Starting phenix.real_space_refine on Tue Aug 26 12:31:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0t_35911/08_2025/8j0t_35911.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0t_35911/08_2025/8j0t_35911.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/8j0t_35911/08_2025/8j0t_35911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0t_35911/08_2025/8j0t_35911.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0t_35911/08_2025/8j0t_35911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0t_35911/08_2025/8j0t_35911.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= 0.009 sd= 1.095 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 121 5.16 5 C 23522 2.51 5 N 6432 2.21 5 O 7115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.02s 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: 37208 Number of models: 1 Model: "" Number of chains: 25 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: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4061 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 509} 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} Time building chain proxies: 8.60, per 1000 atoms: 0.23 Number of scatterers: 37208 At special positions: 0 Unit cell: (126.29, 135.05, 248.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 121 16.00 P 13 15.00 Mg 5 11.99 O 7115 8.00 N 6432 7.00 C 23522 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: 2.78 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 476.8 nanoseconds 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8866 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 23 sheets defined 59.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 removed outlier: 3.517A pdb=" N SER A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.693A 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 227 through 230 removed outlier: 4.169A pdb=" N ASP A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 256 Proline residue: A 250 - end of helix Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.672A 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: 3.811A pdb=" N LEU A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 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: 3.847A 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 392 through 404 removed outlier: 3.578A pdb=" N ASP A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.689A pdb=" N ALA A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 410 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER A 411 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 454 removed outlier: 3.803A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 478 Processing helix chain 'A' and resid 479 through 490 removed outlier: 4.523A 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 19 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.784A pdb=" N ASN B 84 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.544A pdb=" N PHE B 106 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.008A pdb=" N ARG B 142 " --> pdb=" O VAL B 139 " (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: 3.554A 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: 3.822A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 288 removed outlier: 3.821A 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: 3.800A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.520A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.600A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 403 removed outlier: 4.017A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 403 " --> pdb=" O GLN B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 432 removed outlier: 3.603A 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 480 through 490 Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.710A pdb=" N LYS B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY B 510 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 removed outlier: 3.826A pdb=" N TYR C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.860A pdb=" N PHE C 106 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.769A 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: 3.938A 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 242 through 262 Proline residue: C 250 - end of helix removed outlier: 3.774A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.710A 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: 3.639A pdb=" N THR C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.858A 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 414 through 432 Processing helix chain 'C' and resid 440 through 453 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: 4.265A pdb=" N LEU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.806A pdb=" N LYS C 509 " --> pdb=" O LYS C 505 " (cutoff:3.500A) 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 189 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: 5.080A pdb=" N ALA D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU D 243 " --> pdb=" O MET D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.895A pdb=" N THR D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 3.605A 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: 4.746A pdb=" N ASP D 395 " --> pdb=" O LYS D 391 " (cutoff:3.500A) removed outlier: 5.025A 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 424 removed outlier: 4.096A pdb=" N SER D 424 " --> pdb=" O GLU D 420 " (cutoff:3.500A) 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 481 Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.675A pdb=" N VAL E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 141 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 234 through 255 removed outlier: 3.775A pdb=" N ARG E 238 " --> pdb=" O PRO E 234 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA E 242 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU E 243 " --> pdb=" O MET E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 281 removed outlier: 3.713A 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 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 373 through 401 removed outlier: 4.407A pdb=" N ASP E 395 " --> pdb=" O LYS E 391 " (cutoff:3.500A) removed outlier: 4.636A 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 467 Processing helix chain 'E' and resid 471 through 481 removed outlier: 3.510A pdb=" N LEU E 475 " --> pdb=" O GLY E 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 removed outlier: 3.591A pdb=" N LYS F 106 " --> pdb=" O GLU F 103 " (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 190 removed outlier: 3.872A pdb=" N ARG F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) 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: 5.087A pdb=" N ALA F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LEU F 243 " --> pdb=" O MET F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 281 removed outlier: 3.922A pdb=" N PHE F 270 " --> pdb=" O