Starting phenix.real_space_refine on Sun Aug 9 08:52:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sm2_55024/08_2026/9sm2_55024.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sm2_55024/08_2026/9sm2_55024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sm2_55024/08_2026/9sm2_55024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sm2_55024/08_2026/9sm2_55024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sm2_55024/08_2026/9sm2_55024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sm2_55024/08_2026/9sm2_55024.map" } resolution = 2.5 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= 0.006 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 150 5.16 5 C 20706 2.51 5 N 5508 2.21 5 O 6512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32876 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6913 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 30, 'TRANS': 850} Chain: "B" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3776 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain: "C" Number of atoms: 6913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 6913 Classifications: {'peptide': 881} Link IDs: {'PTRANS': 30, 'TRANS': 850} Chain: "D" Number of atoms: 3776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3776 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain: "E" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1044 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain: "F" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1044 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 1, 'TRANS': 132} Chain: "G" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4504 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain: "H" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4504 Classifications: {'peptide': 569} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'GLC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {'GLC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {'GLC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 67 Unusual residues: {'GLC': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {'GLC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "N" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 89 Unusual residues: {'GLC': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 6.60, per 1000 atoms: 0.20 Number of scatterers: 32876 At special positions: 0 Unit cell: (154.566, 178.665, 181.158, 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 150 16.00 O 6512 8.00 N 5508 7.00 C 20706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 ALPHA1-6 " GLC I 1 " - " GLC I 2 " " GLC I 2 " - " GLC I 3 " " GLC I 3 " - " GLC I 4 " " GLC J 1 " - " GLC J 2 " " GLC J 2 " - " GLC J 3 " " GLC J 3 " - " GLC J 4 " " GLC K 1 " - " GLC K 2 " " GLC K 2 " - " GLC K 3 " " GLC K 3 " - " GLC K 4 " " GLC K 4 " - " GLC K 5 " " GLC K 5 " - " GLC K 6 " " GLC L 1 " - " GLC L 2 " " GLC L 2 " - " GLC L 3 " " GLC L 3 " - " GLC L 4 " " GLC L 4 " - " GLC L 5 " " GLC L 5 " - " GLC L 6 " " GLC M 1 " - " GLC M 2 " " GLC M 2 " - " GLC M 3 " " GLC M 3 " - " GLC M 4 " " GLC M 4 " - " GLC M 5 " " GLC M 5 " - " GLC M 6 " " GLC M 6 " - " GLC M 7 " " GLC M 7 " - " GLC M 8 " " GLC N 1 " - " GLC N 2 " " GLC N 2 " - " GLC N 3 " " GLC N 3 " - " GLC N 4 " " GLC N 4 " - " GLC N 5 " " GLC N 5 " - " GLC N 6 " " GLC N 6 " - " GLC N 7 " " GLC N 7 " - " GLC N 8 " Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7592 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 45 sheets defined 27.6% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 218 through 223 removed outlier: 6.511A pdb=" N SER A 221 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 275 Processing helix chain 'A' and resid 281 through 285 Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.680A pdb=" N GLY A 291 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.594A pdb=" N HIS A 417 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 799 through 806 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 888 through 894 removed outlier: 3.553A pdb=" N ASN A 893 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 921 No H-bonds generated for 'chain 'A' and resid 919 through 921' Processing helix chain 'A' and resid 941 through 946 removed outlier: 3.885A pdb=" N LEU A 945 " --> pdb=" O PRO A 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 48 Processing helix chain 'B' and resid 49 through 55 removed outlier: 4.259A pdb=" N THR B 52 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 3.588A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 98 through 122 removed outlier: 4.139A pdb=" N SER B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 155 removed outlier: 3.588A pdb=" N ARG B 152 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 195 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 210 through 226 Processing helix chain 'B' and resid 227 through 230 removed outlier: 5.410A pdb=" N ARG B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.820A pdb=" N GLU B 235 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 327 through 332 removed outlier: 4.095A pdb=" N VAL B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 382 through 396 Processing helix chain 'B' and resid 398 through 413 removed outlier: 4.393A pdb=" N ALA B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) Proline residue: B 405 - end of helix removed outlier: 3.554A pdb=" N VAL B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 439 Processing helix chain 'B' and resid 443 through 452 removed outlier: 4.644A pdb=" N PHE B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 471 through 476 removed outlier: 3.530A pdb=" N LEU B 476 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 212 through 217 Processing helix chain 'C' and resid 218 through 223 removed outlier: 6.425A pdb=" N SER C 221 " --> pdb=" O ILE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 275 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.809A pdb=" N GLY C 291 " --> pdb=" O SER C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 301 Processing helix chain 'C' and resid 376 through 383 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 413 through 419 removed outlier: 3.617A pdb=" N MET C 419 " --> pdb=" O THR C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 538 Processing helix chain 'C' and resid 601 through 603 No H-bonds generated for 'chain 'C' and resid 601 through 603' Processing helix chain 'C' and resid 706 through 710 Processing helix chain 'C' and resid 799 through 806 Processing helix chain 'C' and resid 829 through 833 removed outlier: 3.615A pdb=" N ARG C 833 " --> pdb=" O ASP C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 879 removed outlier: 4.175A pdb=" N ASP C 877 " --> pdb=" O ALA C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 894 Processing helix chain 'C' and resid 919 through 921 No H-bonds generated for 'chain 'C' and resid 919 through 921' Processing helix chain 'C' and resid 941 through 946 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 49 through 55 removed outlier: 4.224A pdb=" N THR D 52 " --> pdb=" O CYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 70 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'D' and resid 98 through 122 removed outlier: 4.164A pdb=" N SER D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Proline residue: D 108 - end of helix Processing helix chain 'D' and resid 128 through 155 removed outlier: 3.597A pdb=" N ARG D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 195 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 210 through 226 Processing helix chain 'D' and resid 227 through 230 removed outlier: 5.439A pdb=" N ARG D 230 " --> pdb=" O PRO D 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.679A pdb=" N GLU D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.100A pdb=" N VAL D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 382 through 396 Processing helix chain 'D' and resid 398 through 413 removed