Starting phenix.real_space_refine on Tue Aug 26 13:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jr0_36589/08_2025/8jr0_36589.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jr0_36589/08_2025/8jr0_36589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jr0_36589/08_2025/8jr0_36589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jr0_36589/08_2025/8jr0_36589.map" model { file = "/net/cci-nas-00/data/ceres_data/8jr0_36589/08_2025/8jr0_36589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jr0_36589/08_2025/8jr0_36589.cif" } resolution = 2.8 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= 0.012 sd= 1.107 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: 8 Type Number sf(0) Gaussians Br 7 7.06 5 P 13 5.49 5 Mg 5 5.21 5 S 121 5.16 5 C 23717 2.51 5 N 6446 2.21 5 O 7144 1.98 5 F 7 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37460 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3916 Classifications: {'peptide': 517} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 494} Chain: "B" Number of atoms: 3740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3740 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 469} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4033 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 505} Chain breaks: 2 Chain: "D" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "E" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "F" Number of atoms: 3614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3614 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 445} Chain: "G" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2251 Classifications: {'peptide': 287} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 276} Chain breaks: 1 Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 906 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "1" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "2" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "3" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "4" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "5" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "6" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "7" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "8" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "9" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 567 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "a" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1706 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 2 Chain: "b" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1107 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "d" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 433} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'UTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.77, per 1000 atoms: 0.23 Number of scatterers: 37460 At special positions: 0 Unit cell: (126.29, 134.32, 247.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Br 7 34.99 S 121 16.00 P 13 15.00 Mg 5 11.99 F 7 9.00 O 7144 8.00 N 6446 7.00 C 23717 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 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8860 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 23 sheets defined 59.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.531A pdb=" N ILE A 15 " --> pdb=" O ILE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.577A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 242 through 256 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.678A pdb=" N GLN A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.747A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.517A pdb=" N GLY A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.926A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 390 through 404 removed outlier: 4.088A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 463 through 478 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.493A pdb=" N LEU A 483 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.952A pdb=" N ASN B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.614A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 177 through 188 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.921A pdb=" N GLY B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 226 Processing helix chain 'B' and resid 242 through 262 Proline residue: B 250 - end of helix removed outlier: 3.805A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.797A pdb=" N GLN B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 300 through 310 removed outlier: 3.764A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.688A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 400 removed outlier: 3.789A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 432 removed outlier: 3.680A pdb=" N LYS B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.615A pdb=" N LEU B 483 " --> pdb=" O GLU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.559A pdb=" N TYR C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.009A pdb=" N ASN C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 85 " --> pdb=" O PHE C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 85' Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.582A pdb=" N LEU C 107 " --> pdb=" O ASP C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.818A pdb=" N ARG C 142 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 189 through 196 removed outlier: 4.010A pdb=" N GLY C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 230 removed outlier: 4.011A pdb=" N ASP C 230 " --> pdb=" O GLY C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.826A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.698A pdb=" N GLN C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.514A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.782A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 440 through 454 removed outlier: 3.759A pdb=" N GLY C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 Processing helix chain 'C' and resid 479 through 490 removed outlier: 4.006A pdb=" N LEU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.700A pdb=" N LYS C 509 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 152 through 159 Processing helix chain 'D' and resid 176 through 188 Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 234 through 255 removed outlier: 5.137A pdb=" N ALA D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU D 243 " --> pdb=" O MET D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 277 removed outlier: 3.735A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 303 Processing helix chain 'D' and resid 322 through 325 Processing helix chain 'D' and resid 328 through 335 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 373 through 401 removed outlier: 4.794A pdb=" N ASP D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE D 396 " --> pdb=" O ASP D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 405 Processing helix chain 'D' and resid 406 through 423 Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 430 through 435 Processing helix chain 'D' and resid 442 through 456 Processing helix chain 'D' and resid 471 through 482 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 176 through 191 Processing helix chain 'E' and resid 204 through 218 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.749A pdb=" N ARG E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ALA E 242 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LEU E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 281 removed outlier: 3.645A pdb=" N PHE E 270 " --> pdb=" O ASN E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 303 Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 345 through 351 removed outlier: 3.658A pdb=" N LYS E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 401 removed outlier: 3.561A pdb=" N TYR E 377 " --> pdb=" O GLY E 373 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASP E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE E 396 " --> pdb=" O ASP E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 405 Processing helix chain 'E' and resid 406 through 423 Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 430 through 435 Processing helix chain 'E' and resid 442 through 456 Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 471 through 481 removed outlier: 3.638A pdb=" N LEU E 475 " --> pdb=" O GLY E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.556A pdb=" N VAL F 105 " --> pdb=" O GLY F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 176 through 189 Processing helix chain 'F' and resid 204 through 218 Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 234 through 255 removed outlier: 5.189A pdb=" N ALA F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU F 243 " --> pdb=" O MET F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 281 removed outlier: 3.843A pdb=" N PHE F 270 " --> pdb=" O ASN F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 303 Processing helix chain 'F' and resid 322 through 325 Processing helix chain 'F' and resid 328 through 335 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 345 through 351 removed outlier: 3.607A pdb=" N LYS F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 401 removed outlier: 4.726A pdb=" N ASP F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE F 396 " --> pdb=" O ASP F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 405 Processing helix chain 'F' and resid 406 through 423 Processing helix chain 'F' and resid 427 through 429 No H-bonds generated for 'chain 'F' and resid 427 through 429' Processing helix chain 'F' and resid 430 through 435 Processing helix chain 'F' and resid 442 through 456 Processing helix chain 'F' and resid 471 through 482 Processing helix chain 'G' and resid 4 through 60 Proline residue: G 45 - end of helix removed outlier: 4.024A pdb=" N GLU G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 109 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.700A pdb=" N GLN G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 Processing helix chain 'G' and resid 225 through 302 Proline residue: G 235 - end of helix Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 91 through 100 removed outlier: 4.175A pdb=" N GLU H 100 " --> pdb=" O LYS H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.617A pdb=" N VAL H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 42 removed outlier: 3.733A pdb=" N ALA 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 48 removed outlier: 3.981A pdb=" N GLY 1 47 " --> pdb=" O GLU 1 44 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 76 removed outlier: 3.510A pdb=" N PHE 1 53 " --> pdb=" O LEU 1 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE 1 55 " --> pdb=" O THR 1 51 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY 1 58 " --> pdb=" O PHE 1 54 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN 1 67 " --> pdb=" O ALA 1 63 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 42 removed outlier: 3.565A pdb=" N ILE 2 26 " --> pdb=" O ILE 2 22 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY 2 29 " --> pdb=" O GLY 2 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 77 removed outlier: 4.743A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix removed outlier: 3.624A pdb=" N ILE 2 55 " --> pdb=" O THR 2 51 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA 2 62 " --> pdb=" O GLY 2 58 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA 2 72 " --> pdb=" O LEU 2 68 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 42 removed outlier: 3.845A pdb=" N ALA 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER 3 37 " --> pdb=" O ASN 3 33 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 76 removed outlier: 4.878A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix removed outlier: 3.753A pdb=" N ILE 3 55 " --> pdb=" O THR 3 51 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA 3 62 " --> pdb=" O GLY 3 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR 3 64 " --> pdb=" O VAL 3 60 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN 3 67 " --> pdb=" O ALA 3 63 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 42 removed outlier: 3.529A pdb=" N ALA 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 76 removed outlier: 4.762A pdb=" N THR 