ASN F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 removed outlier: 4.088A pdb=" N ARG F 304 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) 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: 3.624A pdb=" N LYS F 351 " --> pdb=" O ALA F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 400 removed outlier: 4.728A pdb=" N ASP F 395 " --> pdb=" O LYS F 391 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ILE F 396 " --> pdb=" O ASP F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 405 removed outlier: 4.142A pdb=" N GLU F 404 " --> pdb=" O GLY F 401 " (cutoff:3.500A) 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 59 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 65 through 69 removed outlier: 3.703A pdb=" N VAL G 69 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 109 Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.967A pdb=" N GLN G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 Processing helix chain 'G' and resid 225 through 302 removed outlier: 3.995A pdb=" N LEU G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) 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 Processing helix chain 'H' and resid 103 through 118 Processing helix chain '1' and resid 2 through 42 removed outlier: 3.736A pdb=" N ALA 1 34 " --> pdb=" O VAL 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 76 removed outlier: 4.695A pdb=" N THR 1 51 " --> pdb=" O GLY 1 47 " (cutoff:3.500A) Proline residue: 1 52 - end of helix Processing helix chain '2' and resid 2 through 42 removed outlier: 3.736A pdb=" N ALA 2 34 " --> pdb=" O VAL 2 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG 2 41 " --> pdb=" O SER 2 37 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 76 removed outlier: 4.205A pdb=" N ARG 2 48 " --> pdb=" O GLU 2 44 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR 2 51 " --> pdb=" O GLY 2 47 " (cutoff:3.500A) Proline residue: 2 52 - end of helix Processing helix chain '3' and resid 2 through 42 removed outlier: 3.735A pdb=" N ALA 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 76 removed outlier: 4.694A pdb=" N THR 3 51 " --> pdb=" O GLY 3 47 " (cutoff:3.500A) Proline residue: 3 52 - end of helix Processing helix chain '4' and resid 2 through 42 removed outlier: 3.736A pdb=" N ALA 4 34 " --> pdb=" O VAL 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 45 through 76 removed outlier: 4.694A pdb=" N THR 4 51 " --> pdb=" O GLY 4 47 " (cutoff:3.500A) Proline residue: 4 52 - end of helix Processing helix chain '5' and resid 2 through 42 removed outlier: 3.736A pdb=" N ALA 5 34 " --> pdb=" O VAL 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 45 through 76 removed outlier: 4.694A pdb=" N THR 5 51 " --> pdb=" O GLY 5 47 " (cutoff:3.500A) Proline residue: 5 52 - end of helix Processing helix chain '6' and resid 2 through 42 removed outlier: 3.735A pdb=" N ALA 6 34 " --> pdb=" O VAL 6 30 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 76 removed outlier: 4.695A pdb=" N THR 6 51 " --> pdb=" O GLY 6 47 " (cutoff:3.500A) Proline residue: 6 52 - end of helix Processing helix chain '7' and resid 2 through 42 removed outlier: 3.735A pdb=" N ALA 7 34 " --> pdb=" O VAL 7 30 " (cutoff:3.500A) Processing helix chain '7' and resid 45 through 76 removed outlier: 4.694A pdb=" N THR 7 51 " --> pdb=" O GLY 7 47 " (cutoff:3.500A) Proline residue: 7 52 - end of helix Processing helix chain '8' and resid 2 through 42 removed outlier: 3.736A pdb=" N ALA 8 34 " --> pdb=" O VAL 8 30 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 76 removed outlier: 4.694A pdb=" N THR 8 51 " --> pdb=" O GLY 8 47 " (cutoff:3.500A) Proline residue: 8 52 - end of helix Processing helix chain '9' and resid 2 through 42 removed outlier: 3.735A pdb=" N ALA 9 34 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 45 through 76 removed outlier: 4.695A pdb=" N THR 9 51 " --> pdb=" O GLY 9 47 " (cutoff:3.500A) Proline residue: 9 52 - end of helix Processing helix chain 'a' and resid 30 through 51 Processing helix chain 'a' and resid 58 through 79 Processing helix chain 'a' and resid 80 through 85 Proline residue: a 85 - end of helix Processing helix chain 'a' and resid 86 through 104 removed outlier: 3.622A pdb=" N LEU a 90 " --> pdb=" O PHE a 86 " (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 128 through 152 removed outlier: 3.635A pdb=" N VAL a 132 " --> pdb=" O ASP a 128 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 201 removed outlier: 3.604A pdb=" N ASN a 172 " --> pdb=" O LEU a 168 " (cutoff:3.500A) Proline residue: a 180 - end of helix removed outlier: 3.678A pdb=" N LEU a 187 " --> pdb=" O LEU a 183 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY a 194 " --> pdb=" O ASN a 190 " (cutoff:3.500A) removed outlier: 4.710A 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 205 through 244 removed outlier: 4.131A pdb=" N TRP a 210 " --> pdb=" O PRO a 206 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA a 211 " --> pdb=" O TYR a 207 " (cutoff:3.500A) Proline residue: a 212 - end of helix Processing helix chain 'b' and resid 29 through 48 removed outlier: 3.808A pdb=" N VAL b 33 " --> pdb=" O GLY b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 99 removed outlier: 3.760A pdb=" N GLN b 82 " --> pdb=" O PHE b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 144 removed outlier: 3.575A pdb=" N ALA b 139 " --> pdb=" O ARG b 135 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 159 removed outlier: 3.797A pdb=" N MET b 151 " --> pdb=" O HIS b 147 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER b 152 " --> pdb=" O VAL b 148 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR b 154 " --> pdb=" O THR b 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 21 removed outlier: 3.707A pdb=" N VAL d 13 " --> pdb=" O PHE d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 138 removed outlier: 3.634A pdb=" N VAL d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG d 97 " --> pdb=" O VAL d 93 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP d 107 " --> pdb=" O ALA d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 156 removed outlier: 3.643A pdb=" N GLN d 143 " --> pdb=" O ASP d 139 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG d 149 " --> pdb=" O ALA d 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 172 Processing helix chain 'd' and resid 176 through 191 Processing helix chain 'd' and resid 192 through 194 No H-bonds generated for 'chain 'd' and resid 192 through 194' Processing helix chain 'd' and resid 195 through 216 removed outlier: 3.881A pdb=" N SER d 208 " --> pdb=" O GLY d 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 223 removed outlier: 3.659A pdb=" N THR d 220 " --> pdb=" O GLU d 216 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR d 222 " --> pdb=" O VAL d 218 " (cutoff:3.500A) Processing helix chain 'd' and resid 230 through 242 Processing helix chain 'd' and resid 246 through 