outlier: 3.509A pdb=" N ALA D 403 " --> pdb=" O PRO D 399 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Proline residue: D 405 - end of helix removed outlier: 3.516A pdb=" N VAL D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 412 " --> pdb=" O ILE D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 439 Processing helix chain 'D' and resid 443 through 452 removed outlier: 4.721A pdb=" N PHE D 447 " --> pdb=" O GLY D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 466 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.530A pdb=" N LEU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'E' and resid 47 through 51 Processing helix chain 'E' and resid 104 through 116 removed outlier: 3.533A pdb=" N ASN E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 51 Processing helix chain 'F' and resid 104 through 114 Processing helix chain 'G' and resid 148 through 162 Processing helix chain 'G' and resid 201 through 214 Processing helix chain 'G' and resid 228 through 233 removed outlier: 4.415A pdb=" N ALA G 232 " --> pdb=" O LYS G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 241 Processing helix chain 'G' and resid 271 through 289 Processing helix chain 'G' and resid 314 through 330 removed outlier: 3.631A pdb=" N GLY G 318 " --> pdb=" O ASN G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 Processing helix chain 'G' and resid 344 through 352 removed outlier: 3.564A pdb=" N GLY G 352 " --> pdb=" O ILE G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 366 removed outlier: 4.047A pdb=" N ALA G 366 " --> pdb=" O ALA G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 382 removed outlier: 3.719A pdb=" N LEU G 371 " --> pdb=" O ASP G 367 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 372 " --> pdb=" O PHE G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 Processing helix chain 'G' and resid 406 through 420 Processing helix chain 'G' and resid 446 through 463 removed outlier: 3.583A pdb=" N HIS G 455 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 468 Processing helix chain 'G' and resid 559 through 563 Processing helix chain 'H' and resid 148 through 162 Processing helix chain 'H' and resid 201 through 215 Processing helix chain 'H' and resid 230 through 234 Processing helix chain 'H' and resid 237 through 241 Processing helix chain 'H' and resid 271 through 289 Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'H' and resid 344 through 350 Processing helix chain 'H' and resid 362 through 366 removed outlier: 4.015A pdb=" N ALA H 366 " --> pdb=" O ALA H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 382 removed outlier: 3.624A pdb=" N LEU H 371 " --> pdb=" O ASP H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 401 removed outlier: 3.502A pdb=" N ASP H 400 " --> pdb=" O ASN H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 406 through 420 Processing helix chain 'H' and resid 446 through 463 removed outlier: 3.709A pdb=" N HIS H 455 " --> pdb=" O THR H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 468 Processing helix chain 'H' and resid 559 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 133 removed outlier: 6.604A pdb=" N LEU A 184 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A 230 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 186 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N SER A 232 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A 185 " --> pdb=" O THR A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 253 removed outlier: 5.419A pdb=" N ALA A 239 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY A 316 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 474 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASN A 525 " --> pdb=" O MET A 541 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET A 541 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N THR A 590 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY A 626 " --> pdb=" O THR A 590 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 698 " --> pdb=" O GLY A 722 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY A 722 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A 700 " --> pdb=" O ASN A 720 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN A 720 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS A 723 " --> pdb=" O LEU A 758 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP A 744 " --> pdb=" O ASN A 737 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU A 857 " --> pdb=" O LEU A 936 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 936 " --> pdb=" O GLU A 857 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER A 859 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE A 934 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N PHE A 861 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR A 928 " --> pdb=" O ILE A 965 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 965 " --> pdb=" O TYR A 928 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 930 " --> pdb=" O ALA A 963 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 963 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS A 932 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A 962 " --> pdb=" O SER A 988 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER A 988 " --> pdb=" O VAL A 962 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 242 " --> pdb=" O PHE A 999 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 643 through 644 Processing sheet with id=AA5, first strand: chain 'A' and resid 766 through 771 removed outlier: 6.695A pdb=" N PHE A 767 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N MET A 778 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ASN A 769 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 13.640A pdb=" N SER A 774 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 11.071A pdb=" N TYR A 791 " --> pdb=" O SER A 774 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL A 776 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 787 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A 788 " --> pdb=" O LEU A 836 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 793 through 796 removed outlier: 4.928A pdb=" N ARG A 818 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 923 through 925 removed outlier: 7.935A pdb=" N ASP A 981 " --> pdb=" O LYS A 869 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR A 871 " --> pdb=" O ASP A 981 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.531A pdb=" N GLY B 76 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP B 311 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 273 removed outlier: 6.983A pdb=" N SER B 269 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG B 381 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE B 271 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 333 through 334 Processing sheet with id=AB2, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.107A pdb=" N VAL C 185 " --> pdb=" O THR C 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 253 removed outlier: 5.430A pdb=" N ALA C 239 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N GLY C 316 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 543 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN C 525 " --> pdb=" O MET C 541 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET C 541 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N THR C 590 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY C 626 " --> pdb=" O THR C 590 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LYS C 723 " --> pdb=" O LEU C 758 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TRP C 744 " --> pdb=" O ASN C 737 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU C 857 " --> pdb=" O LEU C 936 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU C 936 " --> pdb=" O GLU C 857 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER C 859 " --> pdb=" O ILE C 934 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE C 934 " --> pdb=" O