4 51 " --> pdb=" O GLY 4 47 " (cutoff:3.500A) Proline residue: 4 52 - end of helix removed outlier: 3.789A pdb=" N ILE 4 55 " --> pdb=" O THR 4 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR 4 56 " --> pdb=" O PRO 4 52 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA 4 63 " --> pdb=" O LEU 4 59 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN 4 67 " --> pdb=" O ALA 4 63 " (cutoff:3.500A) Processing helix chain '5' and resid 2 through 42 removed outlier: 3.559A pdb=" N ILE 5 26 " --> pdb=" O ILE 5 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER 5 37 " --> pdb=" O ASN 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 76 removed outlier: 3.950A pdb=" N PHE 5 50 " --> pdb=" O GLN 5 46 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N THR 5 51 " --> pdb=" O GLY 5 47 " (cutoff:3.500A) Proline residue: 5 52 - end of helix removed outlier: 3.824A pdb=" N ILE 5 55 " --> pdb=" O THR 5 51 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN 5 67 " --> pdb=" O ALA 5 63 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 42 removed outlier: 4.021A pdb=" N ALA 6 6 " --> pdb=" O ASP 6 2 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE 6 26 " --> pdb=" O ILE 6 22 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA 6 31 " --> pdb=" O GLY 6 27 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA 6 34 " --> pdb=" O VAL 6 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER 6 37 " --> pdb=" O ASN 6 33 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 46 Processing helix chain '6' and resid 49 through 76 removed outlier: 3.502A pdb=" N ILE 6 55 " --> pdb=" O THR 6 51 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY 6 58 " --> pdb=" O PHE 6 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 6 62 " --> pdb=" O GLY 6 58 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN 6 67 " --> pdb=" O ALA 6 63 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 42 removed outlier: 3.782A pdb=" N ALA 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 45 through 76 removed outlier: 4.909A pdb=" N THR 7 51 " --> pdb=" O GLY 7 47 " (cutoff:3.500A) Proline residue: 7 52 - end of helix removed outlier: 3.562A pdb=" N ILE 7 55 " --> pdb=" O THR 7 51 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY 7 58 " --> pdb=" O PHE 7 54 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA 7 63 " --> pdb=" O LEU 7 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 42 removed outlier: 3.536A pdb=" N GLY 8 20 " --> pdb=" O ILE 8 16 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE 8 26 " --> pdb=" O ILE 8 22 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU 8 35 " --> pdb=" O ALA 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 76 removed outlier: 4.775A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix removed outlier: 3.666A pdb=" N ASN 8 67 " --> pdb=" O ALA 8 63 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 42 removed outlier: 3.517A pdb=" N ALA 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 45 through 76 removed outlier: 4.425A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix removed outlier: 3.646A pdb=" N ILE 9 55 " --> pdb=" O THR 9 51 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN 9 67 " --> pdb=" O ALA 9 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 50 Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 86 through 104 removed outlier: 3.563A pdb=" N ILE a 98 " --> pdb=" O ILE a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 105 through 107 No H-bonds generated for 'chain 'a' and resid 105 through 107' Processing helix chain 'a' and resid 124 through 127 Processing helix chain 'a' and resid 128 through 152 removed outlier: 4.129A pdb=" N VAL a 132 " --> pdb=" O ASP a 128 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG a 151 " --> pdb=" O GLY a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 167 No H-bonds generated for 'chain 'a' and resid 165 through 167' Processing helix chain 'a' and resid 168 through 201 removed outlier: 3.610A pdb=" N LYS a 179 " --> pdb=" O GLU a 175 " (cutoff:3.500A) Proline residue: a 180 - end of helix removed outlier: 3.779A pdb=" N LEU a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE a 191 " --> pdb=" O LEU a 187 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY a 194 " --> pdb=" O ASN a 190 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA a 199 " --> pdb=" O GLY a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 204 No H-bonds generated for 'chain 'a' and resid 202 through 204' Processing helix chain 'a' and resid 209 through 243 removed outlier: 3.844A pdb=" N LEU a 221 " --> pdb=" O LYS a 217 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE a 222 " --> pdb=" O ALA a 218 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 49 removed outlier: 3.642A pdb=" N VAL b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 99 removed outlier: 3.712A pdb=" N GLN b 82 " --> pdb=" O PHE b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 141 removed outlier: 3.717A pdb=" N VAL b 122 " --> pdb=" O ALA b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 146 Processing helix chain 'b' and resid 147 through 161 Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 21 through 137 removed outlier: 3.780A pdb=" N LEU d 25 " --> pdb=" O PHE d 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR d 59 " --> pdb=" O SER d 55 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU d 81 " --> pdb=" O ARG d 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU d 124 " --> pdb=" O GLU d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 156 removed outlier: 3.853A pdb=" N SER d 144 " --> pdb=" O GLN d 140 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP d 152 " --> pdb=" O ASP d 148 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN d 153 " --> pdb=" O ARG d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 191 Processing helix chain 'd' and resid 195 through 216 Processing helix chain 'd' and resid 216 through 224 removed outlier: 3.509A pdb=" N THR d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 241 Processing helix chain 'd' and resid 246 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.519A pdb=" N GLU d 272 " --> pdb=" O ILE d 268 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 306 removed outlier: 3.960A pdb=" N GLN d 306 " --> pdb=" O ILE d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 312 removed outlier: 4.307A pdb=" N ALA d 310 " --> pdb=" O GLN d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 319 through 332 removed outlier: 4.100A pdb=" N ARG d 323 " --> pdb=" O PRO d 319 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 351 Processing helix chain 'd' and resid 357 through 372 removed outlier: 4.509A pdb=" N LEU d 363 " --> pdb=" O GLU d 359 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 403 Processing helix chain 'd' and resid 414 through 417 Processing helix chain 'd' and resid 432 through 443 Processing sheet with id=AA1, first strand: chain 'd' and resid 406 through 412 removed outlier: 4.063A pdb=" N ALA d 382 " --> pdb=" O HIS d 411 " (cutoff:3.500A) removed outlier: 14.243A pdb=" N ARG A 28 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N GLY A 95 " --> pdb=" O ARG A 28 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU A 30 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 94 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N GLU A 57 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU A 96 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASP A 36 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 8.672A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 209 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 267 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU A 327 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE A 269 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 329 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE A 271 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N GLU A 331 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.058A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS B 43 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 90 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU F 89 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU F 50 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA F 46 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN F 45 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG F 74 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N HIS F 67 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU F 72 " --> pdb=" O HIS F 67 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP F 32 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 102 removed outlier: 4.130A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 69 removed outlier: 4.122A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS C 43 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU D 89 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA D 46 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN D 45 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG D 74 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N HIS D 67 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU D 72 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP D 32 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AA9, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.311A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 209 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 534 through 540 removed outlier: 6.541A pdb=" N ALA C 534 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA G 203 " --> pdb=" O ALA C 534 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLU C 536 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N MET G 205 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL C 538 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL G 207 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 540 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR G 209 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN G 195 " --> pdb=" O LYS G 190 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LYS G 190 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA G 197 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU G 188 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 199 " --> pdb=" O TYR G 186 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N TYR G 186 " --> pdb=" O ALA G 199 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG G 201 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE G 184 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR G 187 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU G 116 " --> pdb=" O THR G 135 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER G 137 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 118 " --> pdb=" O SER G 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.048A pdb=" N GLU D 127 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 109 through 110 removed outlier: 6.742A pdb=" N SER D 196 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL D 227 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE D 198 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLY D 229 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLY D 200 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 201 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N MET D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D 262 " --> pdb=" O MET D 316 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA D 318 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE D 264 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR D 320 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE D 167 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL D 319 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 169 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS D 166 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR D 342 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 168 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 147 through 148 removed outlier: 4.180A pdb=" N TYR D 161 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 21 through 27 removed outlier: 5.653A pdb=" N VAL