57 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 104 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 556 ASN D 42 GLN D 250 ASN D 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.127852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108963 restraints weight = 14880.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112607 restraints weight = 6943.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114949 restraints weight = 4240.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116529 restraints weight = 3065.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117285 restraints weight = 2457.121| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9956 Z= 0.173 Angle : 0.638 9.874 13580 Z= 0.320 Chirality : 0.046 0.258 1505 Planarity : 0.005 0.055 1718 Dihedral : 5.861 52.385 1719 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 5.15 % Allowed : 17.57 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.25), residues: 1156 helix: 0.85 (0.27), residues: 404 sheet: -0.85 (0.37), residues: 193 loop : -1.53 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.030 0.002 TYR A 473 PHE 0.030 0.002 PHE D 285 TRP 0.032 0.002 TRP D 610 HIS 0.005 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9924) covalent geometry : angle 0.63024 (13495) SS BOND : bond 0.00155 ( 11) SS BOND : angle 0.63899 ( 22) hydrogen bonds : bond 0.03898 ( 362) hydrogen bonds : angle 4.69782 ( 1041) link_BETA1-4 : bond 0.00232 ( 6) link_BETA1-4 : angle 1.48134 ( 18) link_NAG-ASN : bond 0.00251 ( 15) link_NAG-ASN : angle 1.61324 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2162.15 seconds wall clock time: 38 minutes 0.27 seconds (2280.27 seconds total)