SER C 859 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N PHE C 861 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR C 928 " --> pdb=" O ILE C 965 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE C 965 " --> pdb=" O TYR C 928 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG C 930 " --> pdb=" O ALA C 963 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 963 " --> pdb=" O ARG C 930 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS C 932 " --> pdb=" O ASN C 961 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 962 " --> pdb=" O SER C 988 " (cutoff:3.500A) removed outlier: 10.443A pdb=" N SER C 988 " --> pdb=" O VAL C 962 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL C 242 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 643 through 644 Processing sheet with id=AB6, first strand: chain 'C' and resid 700 through 702 Processing sheet with id=AB7, first strand: chain 'C' and resid 766 through 771 removed outlier: 6.755A pdb=" N PHE C 767 " --> pdb=" O MET C 778 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET C 778 " --> pdb=" O PHE C 767 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ASN C 769 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N VAL C 776 " --> pdb=" O TYR C 789 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 787 " --> pdb=" O MET C 778 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE C 788 " --> pdb=" O LEU C 836 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 793 through 796 removed outlier: 4.011A pdb=" N GLY C 795 " --> pdb=" O ARG C 818 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 869 through 871 Processing sheet with id=AC1, first strand: chain 'D' and resid 73 through 76 removed outlier: 6.397A pdb=" N GLY D 76 " --> pdb=" O TRP D 311 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP D 311 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 269 through 273 removed outlier: 6.398A pdb=" N TYR D 380 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU D 272 " --> pdb=" O VAL D 378 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 378 " --> pdb=" O GLU D 272 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AC4, first strand: chain 'E' and resid 37 through 39 Processing sheet with id=AC5, first strand: chain 'E' and resid 43 through 44 removed outlier: 8.127A pdb=" N ILE E 72 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR E 95 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR E 74 " --> pdb=" O LEU E 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 37 through 39 Processing sheet with id=AC7, first strand: chain 'F' and resid 43 through 44 removed outlier: 7.081A pdb=" N ILE F 44 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN F 141 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR F 74 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 39 through 41 removed outlier: 6.906A pdb=" N THR G 40 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N GLY G 121 " --> pdb=" O THR G 40 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ASP G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU G 113 " --> pdb=" O ASP G 117 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ILE G 119 " --> pdb=" O ARG G 111 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG G 111 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL G 74 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU G 85 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR G 76 " --> pdb=" O VAL G 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 47 through 49 Processing sheet with id=AD1, first strand: chain 'G' and resid 137 through 140 removed outlier: 6.120A pdb=" N VAL G 167 " --> pdb=" O MET G 219 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR G 221 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE G 169 " --> pdb=" O TYR G 221 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N LEU G 223 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER G 218 " --> pdb=" O GLY G 293 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN G 295 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE G 220 " --> pdb=" O GLN G 295 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA G 297 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN G 222 " --> pdb=" O ALA G 297 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 190 through 192 Processing sheet with id=AD3, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AD4, first strand: chain 'G' and resid 305 through 306 removed outlier: 4.648A pdb=" N LEU G 305 " --> pdb=" O VAL G 313 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 357 through 360 removed outlier: 6.610A pdb=" N PHE G 357 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA G 391 " --> pdb=" O PHE G 357 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN G 359 " --> pdb=" O ALA G 391 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU G 425 " --> pdb=" O THR G 388 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE G 390 " --> pdb=" O LEU G 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'G' and resid 403 through 404 removed outlier: 6.716A pdb=" N GLY G 403 " --> pdb=" O THR G 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 472 through 474 removed outlier: 3.951A pdb=" N ALA G 501 " --> pdb=" O ASN G 474 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 472 through 474 removed outlier: 3.951A pdb=" N ALA G 501 " --> pdb=" O ASN G 474 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS G 551 " --> pdb=" O GLU G 592 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU G 552 " --> pdb=" O LEU G 567 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 478 through 480 removed outlier: 6.558A pdb=" N THR G 537 " --> pdb=" O ALA G 582 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA G 582 " --> pdb=" O THR G 537 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA G 539 " --> pdb=" O LEU G 580 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 39 through 41 removed outlier: 6.879A pdb=" N LEU H 109 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR H 122 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA H 107 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA H 124 " --> pdb=" O TYR H 105 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR H 105 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP H 126 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS H 103 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 74 " --> pdb=" O GLU H 85 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU H 85 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR H 76 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 47 through 49 Processing sheet with id=AE3, first strand: chain 'H' and resid 137 through 140 removed outlier: 6.071A pdb=" N VAL H 167 " --> pdb=" O MET H 219 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N TYR H 221 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE H 169 " --> pdb=" O TYR H 221 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LEU H 223 " --> pdb=" O PHE H 169 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N SER H 218 " --> pdb=" O GLY H 293 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLN H 295 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE H 220 " --> pdb=" O GLN H 295 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA H 297 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN H 222 " --> pdb=" O ALA H 297 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR H 358 " --> pdb=" O MET H 337 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE H 357 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ALA H 391 " --> pdb=" O PHE H 357 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN H 359 " --> pdb=" O ALA H 391 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU H 425 " --> pdb=" O THR H 388 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE H 390 " --> pdb=" O LEU H 425 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 190 through 192 Processing sheet with id=AE5, first strand: chain 'H' and resid 226 through 228 Processing sheet with id=AE6, first strand: chain 'H' and resid 403 through 404 removed outlier: 6.866A pdb=" N GLY H 403 " --> pdb=" O THR H 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 472 through 474 removed outlier: 3.932A pdb=" N ALA H 501 " --> pdb=" O ASN H 474 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN H 488 " --> pdb=" O THR H 499 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ALA H 501 " --> pdb=" O ASN H 488 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 472 through 474 removed outlier: 3.932A pdb=" N ALA H 501 " --> pdb=" O ASN H 474 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER H 496 " --> pdb=" O PHE H 515 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 478 through 480 removed outlier: 6.439A pdb=" N THR H 537 " --> pdb=" O ALA H 582 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA H 582 " --> pdb=" O THR H 537 " (cutoff:3.500A) 1498 hydrogen bonds defined for protein. 