E 23 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLU E 34 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG E 25 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU E 72 " --> pdb=" O HIS E 67 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS E 67 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG E 74 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU E 50 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU E 89 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 98 through 101 removed outlier: 4.043A pdb=" N GLU E 127 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 109 through 111 removed outlier: 6.503A pdb=" N PHE E 110 " --> pdb=" O PHE E 228 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN E 230 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER E 196 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL E 227 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N PHE E 198 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLY E 229 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY E 200 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR E 195 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE E 263 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E 197 " --> pdb=" O PHE E 263 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ASP E 265 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA E 199 " --> pdb=" O ASP E 265 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N MET E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU E 262 " --> pdb=" O MET E 316 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA E 318 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE E 264 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 167 " --> pdb=" O GLN E 317 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS E 166 " --> pdb=" O ALA E 340 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR E 342 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA E 168 " --> pdb=" O THR E 342 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 147 through 148 removed outlier: 4.249A pdb=" N TYR E 161 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 98 through 101 removed outlier: 4.085A pdb=" N GLU F 127 " --> pdb=" O VAL F 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 109 through 110 removed outlier: 6.791A pdb=" N SER F 196 " --> pdb=" O ALA F 225 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N VAL F 227 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE F 198 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLY F 229 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLY F 200 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N MET F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU F 262 " --> pdb=" O MET F 316 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA F 318 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE F 264 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N TYR F 320 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE F 167 " --> pdb=" O GLN F 317 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL F 319 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU F 169 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS F 166 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N THR F 342 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA F 168 " --> pdb=" O THR F 342 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU F 344 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE F 170 " --> pdb=" O LEU F 344 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.973A pdb=" N TYR F 161 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 221 through 223 removed outlier: 6.326A pdb=" N SER G 221 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLN H 44 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLU G 223 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ALA H 10 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASN H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 30 through 34 removed outlier: 4.176A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 17 through 19 2284 hydrogen bonds defined for protein. 6612 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: 7.66 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 12763 1.35 - 1.50: 9560 1.50 - 1.65: 15543 1.65 - 1.79: 116 1.79 - 1.94: 112 Bond restraints: 38094 Sorted by residual: bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.94e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.90e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 ... (remaining 38089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 51477 3.73 - 7.46: 201 7.46 - 11.19: 17 11.19 - 14.92: 0 14.92 - 18.65: 6 Bond angle restraints: 51701 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.22 18.65 1.00e+00 1.00e+00 3.48e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 121.24 18.63 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 121.23 15.60 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 121.24 15.59 1.00e+00 1.00e+00 2.43e+02 ... (remaining 51696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.86: 21358 20.86 - 41.72: 1405 41.72 - 62.58: 174 62.58 - 83.44: 32 83.44 - 104.30: 15 Dihedral angle restraints: 22984 sinusoidal: 9180 harmonic: 13804 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 44.30 -104.30 1 2.00e+01 2.50e-03 2.99e+01 dihedral pdb=" CA GLN D 258 " pdb=" C GLN D 258 " pdb=" N ASP D 259 " pdb=" CA ASP D 259 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLN F 258 " pdb=" C GLN F 258 " pdb=" N ASP F 259 " pdb=" CA ASP F 259 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 22981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5488 0.083 - 0.166: 468 0.166 - 0.250: 19 0.250 - 0.333: 1 0.333 - 0.416: 1 Chirality restraints: 5977 Sorted by residual: chirality pdb=" C17 UTI 1 600 " pdb=" C06 UTI 1 600 " pdb=" C18 UTI 1 600 " pdb=" C27 UTI 1 600 " both_signs ideal model delta sigma weight residual False 2.42 2.84 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C06 UTI 1 600 " pdb=" C05 UTI 1 600 " pdb=" C07 UTI 1 600 " pdb=" C17 UTI 1 600 " both_signs ideal model delta sigma weight residual False -2.86 -2.61 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE a 171 " pdb=" N ILE a 171 " pdb=" C ILE a 171 " pdb=" CB ILE a 171 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5974 not shown) Planarity restraints: 6720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG b 100 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG b 100 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG b 100 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP b 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 328 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C ARG d 328 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG d 328 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS d 329 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO b 51 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO b 52 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO b 52 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO b 52 " 0.032 5.00e-02 4.00e+02 ... (remaining 6717 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 83 2.38 - 3.01: 22123 3.01 - 3.64: 56139 3.64 - 4.27: 90125 4.27 - 4.90: 149831 Nonbonded interactions: 318301 Sorted by model distance: nonbonded pdb=" O3B ADP D 600 " pdb="MG MG D 601 " model vdw 1.747 2.170 nonbonded pdb=" O3B ADP F 600 " pdb="MG MG F 601 " model vdw 1.805 2.170 nonbonded pdb=" OG1 THR D 178 " pdb="MG MG D 601 " model vdw 1.815 2.170 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 1.918 2.170 nonbonded pdb=" OG1 THR B 179 " pdb="MG MG B 601 " model vdw 2.015 2.170 ... (remaining 318296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain '1' and resid 1 through 81) selection = chain '2' selection = chain '3' selection = (chain '4' and resid 1 through 81) selection = (chain '5' and resid 1 through 81) selection = (chain '6' and resid 1 through 81) selection = (chain '7' and resid 1 through 81) selection = (chain '8' and resid 1 through 81) selection = (chain '9' and resid 1 through 81) } ncs_group { reference = (chain 'A' and (resid 5 through 22 or resid 29 through 404 or resid 417 or (resi \ d 418 through 419 and (name N or name CA or name C or name O or name CB )) or re \ sid 420 through 513 or resid 600 through 601)) selection = chain 'B' selection = (chain 'C' and (resid 5 through 404 or resid 417 or (resid 418 through 419 and ( \ name N or name CA or name C or name O or name CB )) or resid 420 through 513 or \ resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 18 through 486) selection = chain 'E' selection = (chain 'F' and resid 18 through 486) } 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: 9.750 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: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 33.720 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.150 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.006 0.081 38094 Z= 0.303 Angle : 0.734 18.648 51701 Z= 0.458 Chirality : 0.046 0.416 5977 Planarity : 0.005 0.081 6720 Dihedral : 13.792 104.296 14124 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.10), residues: 4835 helix: -1.63 (0.09), residues: 2562 sheet: -1.48 (0.19), residues: 578 loop : -1.87 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG d 221 TYR 0.018 0.001 TYR a 143 PHE 0.021 0.001 PHE 1 74 TRP 0.012 0.001 TRP a 216 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00581 (38094) covalent geometry : angle 0.73353 (51701) hydrogen bonds : bond 0.15380 ( 2284) hydrogen bonds : angle 7.83962 ( 6612) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 758 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.7382 (pp20) cc_final: 0.7008 (tm-30) REVERT: A 418 LYS cc_start: 0.7805 (tttm) cc_final: 0.7603 (ttmt) REVERT: B 70 ASP cc_start: 0.8010 (t0) cc_final: 0.7732 (t0) REVERT: B 146 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7995 (pttp) REVERT: B 473 ASP cc_start: 0.7476 (m-30) cc_final: 0.7270 (m-30) REVERT: C 146 LYS cc_start: 0.8863 (pttp) cc_final: 0.8544 (ptpt) REVERT: C 184 ASP cc_start: 0.7744 (m-30) cc_final: 0.7531 (m-30) REVERT: C 199 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8394 (mtmt) REVERT: C 491 LYS cc_start: 0.8165 (mttt) cc_final: 0.7742 (mtmt) REVERT: C 541 LYS cc_start: 0.7598 (ptpt) cc_final: 0.7339 (ttpp) REVERT: D 22 ARG cc_start: 0.7892 (ttp-110) cc_final: 0.7042 (tpp-160) REVERT: D 214 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7450 (tp30) REVERT: D 316 MET cc_start: 0.8560 (ttt) cc_final: 0.8250 (ttp) REVERT: D 391 LYS cc_start: 0.8279 (tttt) cc_final: 0.7993 (ttpt) REVERT: D 474 ASP cc_start: 0.7931 (m-30) cc_final: 0.7476 (m-30) REVERT: D 480 GLU cc_start: 0.7539 (tt0) cc_final: 0.6925 (mp0) REVERT: E 184 MET cc_start: 0.8431 (mmm) cc_final: 0.8180 (mmt) REVERT: E 309 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7407 (mtm180) REVERT: E 346 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7362 (tpp80) REVERT: E 389 ARG cc_start: 0.7790 (tpt170) cc_final: 0.7381 (tpt-90) REVERT: E 464 GLN cc_start: 0.7891 (tp40) cc_final: 0.7479 (mp10) REVERT: F 231 MET cc_start: 0.9203 (mtm) cc_final: 0.8939 (mtt) REVERT: F 417 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6866 (mtp180) REVERT: F 477 LYS cc_start: 0.7195 (mtmm) cc_final: 0.6912 (mtpp) REVERT: F 480 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7105 (pt0) REVERT: G 121 ARG cc_start: 0.6973 (mtt90) cc_final: 0.6710 (mtt-85) REVERT: G 139 MET cc_start: 0.7721 (mtm) cc_final: 0.7354 (mtm) REVERT: G 198 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6873 (mm-30) REVERT: G 200 HIS cc_start: 0.7815 (m170) cc_final: 0.7395 (m90) REVERT: H 73 THR cc_start: 0.8612 (p) cc_final: 0.8390 (t) REVERT: b 109 LYS cc_start: 0.9109 (mmpt) cc_final: 0.8748 (tmmt) REVERT: b 127 GLN cc_start: 0.8813 (tp40) cc_final: 0.8259 (tm-30) REVERT: b 142 LEU cc_start: 0.9211 (pp) cc_final: 0.8891 (mp) REVERT: b 147 HIS cc_start: 0.7635 (m-70) cc_final: 0.7427 (m-70) REVERT: d 1 MET cc_start: 0.6733 (tmm) cc_final: 0.6124 (tmt) REVERT: d 168 LEU cc_start: 0.8335 (tt) cc_final: 0.8112 (tt) REVERT: d 272 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8219 (tp30) outliers start: 0 outliers final: 1 residues processed: 758 average time/residue: 0.7528 time to fit residues: 677.4294 Evaluate side-chains 571 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 570 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 143 GLN A 437 GLN B 53 GLN B 72 HIS B 335 ASN B 382 GLN C 192 ASN C 506 ASN D 71 ASN D 128 HIS D 209 ASN D 388 GLN E 219 ASN E 394 GLN E 414 ASN F 128 HIS F 209 ASN F 388 GLN F 464 GLN G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 HIS 4 46 GLN ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 42 GLN ** 8 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 130 HIS ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 411 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119905 restraints weight = 50143.142| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.09 r_work: 0.3297 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38094 Z= 0.140 Angle : 0.593 9.468 51701 Z= 0.303 Chirality : 0.043 0.210 5977 Planarity : 0.004 0.052 6720 Dihedral : 6.693 87.122 5603 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.02 % Allowed : 12.48 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.12), residues: 4835 helix: 0.39 (0.10), residues: 2586 sheet: -1.02 (0.20), residues: 570 loop : -1.09 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 72 TYR 0.032 0.001 TYR a 238 PHE 0.017 0.001 PHE d 11 TRP 0.010 0.001 TRP a 216 HIS 0.007 0.001 HIS d 273 Details of bonding type rmsd covalent geometry : bond 0.00302 (38094) covalent geometry : angle 0.59322 (51701) hydrogen bonds : bond 0.04392 ( 2284) hydrogen bonds : angle 4.87753 ( 6612) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 644 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8414 (ttt-90) REVERT: A 279 GLU cc_start: 0.8197 (mp0) cc_final: 0.7927 (mp0) REVERT: A 494 GLU cc_start: 0.7115 (pm20) cc_final: 0.6765 (mm-30) REVERT: B 146 LYS cc_start: 0.8431 (ptmt) cc_final: 0.8043 (pttp) REVERT: B 470 GLU cc_start: 0.7369 (tp30) cc_final: 0.7026 (tp30) REVERT: B 473 ASP cc_start: 0.7584 (m-30) cc_final: 0.7357 (m-30) REVERT: C 45 GLU cc_start: 0.8692 (tt0) cc_final: 0.8332 (pt0) REVERT: C 71 GLU cc_start: 0.8539 (pm20) cc_final: 0.8014 (pm20) REVERT: C 146 LYS cc_start: 0.8944 (pttp) cc_final: 0.8483 (ptpt) REVERT: C 173 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: C 199 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8015 (mmpt) REVERT: C 491 LYS cc_start: 0.8099 (mttt) cc_final: 0.7810 (mtmt) REVERT: C 541 LYS cc_start: 0.7495 (ptpt) cc_final: 0.7170 (ttpt) REVERT: D 22 ARG cc_start: 0.8143 (ttp-110) cc_final: 0.6943 (ttm-80) REVERT: D 163 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7771 (ttm-80) REVERT: D 190 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7370 (mtt-85) REVERT: D 214 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7560 (tp30) REVERT: D 316 MET cc_start: 0.9061 (ttt) cc_final: 0.8796 (ttp) REVERT: D 391 LYS cc_start: 0.8184 (tttt) cc_final: 0.7786 (ttpt) REVERT: D 474 ASP cc_start: 0.7965 (m-30) cc_final: 0.7424 (m-30) REVERT: D 480 GLU cc_start: 0.7604 (tt0) cc_final: 0.6601 (mm-30) REVERT: E 230 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.6856 (mm110) REVERT: E 389 ARG cc_start: 0.7749 (tpt170) cc_final: 0.7365 (tpt-90) REVERT: E 464 GLN cc_start: 0.7970 (tp40) cc_final: 0.7365 (mp10) REVERT: F 127 GLU cc_start: 0.8075 (tt0) cc_final: 0.7872 (tt0) REVERT: F 217 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: F 417 ARG cc_start: 0.7514 (mtt90) cc_final: 0.6927 (mtp180) REVERT: F 464 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6929 (mt0) REVERT: F 477 LYS cc_start: 0.6876 (mtmm) cc_final: 0.6595 (mtpp) REVERT: F 480 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6959 (pt0) REVERT: G 121 ARG cc_start: 0.7030 (mtt90) cc_final: 0.6701 (mtt-85) REVERT: G 124 GLN cc_start: 0.7738 (mt0) cc_final: 0.7180 (mt0) REVERT: G 139 MET cc_start: 0.8445 (mtm) cc_final: 0.8235 (mtt) REVERT: G 198 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7294 (mm-30) REVERT: G 200 HIS cc_start: 0.7692 (m170) cc_final: 0.7394 (m90) REVERT: H 73 THR cc_start: 0.8907 (p) cc_final: 0.8644 (t) REVERT: H 96 LYS cc_start: 0.8501 (tppp) cc_final: 0.7856 (mttm) REVERT: 3 71 MET cc_start: 0.8553 (tmm) cc_final: 0.8303 (tmm) REVERT: a 81 MET cc_start: 0.7930 (mmm) cc_final: 0.7693 (tpt) REVERT: a 137 LEU cc_start: 0.9059 (mt) cc_final: 0.8742 (pp) REVERT: a 204 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7376 (t80) REVERT: b 73 LYS cc_start: 0.8954 (pptt) cc_final: 0.8086 (tmmt) REVERT: b 76 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8592 (pp20) REVERT: b 78 PHE cc_start: 0.8890 (t80) cc_final: 0.8616 (t80) REVERT: b 82 GLN cc_start: 0.8410 (mp10) cc_final: 0.8177 (mp10) REVERT: b 89 MET cc_start: 0.8871 (mmm) cc_final: 0.8647 (mmm) REVERT: b 127 GLN cc_start: 0.8892 (tp40) cc_final: 0.8633 (tm-30) REVERT: b 131 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8230 (mm-30) REVERT: b 144 LEU cc_start: 0.8253 (pt) cc_final: 0.7974 (mm) REVERT: d 1 MET cc_start: 0.7172 (tmm) cc_final: 0.5967 (tmt) REVERT: d 202 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8985 (mm) REVERT: d 215 ARG cc_start: 0.8847 (ttm170) cc_final: 0.8521 (mmp-170) REVERT: d 233 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7662 (mtm-85) REVERT: d 259 LYS cc_start: 0.8270 (mmmm) cc_final: 0.7987 (mmmm) REVERT: d 272 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8456 (tp30) REVERT: d 359 GLU cc_start: 0.8085 (pt0) cc_final: 0.7753 (pt0) outliers start: 78 outliers final: 27 residues processed: 682 average time/residue: 0.6891 time to fit residues: 562.0268 Evaluate side-chains 593 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 559 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 358 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 241 optimal weight: 0.1980 chunk 437 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 72 HIS C 192 ASN C 399 GLN D 71 ASN D 432 GLN E 436 GLN F 186 ASN G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 8 42 GLN ** 8 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118129 restraints weight = 50386.800| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.10 r_work: 0.3272 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38094 Z= 0.194 Angle : 0.617 10.427 51701 Z= 0.312 Chirality : 0.045 0.196 5977 Planarity : 0.004 0.053 6720 Dihedral : 6.529 103.552 5601 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.95 % Allowed : 14.16 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.12), residues: 4835 helix: 0.99 (0.10), residues: 2558 sheet: -0.74 (0.21), residues: 575 loop : -0.88 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 1 48 TYR 0.044 0.001 TYR a 238 PHE 0.025 0.001 PHE 6 70 TRP 0.009 0.001 TRP a 103 HIS 0.006 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00461 (38094) covalent geometry : angle 0.61655 (51701) hydrogen bonds : bond 0.04501 ( 2284) hydrogen bonds : angle 4.71188 ( 6612) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 588 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8382 (ttt-90) REVERT: A 404 GLU cc_start: 0.7693 (pp20) cc_final: 0.7290 (tm-30) REVERT: A 494 GLU cc_start: 0.7080 (pm20) cc_final: 0.6787 (mm-30) REVERT: B 146 LYS cc_start: 0.8424 (ptmt) cc_final: 0.7970 (pttp) REVERT: B 470 GLU cc_start: 0.7394 (tp30) cc_final: 0.7078 (tp30) REVERT: C 45 GLU cc_start: 0.8727 (tt0) cc_final: 0.8358 (pt0) REVERT: C 71 GLU cc_start: 0.8522 (pm20) cc_final: 0.8178 (pm20) REVERT: C 146 LYS cc_start: 0.8939 (pttp) cc_final: 0.8467 (ptpt) REVERT: C 173 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8048 (m-30) REVERT: C 199 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8206 (mtmt) REVERT: C 376 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8765 (mtt180) REVERT: C 491 LYS cc_start: 0.8063 (mttt) cc_final: 0.7733 (mtmt) REVERT: C 541 LYS cc_start: 0.7572 (ptpt) cc_final: 0.7341 (ttpp) REVERT: D 22 ARG cc_start: 0.8082 (ttp-110) cc_final: 0.6907 (ttm-80) REVERT: D 125 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8030 (mmtm) REVERT: D 163 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7816 (ttm-80) REVERT: D 190 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7368 (mtt-85) REVERT: D 214 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7495 (tp30) REVERT: D 217 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6850 (mm-30) REVERT: D 316 MET cc_start: 0.9052 (ttt) cc_final: 0.8744 (ttp) REVERT: D 391 LYS cc_start: 0.8134 (tttt) cc_final: 0.7743 (ttpt) REVERT: D 473 ASP cc_start: 0.7526 (t0) cc_final: 0.7103 (t0) REVERT: D 474 ASP cc_start: 0.7996 (m-30) cc_final: 0.7384 (m-30) REVERT: D 480 GLU cc_start: 0.7536 (tt0) cc_final: 0.6601 (mp0) REVERT: E 95 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7288 (ptt-90) REVERT: E 134 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8480 (mmtt) REVERT: E 230 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.6975 (mm110) REVERT: E 382 GLU cc_start: 0.7020 (tt0) cc_final: 0.6737 (tm-30) REVERT: E 389 ARG cc_start: 0.7744 (tpt170) cc_final: 0.7370 (tpt-90) REVERT: E 391 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8325 (ttmt) REVERT: E 464 GLN cc_start: 0.8051 (tp40) cc_final: 0.7412 (mp10) REVERT: F 217 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7391 (tp30) REVERT: F 417 ARG cc_start: 0.7513 (mtt90) cc_final: 0.6876 (mmm160) REVERT: F 467 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: F 477 LYS cc_start: 0.6906 (mtmm) cc_final: 0.6590 (mtpp) REVERT: F 480 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6966 (pt0) REVERT: G 121 ARG cc_start: 0.7010 (mtt90) cc_final: 0.6688 (mtt-85) REVERT: G 124 GLN cc_start: 0.7788 (mt0) cc_final: 0.7227 (mt0) REVERT: G 139 MET cc_start: 0.8436 (mtm) cc_final: 0.8209 (mtt) REVERT: G 198 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7271 (mm-30) REVERT: H 73 THR cc_start: 0.8962 (p) cc_final: 0.8672 (t) REVERT: H 96 LYS cc_start: 0.8594 (tppp) cc_final: 0.7997 (mttm) REVERT: 1 81 LYS cc_start: 0.6629 (tttp) cc_final: 0.6428 (ptmt) REVERT: 3 71 MET cc_start: 0.8616 (tmt) cc_final: 0.8367 (tmm) REVERT: 7 80 VAL cc_start: 0.8287 (t) cc_final: 0.7863 (m) REVERT: a 137 LEU cc_start: 0.9056 (mt) cc_final: 0.8765 (tm) REVERT: a 143 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8162 (p90) REVERT: a 204 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7307 (t80) REVERT: b 72 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8613 (ptpp) REVERT: b 109 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8801 (ttpp) REVERT: b 127 GLN cc_start: 0.8977 (tp40) cc_final: 0.8659 (tm-30) REVERT: b 131 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8189 (mm-30) REVERT: b 151 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8745 (mtp) REVERT: d 1 MET cc_start: 0.7134 (tmm) cc_final: 0.6229 (tmt) REVERT: d 199 LEU cc_start: 0.9127 (mt) cc_final: 0.8889 (mp) REVERT: d 215 ARG cc_start: 0.8912 (ttm170) cc_final: 0.8550 (mtp-110) REVERT: d 259 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7795 (mmmm) REVERT: d 272 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8499 (tp30) REVERT: d 359 GLU cc_start: 0.8111 (pt0) cc_final: 0.7872 (pt0) outliers start: 114 outliers final: 43 residues processed: 647 average time/residue: 0.7753 time to fit residues: 599.2224 Evaluate side-chains 612 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 556 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 316 MET Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 68 LEU Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 143 TYR Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 338 VAL Chi-restraints excluded: chain d residue 358 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 1 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 310 optimal weight: 0.0670 chunk 169 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 373 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 409 optimal weight: 0.1980 chunk 315 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 192 ASN C 399 GLN D 71 ASN E 436 GLN F 108 HIS F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 6 46 GLN 8 42 GLN 8 67 ASN a 74 GLN b 77 GLN ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.119630 restraints weight = 50037.553| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.06 r_work: 0.3334 