4071 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: 7.53 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10722 1.34 - 1.46: 7194 1.46 - 1.58: 15458 1.58 - 1.69: 0 1.69 - 1.81: 268 Bond restraints: 33642 Sorted by residual: bond pdb=" C LYS C 501 " pdb=" N HIS C 502 " ideal model delta sigma weight residual 1.331 1.454 -0.123 1.66e-02 3.63e+03 5.51e+01 bond pdb=" C ALA C 499 " pdb=" N LYS C 500 " ideal model delta sigma weight residual 1.332 1.265 0.068 1.41e-02 5.03e+03 2.30e+01 bond pdb=" C1 GLC J 1 " pdb=" O1 GLC J 1 " ideal model delta sigma weight residual 1.389 1.433 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 GLC L 1 " pdb=" O1 GLC L 1 " ideal model delta sigma weight residual 1.389 1.432 -0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" C1 GLC N 1 " pdb=" O1 GLC N 1 " ideal model delta sigma weight residual 1.389 1.431 -0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 33637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 45220 2.70 - 5.39: 423 5.39 - 8.09: 51 8.09 - 10.78: 2 10.78 - 13.48: 2 Bond angle restraints: 45698 Sorted by residual: angle pdb=" CA ALA C 499 " pdb=" C ALA C 499 " pdb=" N LYS C 500 " ideal model delta sigma weight residual 116.59 123.93 -7.34 1.47e+00 4.63e-01 2.49e+01 angle pdb=" C ALA C 499 " pdb=" N LYS C 500 " pdb=" CA LYS C 500 " ideal model delta sigma weight residual 122.61 129.81 -7.20 1.56e+00 4.11e-01 2.13e+01 angle pdb=" C5 GLC I 1 " pdb=" C6 GLC I 1 " pdb=" O6 GLC I 1 " ideal model delta sigma weight residual 113.12 99.64 13.48 3.00e+00 1.11e-01 2.02e+01 angle pdb=" O ALA C 499 " pdb=" C ALA C 499 " pdb=" N LYS C 500 " ideal model delta sigma weight residual 122.23 115.10 7.13 1.61e+00 3.86e-01 1.96e+01 angle pdb=" C ASN A 525 " pdb=" N ILE A 526 " pdb=" CA ILE A 526 " ideal model delta sigma weight residual 121.97 129.82 -7.85 1.80e+00 3.09e-01 1.90e+01 ... (remaining 45693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 18836 17.77 - 35.55: 1096 35.55 - 53.32: 216 53.32 - 71.09: 65 71.09 - 88.87: 25 Dihedral angle restraints: 20238 sinusoidal: 8320 harmonic: 11918 Sorted by residual: dihedral pdb=" CA LEU A 822 " pdb=" C LEU A 822 " pdb=" N ASN A 823 " pdb=" CA ASN A 823 " ideal model delta harmonic sigma weight residual 180.00 151.27 28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASN C 823 " pdb=" C ASN C 823 " pdb=" N ASN C 824 " pdb=" CA ASN C 824 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLU C 603 " pdb=" C GLU C 603 " pdb=" N ASP C 604 " pdb=" CA ASP C 604 " ideal model delta harmonic sigma weight residual 180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 20235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4360 0.073 - 0.146: 613 0.146 - 0.219: 38 0.219 - 0.292: 6 0.292 - 0.365: 7 Chirality restraints: 5024 Sorted by residual: chirality pdb=" C1 GLC M 3 " pdb=" O6 GLC M 2 " pdb=" C2 GLC M 3 " pdb=" O5 GLC M 3 " both_signs ideal model delta sigma weight residual False 2.40 2.05 0.35 2.00e-02 2.50e+03 3.07e+02 chirality pdb=" C1 GLC J 3 " pdb=" O6 GLC J 2 " pdb=" C2 GLC J 3 " pdb=" O5 GLC J 3 " both_signs ideal model delta sigma weight residual False 2.40 2.12 0.28 2.00e-02 2.50e+03 1.96e+02 chirality pdb=" C1 GLC K 2 " pdb=" O6 GLC K 1 " pdb=" C2 GLC K 2 " pdb=" O5 GLC K 2 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.63e+02 ... (remaining 5021 not shown) Planarity restraints: 5902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 564 " -0.002 2.00e-02 2.50e+03 2.62e-02 1.38e+01 pdb=" CG TYR A 564 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 564 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 564 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 564 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 564 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 564 " -0.037 2.00e-02 2.50e+03 pdb=" OH TYR A 564 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 930 " 0.275 9.50e-02 1.11e+02 1.24e-01 1.20e+01 pdb=" NE ARG C 930 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG C 930 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG C 930 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 930 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 474 " 0.262 9.50e-02 1.11e+02 1.19e-01 1.12e+01 pdb=" NE ARG D 474 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 474 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG D 474 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 474 " 0.000 2.00e-02 2.50e+03 ... (remaining 5899 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4768 2.77 - 3.30: 32576 3.30 - 3.83: 55544 3.83 - 4.37: 69148 4.37 - 4.90: 118246 Nonbonded interactions: 280282 Sorted by model distance: nonbonded pdb=" OE1 GLU E 23 " pdb=" OH TYR E 25 " model vdw 2.233 3.040 nonbonded pdb=" NH1 ARG C 173 " pdb=" OE1 GLN C 671 " model vdw 2.252 3.120 nonbonded pdb=" O MET G 445 " pdb=" NZ LYS G 450 " model vdw 2.262 3.120 nonbonded pdb=" NH1 ARG A 930 " pdb=" OE2 GLU A 974 " model vdw 2.277 3.120 nonbonded pdb=" OG1 THR A 652 " pdb=" N ALA A 653 " model vdw 2.277 3.120 ... (remaining 280277 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.710 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.370 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 0.123 33672 Z= 0.156 Angle : 0.725 13.479 45788 Z= 0.392 Chirality : 0.050 0.365 5024 Planarity : 0.007 0.124 5902 Dihedral : 12.795 88.865 12646 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.58 % Allowed : 4.02 % Favored : 95.40 % Rotamer: Outliers : 1.41 % Allowed : 4.51 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.14 (0.13), residues: 4108 helix: -0.62 (0.16), residues: 858 sheet: 1.21 (0.15), residues: 1138 loop : -0.13 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG D 474 TYR 0.038 0.004 TYR A 564 PHE 0.025 0.002 PHE A 529 TRP 0.034 0.002 TRP B 64 HIS 0.008 0.001 HIS F 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (33642) covalent geometry : angle 0.71686 / 0.39 (45698) hydrogen bonds : bond 0.18166 / 12.20 ( 1492) hydrogen bonds : angle 7.43871 / 5.20 ( 4071) link_ALPHA1-6 : bond 0.01628 / 1.05 ( 30) link_ALPHA1-6 : angle 2.56323 / 1.56 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 271 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.8940 (ttt) cc_final: 0.8696 (ttp) REVERT: A 857 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8232 (mt-10) REVERT: B 473 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8473 (mp0) REVERT: C 247 ASN cc_start: 0.8423 (p0) cc_final: 0.8034 (p0) REVERT: C 337 SER cc_start: 0.8280 (t) cc_final: 0.7744 (p) REVERT: C 614 ASN cc_start: 0.8236 (m110) cc_final: 0.7971 (m110) REVERT: C 650 ASN cc_start: 0.8218 (t0) cc_final: 0.7866 (t0) REVERT: C 967 ARG cc_start: 0.8647 (mmt180) cc_final: 0.8143 (mmt90) REVERT: D 32 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: D 347 ARG cc_start: 0.7967 (mtm-85) cc_final: 0.7687 (mtm-85) REVERT: D 352 ASN cc_start: 0.9013 (m110) cc_final: 0.8749 (t0) REVERT: E 147 LEU cc_start: 0.7340 (tm) cc_final: 0.6779 (tt) REVERT: F 111 LEU cc_start: 0.9057 (mm) cc_final: 0.8703 (mt) REVERT: H 219 MET cc_start: 0.9104 (mmm) cc_final: 0.8773 (mmm) REVERT: H 543 MET cc_start: 0.7993 (tmm) cc_final: 0.7598 (tmt) outliers start: 49 outliers final: 17 residues processed: 314 average time/residue: 0.7420 time to fit residues: 276.0249 Evaluate side-chains 217 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 221 TYR Chi-restraints excluded: chain H residue 340 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN A 770 GLN A 773 ASN B 242 GLN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN E 114 GLN F 109 GLN F 114 GLN G 170 GLN H 440 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.057904 restraints weight = 59412.308| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.38 r_work: 0.2590 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33672 Z= 0.155 Angle : 0.634 9.769 45788 Z= 0.336 Chirality : 0.044 0.160 5024 Planarity : 0.004 0.057 5902 Dihedral : 6.159 59.277 5207 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.19 % Favored : 96.57 % Rotamer: Outliers : 1.84 % Allowed : 6.79 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.72 (0.13), residues: 4108 helix: 0.93 (0.18), residues: 870 sheet: 0.94 (0.14), residues: 1140 loop : 0.13 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 316 TYR 0.021 0.001 TYR A 265 PHE 0.020 0.001 PHE A 529 TRP 0.021 0.001 TRP A 455 HIS 0.004 0.001 HIS H 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (33642) covalent geometry : angle 0.63041 / 0.34 (45698) hydrogen bonds : bond 0.04231 / 2.86 ( 1492) hydrogen bonds : angle 5.38072 / 3.73 ( 4071) link_ALPHA1-6 : bond 0.00347 / 0.18 ( 30) link_ALPHA1-6 : angle 1.66652 / 1.03 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 219 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ASN cc_start: 0.8714 (p0) cc_final: 0.8503 (p0) REVERT: A 507 MET cc_start: 0.9146 (ttt) cc_final: 0.8942 (ttp) REVERT: A 518 ASP cc_start: 0.8938 (p0) cc_final: 0.8649 (p0) REVERT: A 614 ASN cc_start: 0.8706 (m-40) cc_final: 0.8453 (m-40) REVERT: A 667 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: A 857 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 976 ASP cc_start: 0.8698 (t0) cc_final: 0.8326 (t0) REVERT: B 473 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8688 (mp0) REVERT: C 247 ASN cc_start: 0.8164 (p0) cc_final: 0.7804 (p0) REVERT: C 332 SER cc_start: 0.8919 (m) cc_final: 0.8587 (p) REVERT: C 419 MET cc_start: 0.9176 (mtt) cc_final: 0.8946 (mtt) REVERT: C 650 ASN cc_start: 0.8388 (t0) cc_final: 0.8075 (t0) REVERT: C 731 MET cc_start: 0.8749 (ttp) cc_final: 0.8455 (ttp) REVERT: C 967 ARG cc_start: 0.9088 (mmt180) cc_final: 0.8536 (mmt90) REVERT: D 347 ARG cc_start: 0.8041 (mtm-85) cc_final: 0.7811 (mtm180) REVERT: D 352 ASN cc_start: 0.9013 (m110) cc_final: 0.8712 (t0) REVERT: F 33 ASP cc_start: 0.7432 (t70) cc_final: 0.7226 (t70) REVERT: H 219 MET cc_start: 0.8811 (mmm) cc_final: 0.8154 (mmm) REVERT: H 543 MET cc_start: 0.7621 (tmm) cc_final: 0.7202 (tmt) outliers start: 64 outliers final: 27 residues processed: 268 average time/residue: 0.6616 time to fit residues: 215.1874 Evaluate side-chains 223 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 340 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 393 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 236 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN C 886 ASN F 47 ASN G 176 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.055858 restraints weight = 59525.535| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.29 r_work: 0.2537 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2408 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 33672 Z= 0.261 Angle : 0.660 21.410 45788 Z= 0.340 Chirality : 0.046 0.286 5024 Planarity : 0.004 0.065 5902 Dihedral : 5.884 54.954 5194 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.80 % Favored : 95.98 % Rotamer: Outliers : 2.21 % Allowed : 7.36 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.67 (0.13), residues: 4108 helix: 1.23 (0.18), residues: 868 sheet: 0.84 (0.14), residues: 1146 loop : -0.04 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 316 TYR 0.024 0.002 TYR A 265 PHE 0.018 0.002 PHE B 283 TRP 0.022 0.001 TRP A 455 HIS 0.005 0.001 HIS H 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.26 (33642) covalent geometry : angle 0.65618 / 0.34 (45698) hydrogen bonds : bond 0.04333 / 2.92 ( 1492) hydrogen bonds : angle 5.16343 / 3.59 ( 4071) link_ALPHA1-6 : bond 0.00612 / 0.35 ( 30) link_ALPHA1-6 : angle 1.78992 / 1.12 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ASN cc_start: 0.8804 (p0) cc_final: 0.8571 (p0) REVERT: A 518 ASP cc_start: 0.8973 (p0) cc_final: 0.8709 (p0) REVERT: A 614 ASN cc_start: 0.8629 (m-40) cc_final: 0.8391 (m110) REVERT: A 667 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: A 857 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8658 (mt-10) REVERT: A 948 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8677 (mp) REVERT: A 976 ASP cc_start: 0.8895 (t0) cc_final: 0.8609 (t0) REVERT: B 473 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8659 (mp0) REVERT: C 332 SER cc_start: 0.8933 (m) cc_final: 0.8576 (p) REVERT: C 650 ASN cc_start: 0.8505 (t0) cc_final: 0.8130 (t0) REVERT: C 680 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7972 (mt) REVERT: C 716 GLU cc_start: 0.8964 (tp30) cc_final: 0.8748 (tp30) REVERT: C 731 MET cc_start: 0.8800 (ttp) cc_final: 0.8507 (ttp) REVERT: C 967 ARG cc_start: 0.9108 (mmt180) cc_final: 0.8554 (mmt90) REVERT: D 347 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7780 (mtm-85) REVERT: F 33 ASP cc_start: 0.7699 (t70) cc_final: 0.7292 (t70) REVERT: F 44 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8416 (pp) REVERT: F 136 MET cc_start: 0.8612 (mtp) cc_final: 0.8164 (mtp) REVERT: G 485 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.6937 (pmm) REVERT: H 219 MET cc_start: 0.8771 (mmm) cc_final: 0.8102 (mmm) REVERT: H 314 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.8125 (p0) REVERT: H 337 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8214 (ttt) REVERT: H 543 MET cc_start: 0.7663 (tmm) cc_final: 0.7348 (tmt) outliers start: 77 outliers final: 44 residues processed: 257 average time/residue: 0.7007 time to fit residues: 217.4885 Evaluate side-chains 236 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 47 ASN Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 453 MET Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 391 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 85 optimal weight: 0.7980 chunk 135 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 345 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.093885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.055177 restraints weight = 59850.119| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.32 r_work: 0.2567 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33672 Z= 0.229 Angle : 0.616 9.196 45788 Z= 0.320 Chirality : 0.045 0.229 5024 Planarity : 0.004 0.063 5902 Dihedral : 5.754 58.593 5193 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.70 % Favored : 96.11 % Rotamer: Outliers : 2.01 % Allowed : 8.14 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.60 (0.13), residues: 4108 helix: 1.27 (0.18), residues: 876 sheet: 0.73 (0.14), residues: 1164 loop : -0.11 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.025 0.001 TYR A 265 PHE 0.015 0.002 PHE B 283 TRP 0.023 0.001 TRP A 455 HIS 0.004 0.001 HIS G 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (33642) covalent geometry : angle 0.61158 / 0.32 (45698) hydrogen bonds : bond 0.03939 / 2.65 ( 1492) hydrogen bonds : angle 5.01469 / 3.49 ( 4071) link_ALPHA1-6 : bond 0.00519 / 0.29 ( 30) link_ALPHA1-6 : angle 1.69172 / 1.05 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 197 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 ASN cc_start: 0.8834 (p0) cc_final: 0.8596 (p0) REVERT: A 518 ASP cc_start: 