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38094 Z= 0.121 Angle : 0.575 11.164 51701 Z= 0.287 Chirality : 0.043 0.221 5977 Planarity : 0.004 0.051 6720 Dihedral : 5.932 101.721 5601 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.59 % Allowed : 16.16 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.12), residues: 4835 helix: 1.43 (0.10), residues: 2579 sheet: -0.48 (0.21), residues: 585 loop : -0.66 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 6 48 TYR 0.045 0.001 TYR a 238 PHE 0.028 0.001 PHE a 138 TRP 0.010 0.001 TRP a 103 HIS 0.004 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00262 (38094) covalent geometry : angle 0.57506 (51701) hydrogen bonds : bond 0.03877 ( 2284) hydrogen bonds : angle 4.38346 ( 6612) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 627 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8071 (mptt) REVERT: A 200 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8553 (mtmt) REVERT: A 220 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8369 (ttt-90) REVERT: A 331 GLU cc_start: 0.8479 (tt0) cc_final: 0.8112 (tt0) REVERT: A 404 GLU cc_start: 0.7612 (pp20) cc_final: 0.7293 (tm-30) REVERT: B 146 LYS cc_start: 0.8453 (ptmt) cc_final: 0.8038 (pttp) REVERT: B 499 LYS cc_start: 0.7080 (mttt) cc_final: 0.6712 (mttm) REVERT: C 45 GLU cc_start: 0.8711 (tt0) cc_final: 0.8368 (pt0) REVERT: C 71 GLU cc_start: 0.8490 (pm20) cc_final: 0.8017 (pm20) REVERT: C 146 LYS cc_start: 0.8895 (pttp) cc_final: 0.8435 (ptpt) REVERT: C 173 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: C 199 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8219 (mtmt) REVERT: C 376 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8746 (mtt180) REVERT: C 491 LYS cc_start: 0.8017 (mttt) cc_final: 0.7746 (mtmt) REVERT: C 494 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6686 (tm-30) REVERT: C 541 LYS cc_start: 0.7591 (ptpt) cc_final: 0.7289 (mmtt) REVERT: D 22 ARG cc_start: 0.8037 (ttp-110) cc_final: 0.6890 (ttm-80) REVERT: D 163 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7890 (ttm-80) REVERT: D 210 ASP cc_start: 0.8467 (m-30) cc_final: 0.8054 (m-30) REVERT: D 214 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7487 (tp30) REVERT: D 217 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6851 (mm-30) REVERT: D 316 MET cc_start: 0.8980 (ttt) cc_final: 0.8751 (ttp) REVERT: D 345 SER cc_start: 0.8533 (m) cc_final: 0.8252 (p) REVERT: D 391 LYS cc_start: 0.8063 (tttt) cc_final: 0.7672 (ttpt) REVERT: D 474 ASP cc_start: 0.7924 (m-30) cc_final: 0.7280 (m-30) REVERT: D 480 GLU cc_start: 0.7504 (tt0) cc_final: 0.6578 (mm-30) REVERT: E 230 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.6912 (mm110) REVERT: E 382 GLU cc_start: 0.7071 (tt0) cc_final: 0.6783 (tt0) REVERT: E 389 ARG cc_start: 0.7712 (tpt170) cc_final: 0.7340 (tpt-90) REVERT: E 464 GLN cc_start: 0.8001 (tp40) cc_final: 0.7412 (mp10) REVERT: F 203 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7821 (mm-30) REVERT: F 417 ARG cc_start: 0.7395 (mtt90) cc_final: 0.6800 (mtp180) REVERT: F 467 PHE cc_start: 0.8090 (t80) cc_final: 0.7699 (m-80) REVERT: F 480 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6876 (pt0) REVERT: G 41 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7887 (pt0) REVERT: G 121 ARG cc_start: 0.6943 (mtt90) cc_final: 0.6556 (mtt-85) REVERT: G 124 GLN cc_start: 0.7732 (mt0) cc_final: 0.7140 (mt0) REVERT: G 139 MET cc_start: 0.8373 (mtm) cc_final: 0.7923 (mtt) REVERT: G 198 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7255 (mm-30) REVERT: H 73 THR cc_start: 0.8895 (p) cc_final: 0.8615 (t) REVERT: H 96 LYS cc_start: 0.8661 (tppp) cc_final: 0.8022 (mttm) REVERT: H 120 ILE cc_start: 0.7548 (tt) cc_final: 0.7321 (tp) REVERT: 1 46 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7976 (tp-100) REVERT: 1 81 LYS cc_start: 0.6694 (tttp) cc_final: 0.6417 (ptmt) REVERT: 2 44 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7881 (pt0) REVERT: 4 71 MET cc_start: 0.8464 (tmm) cc_final: 0.8263 (tmm) REVERT: 7 80 VAL cc_start: 0.8281 (t) cc_final: 0.7881 (m) REVERT: 8 54 PHE cc_start: 0.8320 (m-80) cc_final: 0.7964 (m-80) REVERT: a 94 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7849 (tt) REVERT: a 137 LEU cc_start: 0.9095 (mt) cc_final: 0.8825 (tm) REVERT: a 143 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8246 (p90) REVERT: b 24 PHE cc_start: 0.7208 (p90) cc_final: 0.5670 (p90) REVERT: b 78 PHE cc_start: 0.8837 (t80) cc_final: 0.8488 (t80) REVERT: b 82 GLN cc_start: 0.8484 (mp10) cc_final: 0.8250 (mp10) REVERT: b 87 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8455 (pp20) REVERT: b 109 LYS cc_start: 0.9020 (mmpt) cc_final: 0.8791 (ttpp) REVERT: b 127 GLN cc_start: 0.8975 (tp40) cc_final: 0.8590 (tm-30) REVERT: b 130 HIS cc_start: 0.9106 (t70) cc_final: 0.8895 (t-90) REVERT: b 131 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8119 (mp0) REVERT: b 151 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8617 (mtp) REVERT: d 1 MET cc_start: 0.7096 (tmm) cc_final: 0.6050 (tmt) REVERT: d 98 ILE cc_start: 0.8768 (mm) cc_final: 0.8378 (tp) REVERT: d 215 ARG cc_start: 0.8896 (ttm170) cc_final: 0.8668 (mtp-110) REVERT: d 219 VAL cc_start: 0.9026 (p) cc_final: 0.8607 (t) REVERT: d 272 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8581 (tp30) REVERT: d 359 GLU cc_start: 0.8142 (pt0) cc_final: 0.7862 (mp0) outliers start: 100 outliers final: 40 residues processed: 683 average time/residue: 0.7322 time to fit residues: 599.3339 Evaluate side-chains 625 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 575 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain 1 residue 46 GLN Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 2 residue 68 LEU Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 8 residue 78 THR Chi-restraints excluded: chain 9 residue 70 PHE Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain a residue 104 LEU Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 143 TYR Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 312 LEU Chi-restraints excluded: chain d residue 326 LEU Chi-restraints excluded: chain d residue 358 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 296 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 100 optimal weight: 30.0000 chunk 121 optimal weight: 0.5980 chunk 378 optimal weight: 1.9990 chunk 317 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 357 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 chunk 238 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 72 HIS C 192 ASN C 399 GLN C 490 GLN D 71 ASN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 6 46 GLN a 15 HIS a 74 GLN ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.152297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118980 restraints weight = 50160.371| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.13 r_work: 0.3273 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 38094 Z= 0.184 Angle : 0.621 11.784 51701 Z= 0.311 Chirality : 0.045 0.338 5977 Planarity : 0.004 0.050 6720 Dihedral : 6.098 109.559 5601 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.77 % Favored : 97.21 % Rotamer: Outliers : 3.00 % Allowed : 17.17 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.12), residues: 4835 helix: 1.43 (0.10), residues: 2580 sheet: -0.47 (0.21), residues: 572 loop : -0.61 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 71 TYR 0.036 0.001 TYR a 238 PHE 0.038 0.001 PHE 9 70 TRP 0.017 0.001 TRP a 103 HIS 0.006 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00436 (38094) covalent geometry : angle 0.62083 (51701) hydrogen bonds : bond 0.04267 ( 2284) hydrogen bonds : angle 4.48216 ( 6612) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 572 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8036 (mptt) REVERT: A 220 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8354 (ttt-90) REVERT: A 304 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8678 (tp) REVERT: A 331 GLU cc_start: 0.8531 (tt0) cc_final: 0.8237 (tt0) REVERT: A 404 GLU cc_start: 0.7626 (pp20) cc_final: 0.7318 (tm-30) REVERT: B 146 LYS cc_start: 0.8431 (ptmt) cc_final: 0.8006 (pttp) REVERT: B 470 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7146 (mm-30) REVERT: B 472 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6604 (mm) REVERT: B 499 LYS cc_start: 0.7105 (mttt) cc_final: 0.6729 (mttm) REVERT: C 45 GLU cc_start: 0.8732 (tt0) cc_final: 0.8380 (pt0) REVERT: C 71 GLU cc_start: 0.8497 (pm20) cc_final: 0.8079 (pm20) REVERT: C 146 LYS cc_start: 0.8910 (pttp) cc_final: 0.8452 (ptpt) REVERT: C 173 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: C 199 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8203 (mtmt) REVERT: C 376 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8745 (mtt180) REVERT: C 491 LYS cc_start: 0.7999 (mttt) cc_final: 0.7700 (mtmt) REVERT: C 494 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6681 (tm-30) REVERT: C 541 LYS cc_start: 0.7582 (ptpt) cc_final: 0.7260 (mmtt) REVERT: D 22 ARG cc_start: 0.8076 (ttp-110) cc_final: 0.6925 (ttm-80) REVERT: D 163 ARG cc_start: 0.8331 (ttm110) cc_final: 0.7893 (ttm-80) REVERT: D 190 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7333 (mtt-85) REVERT: D 214 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7422 (tp30) REVERT: D 217 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6808 (mm-30) REVERT: D 316 MET cc_start: 0.9018 (ttt) cc_final: 0.8733 (ttp) REVERT: D 391 LYS cc_start: 0.8083 (tttt) cc_final: 0.7692 (ttpt) REVERT: D 474 ASP cc_start: 0.7964 (m-30) cc_final: 0.7359 (m-30) REVERT: D 480 GLU cc_start: 0.7526 (tt0) cc_final: 0.6563 (mm-30) REVERT: E 40 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8312 (mt) REVERT: E 95 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7278 (ptt-90) REVERT: E 134 LYS cc_start: 0.8797 (mmtp) cc_final: 0.8450 (mmtt) REVERT: E 230 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7053 (mm110) REVERT: E 382 GLU cc_start: 0.7078 (tt0) cc_final: 0.6790 (tt0) REVERT: E 389 ARG cc_start: 0.7734 (tpt170) cc_final: 0.7361 (tpt-90) REVERT: E 391 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: E 464 GLN cc_start: 0.7895 (tp40) cc_final: 0.7319 (mp10) REVERT: F 417 ARG cc_start: 0.7510 (mtt90) cc_final: 0.6870 (mtp180) REVERT: F 464 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7060 (tp40) REVERT: F 467 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: F 480 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6866 (pt0) REVERT: G 121 ARG cc_start: 0.7045 (mtt90) cc_final: 0.6685 (mtt-85) REVERT: G 124 GLN cc_start: 0.7757 (mt0) cc_final: 0.7179 (mt0) REVERT: G 139 MET cc_start: 0.8449 (mtm) cc_final: 0.8115 (mtt) REVERT: G 198 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7297 (mm-30) REVERT: H 73 THR cc_start: 0.8963 (p) cc_final: 0.8657 (t) REVERT: H 96 LYS cc_start: 0.8678 (tppp) cc_final: 0.8053 (mttm) REVERT: H 120 ILE cc_start: 0.7735 (tt) cc_final: 0.7471 (tp) REVERT: 1 46 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8004 (tp-100) REVERT: 1 81 LYS cc_start: 0.6812 (tttp) cc_final: 0.6399 (ptmt) REVERT: 2 44 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7989 (pt0) REVERT: 6 46 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: 7 80 VAL cc_start: 0.8296 (t) cc_final: 0.7979 (m) REVERT: 8 1 MET cc_start: 0.7264 (tpt) cc_final: 0.6910 (mmm) REVERT: 8 54 PHE cc_start: 0.8414 (m-80) cc_final: 0.7993 (m-80) REVERT: a 94 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.7909 (tt) REVERT: a 137 LEU cc_start: 0.9115 (mt) cc_final: 0.8820 (tp) REVERT: a 143 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8358 (p90) REVERT: b 24 PHE cc_start: 0.7308 (p90) cc_final: 0.5922 (p90) REVERT: b 78 PHE cc_start: 0.8864 (t80) cc_final: 0.8566 (t80) REVERT: b 82 GLN cc_start: 0.8347 (mp10) cc_final: 0.8105 (mp10) REVERT: b 87 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8421 (pp20) REVERT: b 109 LYS cc_start: 0.9030 (mmpt) cc_final: 0.8799 (ttpp) REVERT: b 127 GLN cc_start: 0.9009 (tp40) cc_final: 0.8610 (tm-30) REVERT: b 130 HIS cc_start: 0.9107 (t70) cc_final: 0.8895 (t-90) REVERT: b 131 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8139 (mp0) REVERT: b 151 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: d 1 MET cc_start: 0.7232 (tmm) cc_final: 0.6547 (tmt) REVERT: d 199 LEU cc_start: 0.9109 (mt) cc_final: 0.8820 (mp) REVERT: d 215 ARG cc_start: 0.8973 (ttm170) cc_final: 0.8686 (mtp-110) REVERT: d 272 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8471 (tp30) outliers start: 116 outliers final: 57 residues processed: 638 average time/residue: 0.7286 time to fit residues: 556.7226 Evaluate side-chains 631 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 556 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 40 ILE Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 464 GLN Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain 1 residue 46 GLN Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 6 residue 46 GLN Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 8 residue 78 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 94 ILE Chi-restraints excluded: chain a residue 143 TYR Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 151 MET Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 182 SER Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 341 VAL Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 434 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 351 optimal weight: 0.5980 chunk 413 optimal weight: 2.9990 chunk 410 optimal weight: 0.9990 chunk 137 optimal weight: 0.0000 chunk 366 optimal weight: 6.9990 chunk 393 optimal weight: 0.6980 chunk 285 optimal weight: 0.0980 chunk 463 optimal weight: 0.1980 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 192 ASN C 399 GLN C 490 GLN D 71 ASN E 414 ASN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 74 GLN a 172 ASN ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.117017 restraints weight = 48942.108| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.04 r_work: 0.3335 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 38094 Z= 0.114 Angle : 0.588 12.487 51701 Z= 0.290 Chirality : 0.043 0.365 5977 Planarity : 0.004 0.050 6720 Dihedral : 5.561 103.129 5601 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 2.05 % Allowed : 18.64 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.12), residues: 4835 helix: 1.79 (0.10), residues: 2567 sheet: -0.20 (0.21), residues: 574 loop : -0.44 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 6 48 TYR 0.015 0.001 TYR a 143 PHE 0.038 0.001 PHE a 138 TRP 0.015 0.001 TRP a 103 HIS 0.004 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00239 (38094) covalent geometry : angle 0.58770 (51701) hydrogen bonds : bond 0.03653 ( 2284) hydrogen bonds : angle 4.22203 ( 6612) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 639 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ARG cc_start: 0.8026 (ptm-80) cc_final: 0.7677 (ttp80) REVERT: A 199 LYS cc_start: 0.8390 (mmmt) cc_final: 0.8040 (mptt) REVERT: A 200 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8518 (mtmt) REVERT: A 220 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8365 (ttt-90) REVERT: A 331 GLU cc_start: 0.8578 (tt0) cc_final: 0.8242 (tt0) REVERT: A 404 GLU cc_start: 0.7652 (pp20) cc_final: 0.7419 (tm-30) REVERT: B 146 LYS cc_start: 0.8407 (ptmt) cc_final: 0.8012 (pttp) REVERT: B 191 GLN cc_start: 0.7784 (mm110) cc_final: 0.7094 (mp-120) REVERT: B 490 GLN cc_start: 0.8366 (mt0) cc_final: 0.8128 (mp10) REVERT: C 45 GLU cc_start: 0.8700 (tt0) cc_final: 0.8361 (pt0) REVERT: C 71 GLU cc_start: 0.8419 (pm20) cc_final: 0.7931 (pm20) REVERT: C 146 LYS cc_start: 0.8870 (pttp) cc_final: 0.8365 (ptpt) REVERT: C 199 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8178 (mmpt) REVERT: C 376 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8813 (mtt180) REVERT: C 491 LYS cc_start: 0.7996 (mttt) cc_final: 0.7719 (mtmt) REVERT: C 494 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6601 (tp30) REVERT: C 498 ASP cc_start: 0.7280 (m-30) cc_final: 0.6921 (m-30) REVERT: C 530 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6412 (tm-30) REVERT: D 22 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.6837 (ttm-80) REVERT: D 163 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8018 (ttm-80) REVERT: D 190 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7329 (mtt-85) REVERT: D 210 ASP cc_start: 0.8417 (m-30) cc_final: 0.8210 (m-30) REVERT: D 214 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7723 (tp30) REVERT: D 217 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6922 (mm-30) REVERT: D 345 SER cc_start: 0.8549 (m) cc_final: 0.8281 (p) REVERT: D 391 LYS cc_start: 0.8095 (tttt) cc_final: 0.7715 (ttpt) REVERT: D 453 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7937 (tt) REVERT: D 463 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8050 (tt0) REVERT: D 474 ASP cc_start: 0.7969 (m-30) cc_final: 0.7301 (m-30) REVERT: D 480 GLU cc_start: 0.7577 (tt0) cc_final: 0.6673 (mm-30) REVERT: E 214 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7581 (pt0) REVERT: E 230 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8188 (mm110) REVERT: E 382 GLU cc_start: 0.7117 (tt0) cc_final: 0.6830 (tt0) REVERT: E 389 ARG cc_start: 0.7792 (tpt170) cc_final: 0.7423 (tpt-90) REVERT: E 391 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8252 (ttmt) REVERT: E 464 GLN cc_start: 0.7838 (tp40) cc_final: 0.7290 (mp10) REVERT: F 203 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: F 217 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: F 417 ARG cc_start: 0.7404 (mtt90) cc_final: 0.6904 (mtp180) REVERT: F 448 GLU cc_start: 0.7951 (tt0) cc_final: 0.7260 (tp30) REVERT: F 467 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: F 480 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6895 (pt0) REVERT: G 33 ILE cc_start: 0.8116 (tt) cc_final: 0.7748 (pt) REVERT: G 41 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7795 (pt0) REVERT: G 121 ARG cc_start: 0.6935 (mtt90) cc_final: 0.6601 (mtt-85) REVERT: G 124 GLN cc_start: 0.7721 (mt0) cc_final: 0.7190 (mt0) REVERT: G 139 MET cc_start: 0.8343 (mtm) cc_final: 0.8139 (mtt) REVERT: G 198 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7260 (mm-30) REVERT: H 73 THR cc_start: 0.8867 (p) cc_final: 0.8586 (t) REVERT: H 96 LYS cc_start: 0.8735 (tppp) cc_final: 0.8121 (mttm) REVERT: H 120 ILE cc_start: 0.7487 (tt) cc_final: 0.7269 (tp) REVERT: 1 42 GLN cc_start: 0.7677 (mp10) cc_final: 0.7450 (pm20) REVERT: 1 46 GLN cc_start: 0.8216 (tt0) cc_final: 0.8009 (tp-100) REVERT: 4 71 MET cc_start: 0.8342 (tmm) cc_final: 0.8088 (tmm) REVERT: 6 46 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7612 (tp40) REVERT: 7 80 VAL cc_start: 0.8251 (t) cc_final: 0.7900 (m) REVERT: 8 1 MET cc_start: 0.7058 (tpt) cc_final: 0.6759 (mmm) REVERT: 8 54 PHE cc_start: 0.8199 (m-80) cc_final: 0.7589 (m-80) REVERT: a 137 LEU cc_start: 0.9068 (mt) cc_final: 0.8831 (tp) REVERT: a 143 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8305 (p90) REVERT: b 24 PHE cc_start: 0.7217 (p90) cc_final: 0.5918 (p90) REVERT: b 82 GLN cc_start: 0.8358 (mp10) cc_final: 0.8088 (mp10) REVERT: b 109 LYS cc_start: 0.8948 (mmpt) cc_final: 0.8734 (ttpp) REVERT: b 127 GLN cc_start: 0.8956 (tp40) cc_final: 0.8537 (tm-30) REVERT: b 130 HIS cc_start: 0.9002 (t70) cc_final: 0.8756 (t-90) REVERT: b 131 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8082 (mp0) REVERT: d 1 MET cc_start: 0.7105 (tmm) cc_final: 0.6211 (tmt) REVERT: d 99 LYS cc_start: 0.9268 (tmmm) cc_final: 0.9019 (mtpm) REVERT: d 199 LEU cc_start: 0.9073 (mt) cc_final: 0.8827 (mp) REVERT: d 215 ARG cc_start: 0.8988 (ttm170) cc_final: 0.8702 (mtp-110) REVERT: d 272 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8418 (tp30) outliers start: 79 outliers final: 38 residues processed: 685 average time/residue: 0.6619 time to fit residues: 548.0067 Evaluate side-chains 626 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 576 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 482 ILE Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 11 ILE Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 6 residue 46 GLN Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 143 TYR Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 313 LEU Chi-restraints excluded: chain d residue 358 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 96 optimal weight: 6.9990 chunk 405 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 145 optimal weight: 0.0970 chunk 455 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 467 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 72 HIS C 141 HIS C 192 ASN C 399 GLN C 490 GLN D 432 GLN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 42 GLN ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 46 GLN 9 42 GLN a 74 GLN b 130 HIS ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112513 restraints weight = 48459.434| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.01 r_work: 0.3216 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 38094 Z= 0.162 Angle : 0.635 12.848 51701 Z= 0.313 Chirality : 0.045 0.375 5977 Planarity : 0.004 0.050 6720 Dihedral : 5.774 109.194 5601 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 2.77 % Allowed : 19.08 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 4835 helix: 1.71 (0.10), residues: 2569 sheet: -0.22 (0.21), residues: 581 loop : -0.43 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 72 TYR 0.026 0.001 TYR B 18 PHE 0.038 0.001 PHE b 78 TRP 0.018 0.001 TRP a 103 HIS 0.005 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00379 (38094) covalent geometry : angle 0.63461 (51701) hydrogen bonds : bond 0.04056 ( 2284) hydrogen bonds : angle 4.33826 ( 6612) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 587 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8023 (mptt) REVERT: A 200 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8512 (mtmt) REVERT: A 220 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8374 (ttt-90) REVERT: A 331 GLU cc_start: 0.8567 (tt0) cc_final: 0.8266 (tt0) REVERT: A 404 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7267 (tm-30) REVERT: A 494 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6916 (pm20) REVERT: B 146 LYS cc_start: 0.8460 (ptmt) cc_final: 0.8050 (pttp) REVERT: B 191 GLN cc_start: 0.7829 (mm110) cc_final: 0.7131 (mp-120) REVERT: B 490 GLN cc_start: 0.8373 (mt0) cc_final: 0.8110 (mp10) REVERT: C 45 GLU cc_start: 0.8717 (tt0) cc_final: 0.8394 (pt0) REVERT: C 70 ASP cc_start: 0.8109 (m-30) cc_final: 0.7875 (m-30) REVERT: C 71 GLU cc_start: 0.8470 (pm20) cc_final: 0.8004 (pm20) REVERT: C 146 LYS cc_start: 0.8902 (pttp) cc_final: 0.8449 (ptpt) REVERT: C 173 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: C 199 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8164 (mmpt) REVERT: C 376 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8794 (mtt180) REVERT: C 491 LYS cc_start: 0.7954 (mttt) cc_final: 0.7673 (mtmm) REVERT: C 494 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6470 (tp30) REVERT: C 530 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: D 22 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.6892 (ttm-80) REVERT: D 37 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7944 (mtm110) REVERT: D 163 ARG cc_start: 0.8370 (ttm110) cc_final: 0.7956 (ttm-80) REVERT: D 214 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7465 (tp30) REVERT: D 217 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6842 (mm-30) REVERT: D 391 LYS cc_start: 0.8067 (tttt) cc_final: 0.7682 (ttpt) REVERT: D 474 ASP cc_start: 0.7939 (m-30) cc_final: 0.7267 (m-30) REVERT: D 480 GLU cc_start: 0.7577 (tt0) cc_final: 0.6644 (mm-30) REVERT: E 230 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.6952 (mm110) REVERT: E 382 GLU cc_start: 0.7121 (tt0) cc_final: 0.6867 (tt0) REVERT: E 389 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7346 (tpt-90) REVERT: E 391 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8194 (ttmt) REVERT: E 464 GLN cc_start: 0.7866 (tp40) cc_final: 0.7303 (mp10) REVERT: F 239 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8615 (mtm) REVERT: F 284 MET cc_start: 0.9156 (ttm) cc_final: 0.8938 (mtt) REVERT: F 417 ARG cc_start: 0.7495 (mtt90) cc_final: 0.6887 (mtp180) REVERT: F 448 GLU cc_start: 0.7893 (tt0) cc_final: 0.7230 (tp30) REVERT: F 464 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.7037 (tp40) REVERT: F 467 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: F 480 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6743 (pt0) REVERT: G 41 