0.8952 (p0) cc_final: 0.8707 (p0) REVERT: A 614 ASN cc_start: 0.8654 (m-40) cc_final: 0.8453 (m110) REVERT: A 667 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: A 948 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8698 (mp) REVERT: A 976 ASP cc_start: 0.8936 (t0) cc_final: 0.8688 (t0) REVERT: B 473 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8710 (mp0) REVERT: C 332 SER cc_start: 0.8938 (m) cc_final: 0.8651 (p) REVERT: C 602 GLN cc_start: 0.9246 (mm110) cc_final: 0.9032 (mm-40) REVERT: C 608 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8850 (mptm) REVERT: C 650 ASN cc_start: 0.8502 (t0) cc_final: 0.8092 (t0) REVERT: C 680 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8003 (mt) REVERT: C 731 MET cc_start: 0.8861 (ttp) cc_final: 0.8607 (ttp) REVERT: C 945 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8195 (pt) REVERT: C 967 ARG cc_start: 0.9149 (mmt180) cc_final: 0.8615 (mmt90) REVERT: F 33 ASP cc_start: 0.7842 (t70) cc_final: 0.7366 (t70) REVERT: F 136 MET cc_start: 0.8656 (mtp) cc_final: 0.8204 (mtp) REVERT: G 485 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.6720 (pmm) REVERT: H 219 MET cc_start: 0.8712 (mmm) cc_final: 0.8088 (mmm) REVERT: H 314 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8092 (p0) REVERT: H 337 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8316 (ttt) REVERT: H 543 MET cc_start: 0.7744 (tmm) cc_final: 0.7362 (tmm) outliers start: 70 outliers final: 37 residues processed: 253 average time/residue: 0.7376 time to fit residues: 222.8298 Evaluate side-chains 234 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 608 LYS Chi-restraints excluded: chain C residue 613 MET Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 277 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 336 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 GLN A 913 ASN C 614 ASN F 47 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.093605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.054897 restraints weight = 59868.255| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 2.32 r_work: 0.2536 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33672 Z= 0.234 Angle : 0.611 9.507 45788 Z= 0.316 Chirality : 0.044 0.166 5024 Planarity : 0.004 0.063 5902 Dihedral : 5.607 55.910 5192 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 2.50 % Allowed : 8.28 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 are not related in a simple way. whole: 0.54 (0.13), residues: 4108 helix: 1.42 (0.18), residues: 860 sheet: 0.66 (0.14), residues: 1174 loop : -0.21 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.025 0.001 TYR A 265 PHE 0.015 0.001 PHE B 283 TRP 0.023 0.001 TRP A 455 HIS 0.004 0.001 HIS G 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.23 (33642) covalent geometry : angle 0.60683 / 0.32 (45698) hydrogen bonds : bond 0.03882 / 2.61 ( 1492) hydrogen bonds : angle 4.96677 / 3.46 ( 4071) link_ALPHA1-6 : bond 0.00511 / 0.30 ( 30) link_ALPHA1-6 : angle 1.69702 / 1.05 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 194 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ASN cc_start: 0.8804 (p0) cc_final: 0.8561 (p0) REVERT: A 518 ASP cc_start: 0.8967 (p0) cc_final: 0.8706 (p0) REVERT: A 667 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8515 (tt0) REVERT: A 948 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 976 ASP cc_start: 0.8930 (t0) cc_final: 0.8688 (t0) REVERT: B 473 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8667 (mp0) REVERT: C 332 SER cc_start: 0.8915 (m) cc_final: 0.8600 (p) REVERT: C 650 ASN cc_start: 0.8557 (t0) cc_final: 0.8065 (t0) REVERT: C 680 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7918 (mt) REVERT: C 731 MET cc_start: 0.8837 (ttp) cc_final: 0.8569 (ttp) REVERT: C 945 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8199 (pt) REVERT: C 967 ARG cc_start: 0.9142 (mmt180) cc_final: 0.8616 (mmt90) REVERT: F 33 ASP cc_start: 0.7822 (t70) cc_final: 0.7346 (t70) REVERT: F 92 ASP cc_start: 0.8602 (t0) cc_final: 0.8380 (m-30) REVERT: F 136 MET cc_start: 0.8652 (mtp) cc_final: 0.8205 (mtp) REVERT: G 122 THR cc_start: 0.7489 (OUTLIER) cc_final: 0.7212 (t) REVERT: G 485 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.6731 (pmm) REVERT: H 219 MET cc_start: 0.8655 (mmm) cc_final: 0.8030 (mmm) REVERT: H 337 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8333 (ttt) REVERT: H 530 MET cc_start: 0.9161 (tpp) cc_final: 0.8942 (tpt) REVERT: H 543 MET cc_start: 0.7717 (tmm) cc_final: 0.7354 (tmm) REVERT: H 580 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8670 (tp) outliers start: 87 outliers final: 50 residues processed: 263 average time/residue: 0.7084 time to fit residues: 225.0862 Evaluate side-chains 242 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 184 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 777 THR Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 584 LYS Chi-restraints excluded: chain C residue 613 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 488 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 509 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 337 MET Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 343 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 364 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 330 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 ASN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 162 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.095396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.057143 restraints weight = 59232.301| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.35 r_work: 0.2598 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33672 Z= 0.137 Angle : 0.561 9.418 45788 Z= 0.290 Chirality : 0.042 0.181 5024 Planarity : 0.003 0.061 5902 Dihedral : 5.279 55.161 5192 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.33 % Favored : 96.47 % Rotamer: Outliers : 2.10 % Allowed : 8.94 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.59 (0.13), residues: 4108 helix: 1.44 (0.18), residues: 880 sheet: 0.68 (0.14), residues: 1164 loop : -0.17 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.022 0.001 TYR A 265 PHE 0.020 0.001 PHE C 997 TRP 0.023 0.001 TRP A 455 HIS 0.003 0.001 HIS G 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (33642) covalent geometry : angle 0.55713 / 0.29 (45698) hydrogen bonds : bond 0.03387 / 2.27 ( 1492) hydrogen bonds : angle 4.81465 / 3.35 ( 4071) link_ALPHA1-6 : bond 0.00334 / 0.18 ( 30) link_ALPHA1-6 : angle 1.50207 / 0.93 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 199 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 ASN cc_start: 0.8641 (p0) cc_final: 0.8211 (p0) REVERT: A 247 ASN cc_start: 0.8746 (p0) cc_final: 0.8484 (p0) REVERT: A 518 ASP cc_start: 0.8872 (p0) cc_final: 0.8642 (p0) REVERT: A 667 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: A 948 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8678 (mp) REVERT: A 976 ASP cc_start: 0.8927 (t0) cc_final: 0.8695 (t0) REVERT: B 473 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8735 (mp0) REVERT: C 247 ASN cc_start: 0.8272 (p0) cc_final: 0.7978 (p0) REVERT: C 650 ASN cc_start: 0.8540 (t0) cc_final: 0.8049 (t0) REVERT: C 680 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7828 (mp) REVERT: C 731 MET cc_start: 0.8884 (ttp) cc_final: 0.8589 (ttp) REVERT: C 945 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8154 (pt) REVERT: C 967 ARG cc_start: 0.9176 (mmt180) cc_final: 0.8665 (mmt90) REVERT: D 316 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8708 (tp30) REVERT: F 33 ASP cc_start: 0.7891 (t70) cc_final: 0.7407 (t70) REVERT: F 109 GLN cc_start: 0.9215 (mm-40) cc_final: 0.9014 (mm-40) REVERT: F 136 MET cc_start: 0.8688 (mtp) cc_final: 0.8312 (mtp) REVERT: G 122 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7212 (t) REVERT: H 219 MET cc_start: 0.8648 (mmm) cc_final: 0.8012 (mmm) REVERT: H 543 MET cc_start: 0.7705 (tmm) cc_final: 