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7867 (pt0) REVERT: G 121 ARG cc_start: 0.6944 (mtt90) cc_final: 0.6586 (mtt-85) REVERT: G 124 GLN cc_start: 0.7721 (mt0) cc_final: 0.7117 (mt0) REVERT: G 139 MET cc_start: 0.8431 (mtm) cc_final: 0.8035 (mtt) REVERT: G 198 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7203 (mm-30) REVERT: H 73 THR cc_start: 0.8913 (p) cc_final: 0.8626 (t) REVERT: H 96 LYS cc_start: 0.8714 (tppp) cc_final: 0.8117 (mttm) REVERT: H 120 ILE cc_start: 0.7686 (tt) cc_final: 0.7414 (tp) REVERT: 1 46 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7994 (tp-100) REVERT: 6 46 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7478 (tp-100) REVERT: 7 80 VAL cc_start: 0.8266 (t) cc_final: 0.7899 (m) REVERT: 8 1 MET cc_start: 0.7156 (tpt) cc_final: 0.6841 (mmm) REVERT: 8 54 PHE cc_start: 0.8325 (m-80) cc_final: 0.7638 (m-80) REVERT: a 128 ASP cc_start: 0.8823 (t0) cc_final: 0.8567 (t0) REVERT: a 133 LEU cc_start: 0.9312 (tp) cc_final: 0.8997 (mt) REVERT: a 137 LEU cc_start: 0.9130 (mt) cc_final: 0.8787 (tp) REVERT: b 24 PHE cc_start: 0.7297 (p90) cc_final: 0.6124 (p90) REVERT: b 91 GLU cc_start: 0.8598 (pp20) cc_final: 0.8257 (pp20) REVERT: b 95 GLN cc_start: 0.8666 (mt0) cc_final: 0.8349 (mp10) REVERT: b 109 LYS cc_start: 0.9008 (mmpt) cc_final: 0.8747 (ttpp) REVERT: b 133 LEU cc_start: 0.9346 (pp) cc_final: 0.9086 (pt) REVERT: b 142 LEU cc_start: 0.9463 (pt) cc_final: 0.9242 (mt) REVERT: d 1 MET cc_start: 0.7301 (tmm) cc_final: 0.6599 (tmt) REVERT: d 199 LEU cc_start: 0.9160 (mt) cc_final: 0.8884 (mp) REVERT: d 215 ARG cc_start: 0.9020 (ttm170) cc_final: 0.8799 (mtp-110) REVERT: d 272 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8427 (tp30) outliers start: 107 outliers final: 56 residues processed: 645 average time/residue: 0.6866 time to fit residues: 532.0201 Evaluate side-chains 621 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 553 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 239 MET Chi-restraints excluded: chain F residue 464 GLN Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain 1 residue 46 GLN Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 6 residue 46 GLN Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 8 residue 78 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 240 LEU Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 313 LEU Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 434 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 257 optimal weight: 6.9990 chunk 278 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 279 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 421 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 309 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS C 192 ASN C 305 HIS C 399 GLN C 490 GLN D 432 GLN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 42 GLN 6 46 GLN 9 42 GLN a 74 GLN ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107525 restraints weight = 48713.456| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.05 r_work: 0.3144 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 38094 Z= 0.303 Angle : 0.733 14.603 51701 Z= 0.367 Chirality : 0.050 0.419 5977 Planarity : 0.005 0.056 6720 Dihedral : 6.634 118.229 5601 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.74 % Allowed : 19.70 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.12), residues: 4835 helix: 1.24 (0.10), residues: 2578 sheet: -0.39 (0.21), residues: 568 loop : -0.53 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 6 48 TYR 0.028 0.002 TYR B 18 PHE 0.034 0.002 PHE 6 70 TRP 0.021 0.002 TRP a 103 HIS 0.007 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00734 (38094) covalent geometry : angle 0.73334 (51701) hydrogen bonds : bond 0.04961 ( 2284) hydrogen bonds : angle 4.71728 ( 6612) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 560 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8374 (ttt-90) REVERT: A 304 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8686 (tp) REVERT: A 404 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: A 494 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6907 (pm20) REVERT: B 81 ASP cc_start: 0.8346 (p0) cc_final: 0.8028 (p0) REVERT: B 146 LYS cc_start: 0.8507 (ptmt) cc_final: 0.8038 (pttp) REVERT: B 499 LYS cc_start: 0.7098 (mttt) cc_final: 0.6673 (mttm) REVERT: C 45 GLU cc_start: 0.8730 (tt0) cc_final: 0.8372 (pt0) REVERT: C 71 GLU cc_start: 0.8520 (pm20) cc_final: 0.8088 (pm20) REVERT: C 146 LYS cc_start: 0.8961 (pttp) cc_final: 0.8486 (ptpt) REVERT: C 199 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8183 (mmpt) REVERT: C 281 TYR cc_start: 0.8686 (t80) cc_final: 0.8428 (t80) REVERT: C 376 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8785 (mtt180) REVERT: C 491 LYS cc_start: 0.7951 (mttt) cc_final: 0.7608 (mtmt) REVERT: C 494 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6586 (tm-30) REVERT: D 22 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.6923 (ttm-80) REVERT: D 163 ARG cc_start: 0.8395 (ttm110) cc_final: 0.8081 (ttm-80) REVERT: D 190 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7304 (mtt-85) REVERT: D 214 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7486 (tp30) REVERT: D 217 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6821 (mm-30) REVERT: D 345 SER cc_start: 0.8730 (m) cc_final: 0.8507 (t) REVERT: D 375 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7691 (tp30) REVERT: D 391 LYS cc_start: 0.8120 (tttt) cc_final: 0.7735 (ttpt) REVERT: D 474 ASP cc_start: 0.8014 (m-30) cc_final: 0.7402 (m-30) REVERT: E 95 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7310 (ptt-90) REVERT: E 103 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8046 (mm-30) REVERT: E 134 LYS cc_start: 0.8824 (mmtp) cc_final: 0.8469 (mmtt) REVERT: E 230 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.6834 (mm110) REVERT: E 382 GLU cc_start: 0.7169 (tt0) cc_final: 0.6932 (tt0) REVERT: E 389 ARG cc_start: 0.7742 (tpt170) cc_final: 0.7358 (tpt-90) REVERT: E 391 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8241 (ttmt) REVERT: E 464 GLN cc_start: 0.7910 (tp40) cc_final: 0.7298 (mp10) REVERT: F 284 MET cc_start: 0.9202 (ttm) cc_final: 0.8914 (mtt) REVERT: F 417 ARG cc_start: 0.7599 (mtt90) cc_final: 0.6934 (mmm160) REVERT: F 448 GLU cc_start: 0.7933 (tt0) cc_final: 0.7266 (tp30) REVERT: F 464 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.7057 (tp40) REVERT: F 467 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: F 480 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6709 (pt0) REVERT: G 108 ARG cc_start: 0.7486 (mtt90) cc_final: 0.7013 (mtt-85) REVERT: G 121 ARG cc_start: 0.7093 (mtt90) cc_final: 0.6739 (mtt-85) REVERT: G 124 GLN cc_start: 0.7766 (mt0) cc_final: 0.7175 (mt0) REVERT: G 139 MET cc_start: 0.8526 (mtm) cc_final: 0.8200 (mtt) REVERT: G 149 ASN cc_start: 0.8570 (m110) cc_final: 0.8047 (m110) REVERT: G 198 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7313 (mm-30) REVERT: H 73 THR cc_start: 0.8976 (p) cc_final: 0.8692 (t) REVERT: H 96 LYS cc_start: 0.8715 (tppp) cc_final: 0.8131 (mttp) REVERT: 1 42 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: 1 46 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7929 (tp-100) REVERT: 2 44 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: 4 48 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7807 (mtt90) REVERT: 6 46 GLN cc_start: 0.7896 (tt0) cc_final: 0.7467 (tp40) REVERT: 7 80 VAL cc_start: 0.8311 (t) cc_final: 0.7937 (m) REVERT: 8 1 MET cc_start: 0.7306 (tpt) cc_final: 0.6912 (mmm) REVERT: 8 54 PHE cc_start: 0.8524 (m-80) cc_final: 0.8009 (m-80) REVERT: a 137 LEU cc_start: 0.9148 (mt) cc_final: 0.8792 (tp) REVERT: b 76 GLU cc_start: 0.8844 (pp20) cc_final: 0.8553 (pp20) REVERT: b 78 PHE cc_start: 0.8892 (t80) cc_final: 0.8673 (t80) REVERT: b 109 LYS cc_start: 0.9035 (mmpt) cc_final: 0.8813 (ttpp) REVERT: b 119 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8102 (mm-30) REVERT: d 1 MET cc_start: 0.7322 (tmm) cc_final: 0.6712 (tmm) REVERT: d 215 ARG cc_start: 0.9023 (ttm170) cc_final: 0.8770 (mtp-110) REVERT: d 272 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8434 (tp30) outliers start: 106 outliers final: 67 residues processed: 619 average time/residue: 0.7451 time to fit residues: 549.3156 Evaluate side-chains 620 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 539 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 214 GLU Chi-restraints excluded: chain F residue 464 GLN Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain 1 residue 42 GLN Chi-restraints excluded: chain 1 residue 46 GLN Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 2 residue 68 LEU Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 8 residue 71 MET Chi-restraints excluded: chain 8 residue 78 THR Chi-restraints excluded: chain 9 residue 70 PHE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 82 GLN Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 183 LEU Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 313 LEU Chi-restraints excluded: chain d residue 358 VAL Chi-restraints excluded: chain d residue 434 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 421 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 222 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 402 optimal weight: 20.0000 chunk 350 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 192 ASN C 399 GLN C 490 GLN D 71 ASN E 414 ASN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 42 GLN ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112146 restraints weight = 48616.932| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.03 r_work: 0.3221 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 38094 Z= 0.147 Angle : 0.668 15.360 51701 Z= 0.328 Chirality : 0.045 0.468 5977 Planarity : 0.004 0.052 6720 Dihedral : 6.024 109.978 5601 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Rotamer: Outliers : 2.10 % Allowed : 21.08 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.12), residues: 4835 helix: 1.51 (0.10), residues: 2568 sheet: -0.28 (0.21), residues: 572 loop : -0.45 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 72 TYR 0.030 0.001 TYR B 18 PHE 0.039 0.001 PHE a 138 TRP 0.024 0.001 TRP a 103 HIS 0.005 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00337 (38094) covalent geometry : angle 0.66760 (51701) hydrogen bonds : bond 0.04112 ( 2284) hydrogen bonds : angle 4.46076 ( 6612) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 574 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8785 (tt0) cc_final: 0.8481 (pt0) REVERT: A 199 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8020 (mptt) REVERT: A 200 LYS cc_start: 0.8833 (mtpp) cc_final: 0.8530 (mtmt) REVERT: A 220 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8389 (ttt-90) REVERT: A 404 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7281 (tm-30) REVERT: A 494 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6897 (pm20) REVERT: B 146 LYS cc_start: 0.8465 (ptmt) cc_final: 0.8046 (pttp) REVERT: B 499 LYS cc_start: 0.7124 (mttt) cc_final: 0.6722 (mttm) REVERT: C 45 GLU cc_start: 0.8740 (tt0) cc_final: 0.8401 (pt0) REVERT: C 71 GLU cc_start: 0.8492 (pm20) cc_final: 0.8064 (pm20) REVERT: C 146 LYS cc_start: 0.8912 (pttp) cc_final: 0.8465 (ptpt) REVERT: C 199 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8178 (mmpt) REVERT: C 376 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8758 (mtt180) REVERT: C 491 LYS cc_start: 0.7949 (mttt) cc_final: 0.7651 (mtmt) REVERT: C 494 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6502 (tp30) REVERT: D 22 ARG cc_start: 0.8078 (ttp-110) cc_final: 0.6905 (ttm-80) REVERT: D 163 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8122 (ttm-80) REVERT: D 190 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.7314 (mtt-85) REVERT: D 214 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7667 (tp30) REVERT: D 217 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6827 (mm-30) REVERT: D 258 GLN cc_start: 0.6774 (pm20) cc_final: 0.6556 (pm20) REVERT: D 391 LYS cc_start: 0.8042 (tttt) cc_final: 0.7654 (ttpt) REVERT: D 453 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7755 (tt) REVERT: D 474 ASP cc_start: 0.8018 (m-30) cc_final: 0.7434 (m-30) REVERT: E 134 LYS cc_start: 0.8811 (mmtp) cc_final: 0.8454 (mmtt) REVERT: E 230 