0.7326 (tmm) REVERT: H 580 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8740 (tp) outliers start: 73 outliers final: 41 residues processed: 256 average time/residue: 0.6989 time to fit residues: 216.6008 Evaluate side-chains 237 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 189 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 488 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 432 MET Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 255 optimal weight: 0.2980 chunk 310 optimal weight: 7.9990 chunk 396 optimal weight: 5.9990 chunk 365 optimal weight: 9.9990 chunk 112 optimal weight: 0.0870 chunk 238 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 383 optimal weight: 9.9990 overall best weight: 2.6764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 ASN ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.094017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.055801 restraints weight = 59608.978| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 2.27 r_work: 0.2542 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33672 Z= 0.227 Angle : 0.601 9.236 45788 Z= 0.310 Chirality : 0.044 0.219 5024 Planarity : 0.004 0.061 5902 Dihedral : 5.384 56.216 5192 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.89 % Favored : 95.89 % Rotamer: Outliers : 2.21 % Allowed : 9.29 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.60 (0.13), residues: 4108 helix: 1.57 (0.18), residues: 858 sheet: 0.66 (0.14), residues: 1164 loop : -0.19 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.025 0.001 TYR A 265 PHE 0.014 0.001 PHE B 283 TRP 0.021 0.001 TRP A 455 HIS 0.004 0.001 HIS G 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (33642) covalent geometry : angle 0.59708 / 0.31 (45698) hydrogen bonds : bond 0.03765 / 2.53 ( 1492) hydrogen bonds : angle 4.87987 / 3.40 ( 4071) link_ALPHA1-6 : bond 0.00498 / 0.29 ( 30) link_ALPHA1-6 : angle 1.67635 / 1.03 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9329 (mmtp) cc_final: 0.8916 (mppt) REVERT: A 245 ASN cc_start: 0.8670 (p0) cc_final: 0.8200 (p0) REVERT: A 247 ASN cc_start: 0.8728 (p0) cc_final: 0.8482 (p0) REVERT: A 518 ASP cc_start: 0.8930 (p0) cc_final: 0.8673 (p0) REVERT: A 667 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8479 (tt0) REVERT: A 948 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 976 ASP cc_start: 0.8926 (t0) cc_final: 0.8709 (t0) REVERT: B 473 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8661 (mp0) REVERT: C 650 ASN cc_start: 0.8579 (t0) cc_final: 0.8075 (t0) REVERT: C 680 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7790 (mt) REVERT: C 731 MET cc_start: 0.8851 (ttp) cc_final: 0.8591 (ttp) REVERT: C 945 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8255 (pt) REVERT: C 967 ARG cc_start: 0.9145 (mmt180) cc_final: 0.8629 (mmt90) REVERT: D 316 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8700 (tp30) REVERT: F 33 ASP cc_start: 0.7850 (t70) cc_final: 0.7370 (t70) REVERT: F 136 MET cc_start: 0.8713 (mtp) cc_final: 0.8345 (mtp) REVERT: G 122 THR cc_start: 0.7577 (OUTLIER) cc_final: 0.7291 (t) REVERT: G 485 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6839 (pmm) REVERT: H 219 MET cc_start: 0.8566 (mmm) cc_final: 0.7917 (mmm) REVERT: H 337 MET cc_start: 0.9181 (tpt) cc_final: 0.8674 (tpt) REVERT: H 507 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8849 (mmtp) REVERT: H 543 MET cc_start: 0.7566 (tmm) cc_final: 0.7144 (tmm) REVERT: H 580 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8618 (tp) outliers start: 77 outliers final: 47 residues processed: 254 average time/residue: 0.7117 time to fit residues: 217.7572 Evaluate side-chains 242 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 187 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 488 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 507 LYS Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 367 optimal weight: 10.0000 chunk 326 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 275 optimal weight: 20.0000 chunk 214 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 284 optimal weight: 0.2980 chunk 61 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 ASN ** C 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.095639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.057384 restraints weight = 59267.977| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.36 r_work: 0.2606 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 33672 Z= 0.126 Angle : 0.558 10.093 45788 Z= 0.288 Chirality : 0.042 0.218 5024 Planarity : 0.003 0.061 5902 Dihedral : 5.149 56.089 5192 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.43 % Favored : 96.35 % Rotamer: Outliers : 1.78 % Allowed : 10.09 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.63 (0.13), residues: 4108 helix: 1.51 (0.18), residues: 880 sheet: 0.73 (0.15), residues: 1146 loop : -0.18 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.021 0.001 TYR A 265 PHE 0.016 0.001 PHE C 997 TRP 0.024 0.001 TRP A 455 HIS 0.003 0.001 HIS G 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (33642) covalent geometry : angle 0.55505 / 0.29 (45698) hydrogen bonds : bond 0.03271 / 2.19 ( 1492) hydrogen bonds : angle 4.74484 / 3.30 ( 4071) link_ALPHA1-6 : bond 0.00310 / 0.16 ( 30) link_ALPHA1-6 : angle 1.44153 / 0.89 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9331 (mmtp) cc_final: 0.8921 (mppt) REVERT: A 245 ASN cc_start: 0.8573 (p0) cc_final: 0.8172 (p0) REVERT: A 247 ASN cc_start: 0.8705 (p0) cc_final: 0.8443 (p0) REVERT: A 518 ASP cc_start: 0.8859 (p0) cc_final: 0.8635 (p0) REVERT: A 667 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: A 948 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 976 ASP cc_start: 0.8924 (t0) cc_final: 0.8690 (t0) REVERT: B 473 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8733 (mp0) REVERT: C 247 ASN cc_start: 0.8259 (p0) cc_final: 0.7969 (p0) REVERT: C 650 ASN cc_start: 0.8554 (t0) cc_final: 0.8081 (t0) REVERT: C 680 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7838 (mp) REVERT: C 731 MET cc_start: 0.8888 (ttp) cc_final: 0.8610 (ttp) REVERT: C 945 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8116 (pt) REVERT: C 967 ARG cc_start: 0.9196 (mmt180) cc_final: 0.8683 (mmt90) REVERT: D 316 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8751 (tp30) REVERT: F 33 ASP cc_start: 0.7889 (t70) cc_final: 0.7414 (t70) REVERT: F 136 MET cc_start: 0.8710 (mtp) cc_final: 0.8384 (mtp) REVERT: G 122 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7486 (t) REVERT: G 485 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.6823 (pmm) REVERT: H 219 MET cc_start: 0.8614 (mmm) cc_final: 0.7978 (mmm) REVERT: H 278 MET cc_start: 0.8932 (mmm) cc_final: 0.8622 (mmm) REVERT: H 337 MET cc_start: 0.9177 (tpt) cc_final: 0.8534 (tpt) REVERT: H 543 MET cc_start: 0.7708 (tmm) cc_final: 0.7338 (tmm) REVERT: H 580 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8740 (tp) outliers start: 62 outliers final: 42 residues processed: 246 average time/residue: 0.7097 time to fit residues: 210.6444 Evaluate side-chains 239 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 316 GLU Chi-restraints excluded: chain D residue 488 ASN Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 267 VAL Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 201 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 384 optimal weight: 0.0870 chunk 236 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.095974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.057771 restraints weight = 59023.855| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 2.42 r_work: 0.2590 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2458 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33672 Z= 0.120 Angle : 0.548 9.488 45788 Z= 0.282 Chirality : 0.041 0.232 5024 Planarity : 0.003 0.061 5902 Dihedral : 5.019 58.348 5192 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.38 % Favored : 96.40 % Rotamer: Outliers : 1.58 % Allowed : 10.24 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.71 (0.13), residues: 4108 helix: 1.65 (0.18), residues: 868 sheet: 0.77 (0.15), residues: 1144 loop : -0.14 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.021 0.001 TYR A 265 PHE 0.018 0.001 PHE C 997 TRP 0.023 0.001 TRP A 455 HIS 0.003 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (33642) covalent geometry : angle 0.54468 / 0.28 (45698) hydrogen bonds : bond 0.03200 / 2.14 ( 1492) hydrogen bonds : angle 4.68578 / 3.26 ( 4071) link_ALPHA1-6 : bond 0.00308 / 0.16 ( 30) link_ALPHA1-6 : angle 1.43207 / 0.88 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 201 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8909 (mppt) REVERT: A 245 ASN cc_start: 0.8506 (p0) cc_final: 0.8110 (p0) REVERT: A 247 ASN cc_start: 0.8621 (p0) cc_final: 0.8354 (p0) REVERT: A 518 ASP cc_start: 0.8777 (p0) cc_final: 0.8556 (p0) REVERT: A 667 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: A 948 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 976 ASP cc_start: 0.8890 (t0) cc_final: 0.8650 (t0) REVERT: B 473 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8703 (mp0) REVERT: C 247 ASN cc_start: 0.8205 (p0) cc_final: 0.7877 (p0) REVERT: C 650 ASN cc_start: 0.8529 (t0) cc_final: 0.8021 (t0) REVERT: C 680 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7627 (mp) REVERT: C 716 GLU cc_start: 0.8614 (tp30) cc_final: 0.8413 (tp30) REVERT: C 731 MET cc_start: 0.8849 (ttp) cc_final: 0.8537 (ttp) REVERT: C 737 ASN cc_start: 0.9200 (m-40) cc_final: 0.8952 (m-40) REVERT: C 945 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8063 (pt) REVERT: C 967 ARG cc_start: 0.9180 (mmt180) cc_final: 0.8650 (mmt90) REVERT: C 976 ASP cc_start: 0.8834 (t0) cc_final: 0.8318 (t0) REVERT: F 33 ASP cc_start: 0.7760 (t70) cc_final: 0.7274 (t70) REVERT: F 136 MET cc_start: 0.8689 (mtp) cc_final: 0.8393 (mtp) REVERT: G 485 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.6803 (pmm) REVERT: H 219 MET cc_start: 0.8578 (mmm) cc_final: 0.7931 (mmm) REVERT: H 278 MET cc_start: 0.8883 (mmm) cc_final: 0.8518 (mmm) REVERT: H 337 MET cc_start: 0.9160 (tpt) cc_final: 0.8488 (tpt) REVERT: H 543 MET cc_start: 0.7671 (tmm) cc_final: 0.7306 (tmm) REVERT: H 580 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8706 (tp) outliers start: 55 outliers final: 37 residues processed: 247 average time/residue: 0.7247 time to fit residues: 215.4572 Evaluate side-chains 237 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 145 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 292 optimal weight: 8.9990 chunk 393 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 303 optimal weight: 5.9990 chunk 358 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 614 ASN ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 571 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.093086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.054336 restraints weight = 59920.616| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.27 r_work: 0.2525 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 33672 Z= 0.319 Angle : 0.660 10.091 45788 Z= 0.338 Chirality : 0.047 0.235 5024 Planarity : 0.004 0.061 5902 Dihedral : 5.506 59.715 5191 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.21 % Favored : 95.57 % Rotamer: Outliers : 1.58 % Allowed : 10.38 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.58 (0.13), residues: 4108 helix: 1.64 (0.18), residues: 846 sheet: 0.70 (0.14), residues: 1160 loop : -0.26 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 206 TYR 0.025 0.002 TYR A 265 PHE 0.017 0.002 PHE C 529 TRP 0.018 0.002 TRP A 455 HIS 0.005 0.001 HIS H 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.32 (33642) covalent geometry : angle 0.65562 / 0.34 (45698) hydrogen bonds : bond 0.04091 / 2.75 ( 1492) hydrogen bonds : angle 4.94244 / 3.45 ( 4071) link_ALPHA1-6 : bond 0.00647 / 0.40 ( 30) link_ALPHA1-6 : angle 1.79950 / 1.10 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7246 (mmm) cc_final: 0.6853 (mtp) REVERT: A 135 LYS cc_start: 0.9341 (mmtp) cc_final: 0.8930 (mppt) REVERT: A 247 ASN cc_start: 0.8822 (p0) cc_final: 0.8567 (p0) REVERT: A 667 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8504 (tt0) REVERT: A 976 ASP cc_start: 0.8966 (t0) cc_final: 0.8751 (t0) REVERT: B 473 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8686 (mp0) REVERT: C 650 ASN cc_start: 0.8586 (t0) cc_final: 0.8098 (t0) REVERT: C 680 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7913 (mp) REVERT: C 731 MET cc_start: 0.8887 (ttp) cc_final: 0.8547 (ttp) REVERT: C 967 ARG cc_start: 0.9174 (mmt180) cc_final: 0.8661 (mmt90) REVERT: F 33 ASP cc_start: 0.7959 (t70) cc_final: 0.7485 (t70) REVERT: F 136 MET cc_start: 0.8718 (mtp) cc_final: 0.8357 (mtp) REVERT: G 485 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.6961 (pmm) REVERT: H 219 MET cc_start: 0.8555 (mmm) cc_final: 0.7935 (mmm) REVERT: H 337 MET cc_start: 0.9198 (tpt) cc_final: 0.8699 (tpt) REVERT: H 543 MET cc_start: 0.7706 (tmm) cc_final: 0.7297 (tmm) REVERT: H 580 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8667 (tp) outliers start: 55 outliers final: 44 residues processed: 231 average time/residue: 0.7147 time to fit residues: 197.9677 Evaluate side-chains 231 residues out of total 3478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 667 GLU Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 652 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 682 ASP Chi-restraints excluded: chain C residue 746 SER Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 787 VAL Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 945 LEU Chi-restraints excluded: chain C residue 962 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 137 TYR Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 247 SER Chi-restraints excluded: chain G residue 250 THR Chi-restraints excluded: chain G residue 340 VAL Chi-restraints excluded: chain G residue 485 MET Chi-restraints excluded: chain G residue 489 VAL Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain H residue 314 ASN Chi-restraints excluded: chain H residue 340 VAL Chi-restraints excluded: chain H residue 425 LEU Chi-restraints excluded: chain H residue 432 MET Chi-restraints excluded: chain H residue 526 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 580 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 403 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 315 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 295 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 277 optimal weight: 0.0670 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.093331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.055023 restraints weight = 59472.469| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.25 r_work: 0.2554 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.174 33672 Z= 0.277 Angle : 0.751 59.190 45788 Z= 0.406 Chirality : 0.045 0.231 5024 Planarity : 0.004 0.061 5902 Dihedral : 5.507 59.654 5191 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.14 % Favored : 95.64 % Rotamer: Outliers : 1.64 % Allowed : 10.35 % Favored : 88.01 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.37 % 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 are not related in a simple way. whole: 0.58 (0.13), residues: 4108 helix: 1.65 (0.18), residues: 846 sheet: 0.68 (0.14), residues: 1160 loop : -0.26 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 451 TYR 0.025 0.001 TYR A 265 PHE 0.017 0.002 PHE C 529 TRP 0.019 0.001 TRP A 455 HIS 0.005 0.001 HIS H 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 (33642) covalent geometry : angle 0.74744 / 0.41 (45698) hydrogen bonds : bond 0.04002 / 2.69 ( 1492) hydrogen bonds : angle 4.94363 / 3.45 ( 4071) link_ALPHA1-6 : bond 0.00568 / 0.33 ( 30) link_ALPHA1-6 : angle 1.79760 / 1.10 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15779.64 seconds wall clock time: 268 minutes 58.99 seconds (16138.99 seconds total)