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.6978 (mm110) REVERT: E 382 GLU cc_start: 0.7105 (tt0) cc_final: 0.6825 (tt0) REVERT: E 389 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7312 (tpt-90) REVERT: E 391 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8215 (ttmt) REVERT: E 464 GLN cc_start: 0.7833 (tp40) cc_final: 0.7263 (mp10) REVERT: F 284 MET cc_start: 0.9173 (ttm) cc_final: 0.8897 (mtt) REVERT: F 417 ARG cc_start: 0.7462 (mtt90) cc_final: 0.6838 (mtp180) REVERT: F 448 GLU cc_start: 0.7929 (tt0) cc_final: 0.7223 (tp30) REVERT: F 467 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: F 480 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6631 (pt0) REVERT: G 41 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7886 (pt0) REVERT: G 121 ARG cc_start: 0.6922 (mtt90) cc_final: 0.6547 (mtt-85) REVERT: G 124 GLN cc_start: 0.7693 (mt0) cc_final: 0.7087 (mt0) REVERT: G 139 MET cc_start: 0.8427 (mtm) cc_final: 0.8067 (mtt) REVERT: G 198 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7228 (mm-30) REVERT: G 217 ARG cc_start: 0.7147 (tpt170) cc_final: 0.6873 (pmt170) REVERT: H 73 THR cc_start: 0.8838 (p) cc_final: 0.8577 (t) REVERT: H 96 LYS cc_start: 0.8754 (tppp) cc_final: 0.8146 (mttm) REVERT: 1 42 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: 1 46 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7964 (tp-100) REVERT: 1 81 LYS cc_start: 0.6602 (mmtt) cc_final: 0.5402 (mtpt) REVERT: 2 44 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: 6 46 GLN cc_start: 0.7940 (tt0) cc_final: 0.7516 (tp40) REVERT: 6 70 PHE cc_start: 0.7813 (m-80) cc_final: 0.7611 (m-10) REVERT: 7 80 VAL cc_start: 0.8161 (t) cc_final: 0.7844 (m) REVERT: 8 1 MET cc_start: 0.7109 (tpt) cc_final: 0.6794 (mmm) REVERT: 8 54 PHE cc_start: 0.8329 (m-80) cc_final: 0.7651 (m-80) REVERT: a 137 LEU cc_start: 0.9124 (mt) cc_final: 0.8849 (tp) REVERT: b 24 PHE cc_start: 0.7018 (p90) cc_final: 0.5947 (p90) REVERT: b 87 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8613 (pp20) REVERT: b 95 GLN cc_start: 0.8660 (mt0) cc_final: 0.8404 (mt0) REVERT: b 127 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8801 (tp-100) REVERT: b 131 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8601 (mm-30) REVERT: d 1 MET cc_start: 0.7136 (tmm) cc_final: 0.6120 (tmt) REVERT: d 215 ARG cc_start: 0.8973 (ttm170) cc_final: 0.8767 (mtp-110) REVERT: d 264 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7647 (t0) REVERT: d 272 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8379 (tp30) outliers start: 81 outliers final: 54 residues processed: 621 average time/residue: 0.7884 time to fit residues: 586.2914 Evaluate side-chains 616 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 550 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain 1 residue 42 GLN Chi-restraints excluded: chain 1 residue 46 GLN Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 8 residue 57 VAL Chi-restraints excluded: chain 8 residue 78 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 131 TYR Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 183 LEU Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 264 ASN Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 313 LEU Chi-restraints excluded: chain d residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 147 optimal weight: 5.9990 chunk 372 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 335 optimal weight: 0.2980 chunk 301 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 461 optimal weight: 4.9990 chunk 387 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 192 ASN C 399 GLN C 490 GLN D 71 ASN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 74 GLN ** d 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.111173 restraints weight = 48371.590| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.05 r_work: 0.3196 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 38094 Z= 0.176 Angle : 0.693 17.412 51701 Z= 0.341 Chirality : 0.046 0.520 5977 Planarity : 0.004 0.053 6720 Dihedral : 6.091 111.724 5601 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 21.36 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.12), residues: 4835 helix: 1.46 (0.10), residues: 2572 sheet: -0.24 (0.21), residues: 571 loop : -0.45 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG a 72 TYR 0.031 0.001 TYR B 18 PHE 0.040 0.001 PHE b 78 TRP 0.030 0.001 TRP a 103 HIS 0.005 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00415 (38094) covalent geometry : angle 0.69288 (51701) hydrogen bonds : bond 0.04299 ( 2284) hydrogen bonds : angle 4.51903 ( 6612) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9670 Ramachandran restraints generated. 4835 Oldfield, 0 Emsley, 4835 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 557 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 GLN cc_start: 0.8811 (tt0) cc_final: 0.8466 (pt0) REVERT: A 199 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8035 (mptt) REVERT: A 200 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8515 (mtmt) REVERT: A 220 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8357 (ttt-90) REVERT: A 331 GLU cc_start: 0.8551 (tt0) cc_final: 0.8274 (tt0) REVERT: A 494 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6946 (pm20) REVERT: B 146 LYS cc_start: 0.8455 (ptmt) cc_final: 0.8026 (pttp) REVERT: B 499 LYS cc_start: 0.7108 (mttt) cc_final: 0.6717 (mttm) REVERT: C 45 GLU cc_start: 0.8740 (tt0) cc_final: 0.8394 (pt0) REVERT: C 71 GLU cc_start: 0.8501 (pm20) cc_final: 0.8073 (pm20) REVERT: C 146 LYS cc_start: 0.8915 (pttp) cc_final: 0.8469 (ptpt) REVERT: C 199 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8183 (mmpt) REVERT: C 376 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8784 (mtt180) REVERT: C 491 LYS cc_start: 0.7945 (mttt) cc_final: 0.7653 (mtmt) REVERT: C 494 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6516 (tp30) REVERT: C 498 ASP cc_start: 0.7370 (m-30) cc_final: 0.7037 (m-30) REVERT: D 22 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.6924 (ttm-80) REVERT: D 163 ARG cc_start: 0.8395 (ttm110) cc_final: 0.8122 (ttm-80) REVERT: D 190 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7322 (mtt-85) REVERT: D 214 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7672 (tp30) REVERT: D 217 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6855 (mm-30) REVERT: D 258 GLN cc_start: 0.6836 (pm20) cc_final: 0.6596 (pm20) REVERT: D 391 LYS cc_start: 0.8085 (tttt) cc_final: 0.7703 (ttpt) REVERT: D 453 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7768 (tt) REVERT: D 474 ASP cc_start: 0.7997 (m-30) cc_final: 0.7419 (m-30) REVERT: E 134 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8456 (mmtt) REVERT: E 230 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7060 (mm110) REVERT: E 382 GLU cc_start: 0.7144 (tt0) cc_final: 0.6912 (tt0) REVERT: E 389 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7323 (tpt-90) REVERT: E 391 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8200 (ttmt) REVERT: E 464 GLN cc_start: 0.7857 (tp40) cc_final: 0.7244 (mp10) REVERT: F 284 MET cc_start: 0.9181 (ttm) cc_final: 0.8901 (mtt) REVERT: F 417 ARG cc_start: 0.7514 (mtt90) cc_final: 0.6889 (mtp180) REVERT: F 448 GLU cc_start: 0.7928 (tt0) cc_final: 0.7242 (tp30) REVERT: F 467 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: F 480 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6649 (pt0) REVERT: G 41 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7884 (pt0) REVERT: G 121 ARG cc_start: 0.6967 (mtt90) cc_final: 0.6596 (mtt-85) REVERT: G 124 GLN cc_start: 0.7763 (mt0) cc_final: 0.7162 (mt0) REVERT: G 139 MET cc_start: 0.8445 (mtm) cc_final: 0.8095 (mtt) REVERT: G 198 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7206 (mm-30) REVERT: G 217 ARG cc_start: 0.7212 (tpt170) cc_final: 0.6884 (pmt170) REVERT: H 73 THR cc_start: 0.8915 (p) cc_final: 0.8635 (t) REVERT: H 96 LYS cc_start: 0.8732 (tppp) cc_final: 0.8151 (mttp) REVERT: 1 42 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: 1 46 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7977 (tp-100) REVERT: 1 81 LYS cc_start: 0.6611 (mmtt) cc_final: 0.5382 (mtpt) REVERT: 2 44 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: 5 1 MET cc_start: 0.5641 (ptm) cc_final: 0.5211 (ptp) REVERT: 6 46 GLN cc_start: 0.7912 (tt0) cc_final: 0.7451 (tp40) REVERT: 7 80 VAL cc_start: 0.8186 (t) cc_final: 0.7824 (m) REVERT: 8 1 MET cc_start: 0.7241 (tpt) cc_final: 0.6921 (mmm) REVERT: 8 54 PHE cc_start: 0.8410 (m-80) cc_final: 0.7650 (m-80) REVERT: 8 71 MET cc_start: 0.8572 (tmm) cc_final: 0.8200 (ttt) REVERT: a 137 LEU cc_start: 0.9161 (mt) cc_final: 0.8833 (tp) REVERT: a 243 MET cc_start: 0.7900 (mmm) cc_final: 0.7677 (tpt) REVERT: b 24 PHE cc_start: 0.7055 (p90) cc_final: 0.5987 (p90) REVERT: b 76 GLU cc_start: 0.8816 (pp20) cc_final: 0.8401 (pp20) REVERT: b 87 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8613 (pp20) REVERT: b 91 GLU cc_start: 0.8630 (pp20) cc_final: 0.8225 (pp20) REVERT: b 95 GLN cc_start: 0.8686 (mt0) cc_final: 0.8317 (mp10) REVERT: b 112 GLU cc_start: 0.8581 (pp20) cc_final: 0.8080 (pp20) REVERT: b 131 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8777 (mm-30) REVERT: d 1 MET cc_start: 0.7260 (tmm) cc_final: 0.6324 (tmt) REVERT: d 215 ARG cc_start: 0.9013 (ttm170) cc_final: 0.8687 (mtp-110) REVERT: d 272 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8391 (tp30) outliers start: 71 outliers final: 55 residues processed: 605 average time/residue: 0.7995 time to fit residues: 579.1352 Evaluate side-chains 612 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 547 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 376 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 502 GLU Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 406 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 467 PHE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 86 PHE Chi-restraints excluded: chain 1 residue 42 GLN Chi-restraints excluded: chain 1 residue 46 GLN Chi-restraints excluded: chain 1 residue 51 THR Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 61 GLU Chi-restraints excluded: chain 3 residue 78 THR Chi-restraints excluded: chain 4 residue 80 VAL Chi-restraints excluded: chain 6 residue 68 LEU Chi-restraints excluded: chain 8 residue 57 VAL Chi-restraints excluded: chain 8 residue 78 THR Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 76 GLU Chi-restraints excluded: chain a residue 93 THR Chi-restraints excluded: chain a residue 131 TYR Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 137 VAL Chi-restraints excluded: chain d residue 183 LEU Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 221 ARG Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 289 VAL Chi-restraints excluded: chain d residue 358 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 387 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 343 optimal weight: 0.7980 chunk 391 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 214 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS C 192 ASN C 399 GLN C 490 GLN D 71 ASN E 414 ASN E 436 GLN F 460 HIS G 37 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 42 GLN ** d 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 404 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113789 restraints weight = 49878.674| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.06 r_work: 0.3235 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 38094 Z= 0.130 Angle : 0.668 16.612 51701 Z= 0.328 Chirality : 0.045 0.505 5977 Planarity : 0.004 0.052 6720 Dihedral : 5.752 107.192 5601 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 1.89 % Allowed : 21.21 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.12), residues: 4835 helix: 1.65 (0.10), residues: 2572 sheet: -0.09 (0.21), residues: 570 loop : -0.38 (0.16), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG a 72 TYR 0.030 0.001 TYR B 18 PHE 0.024 0.001 PHE a 188 TRP 0.034 0.001 TRP d 186 HIS 0.004 0.001 HIS D 376 Details of bonding type rmsd covalent geometry : bond 0.00289 (38094) covalent geometry : angle 0.66833 (51701) hydrogen bonds : bond 0.03906 ( 2284) hydrogen bonds : angle 4.36227 ( 6612) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16967.69 seconds wall clock time: 288 minutes 24.27 seconds (17304.27 seconds total)