259 removed outlier: 3.775A pdb=" N LEU d 250 " --> pdb=" O GLY d 246 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS d 259 " --> pdb=" O THR d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 264 through 286 removed outlier: 4.305A pdb=" N ILE d 268 " --> pdb=" O ASN d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 removed outlier: 3.523A pdb=" N GLU d 293 " --> pdb=" O VAL d 289 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL d 305 " --> pdb=" O ARG d 301 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 313 removed outlier: 3.521A pdb=" N LEU d 312 " --> pdb=" O ARG d 308 " (cutoff:3.500A) Processing helix chain 'd' and resid 320 through 332 removed outlier: 3.907A pdb=" N VAL d 324 " --> pdb=" O ALA d 320 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS d 329 " --> pdb=" O ARG d 325 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 352 Processing helix chain 'd' and resid 357 through 373 removed outlier: 4.517A pdb=" N LEU d 363 " --> pdb=" O GLU d 359 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG d 373 " --> pdb=" O ALA d 369 " (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 'A' and resid 28 through 38 removed outlier: 6.805A pdb=" N HIS A 43 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 46 current: chain 'A' and resid 63 through 69 removed outlier: 5.986A pdb=" N ALA A 66 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A 77 " --> pdb=" O ALA A 66 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 74 through 78 current: chain 'E' and resid 30 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 30 through 34 current: chain 'E' and resid 58 through 69 removed outlier: 6.601A pdb=" N ARG E 74 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N HIS E 67 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU E 72 " --> pdb=" O HIS E 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 72 through 77 current: chain 'd' and resid 406 through 412 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 406 through 412 current: chain 'd' and resid 427 through 430 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: 8.715A pdb=" N THR A 233 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG A 203 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 270 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 205 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASP A 272 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A 207 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 7.928A pdb=" N ILE A 330 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 170 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 69 removed outlier: 4.040A pdb=" N GLU B 54 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 55 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS B 43 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA B 37 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ILE F 91 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU F 50 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR F 93 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N HIS F 48 " --> pdb=" O THR F 93 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ARG F 95 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASN F 45 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG F 74 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N HIS F 67 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU F 72 " --> pdb=" O HIS F 67 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU F 34 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL F 23 " --> pdb=" O GLU F 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 99 through 102 removed outlier: 4.206A pdb=" N THR B 128 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.335A pdb=" N VAL B 111 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA B 238 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 233 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 38 removed outlier: 6.801A pdb=" N HIS C 43 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU C 96 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N GLU C 57 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR C 94 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 111 removed outlier: 6.214A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ALA C 238 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 209 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL C 267 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU C 327 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 269 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 329 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE C 271 " --> pdb=" O ILE C 329 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLU C 331 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 534 through 538 removed outlier: 6.698A pdb=" N ALA C 534 " --> pdb=" O ARG G 201 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA G 203 " --> pdb=" O ALA C 534 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLU C 536 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET G 205 " --> pdb=" O GLU C 536 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 538 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL G 207 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU G 182 " --> pdb=" O ILE G 202 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N HIS G 183 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY G 78 " --> pdb=" O HIS G 183 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL G 185 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 80 " --> pdb=" O VAL G 185 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR G 187 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N VAL G 82 " --> pdb=" O THR G 187 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N PHE G 189 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ALA G 77 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N TYR G 117 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL G 79 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL G 119 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL G 81 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR G 135 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU G 116 " --> pdb=" O THR G 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 27 removed outlier: 6.509A pdb=" N ASP D 32 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU D 72 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS D 67 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG D 74 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU D 50 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU D 89 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 101 removed outlier: 4.178A pdb=" N GLU D 127 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 108 through 110 removed outlier: 6.065A pdb=" N HIS D 108 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE D 228 " --> pdb=" O HIS D 108 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE D 110 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER D 196 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N VAL D 227 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE D 198 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLY D 229 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLY D 200 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N MET D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU D 262 " --> pdb=" O MET D 316 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA D 318 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 264 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR D 320 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE D 167 " --> pdb=" O GLN D 317 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL D 319 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU D 169 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS D 166 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR D 342 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ALA D 168 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 147 through 148 removed outlier: 4.057A pdb=" N TYR D 161 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 98 through 101 removed outlier: 4.170A pdb=" N GLU E 127 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 109 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 109 through 110 current: chain 'E' and resid 224 through 230 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 224 through 230 current: chain 'E' and resid 311 through 318 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 311 through 318 current: chain 'E' and resid 363 through 364 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 98 through 101 removed outlier: 4.122A 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: 6.796A pdb=" N SER F 196 " --> pdb=" O ALA F 225 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL F 227 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE F 198 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N GLY F 229 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY F 200 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 201 " --> pdb=" O ASP F 265 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N MET F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU F 262 " --> pdb=" O MET F 316 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ALA F 318 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE F 264 " --> pdb=" O ALA F 318 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR F 320 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 167 " --> pdb=" O GLN F 317 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL F 319 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU F 169 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS F 166 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR F 342 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 168 " --> pdb=" O THR F 342 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 147 through 148 removed outlier: 4.028A 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: 5.959A pdb=" N SER G 221 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N GLN H 44 " --> pdb=" O SER G 221 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N GLU G 223 " --> pdb=" O GLN H 44 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ALA H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL H 9 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA H 10 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 5.243A 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: 4.194A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER H 83 " --> pdb=" O ASP H 66 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 17 through 19 2259 hydrogen bonds defined for protein. 6555 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: 7.37 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11542 1.33 - 1.45: 5111 1.45 - 1.57: 20926 1.57 - 1.69: 21 1.69 - 1.81: 221 Bond restraints: 37821 Sorted by residual: bond pdb=" C LEU d 113 " pdb=" N THR d 114 " ideal model delta sigma weight residual 1.335 1.436 -0.101 1.31e-02 5.83e+03 5.90e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.73e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.68e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.60e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.28e+01 ... (remaining 37816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 51027 3.73 - 7.46: 245 7.46 - 11.19: 26 11.19 - 14.93: 3 14.93 - 18.66: 3 Bond angle restraints: 51304 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 121.21 18.66 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 139.87 121.23 18.64 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 122.06 14.77 1.00e+00 1.00e+00 2.18e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 122.08 14.75 1.00e+00 1.00e+00 2.18e+02 ... (remaining 51299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.76: 21562 23.76 - 47.52: 1079 47.52 - 71.28: 93 71.28 - 95.04: 27 95.04 - 118.80: 2 Dihedral angle restraints: 22763 sinusoidal: 8949 harmonic: 13814 Sorted by residual: dihedral pdb=" C5' ADP F 600 " pdb=" O5' ADP F 600 " pdb=" PA ADP F 600 " pdb=" O2A ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 58.81 -118.80 1 2.00e+01 2.50e-03 3.56e+01 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 58.78 -118.77 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" CA VAL G 210 " pdb=" C VAL G 210 " pdb=" N GLU G 211 " pdb=" CA GLU G 211 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 22760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4570 0.054 - 0.108: 1148 0.108 - 0.162: 219 0.162 - 0.216: 28 0.216 - 0.270: 2 Chirality restraints: 5967 Sorted by residual: chirality pdb=" CG LEU d 8 " pdb=" CB LEU d 8 " pdb=" CD1 LEU d 8 " pdb=" CD2 LEU d 8 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB ILE C 6 " pdb=" CA ILE C 6 " pdb=" CG1 ILE C 6 " pdb=" CG2 ILE C 6 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LEU d 108 " pdb=" N LEU d 108 " pdb=" C LEU d 108 " pdb=" CB LEU d 108 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 5964 not shown) Planarity restraints: 6704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL d 225 " 0.054 5.00e-02 4.00e+02 8.18e-02 1.07e+01 pdb=" N PRO d 226 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO d 226 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO d 226 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 323 " -0.287 9.50e-02 1.11e+02 1.29e-01 1.02e+01 pdb=" NE ARG d 323 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG d 323 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG d 323 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG d 323 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 145 " 0.271 9.50e-02 1.11e+02 1.21e-01 9.04e+00 pdb=" NE ARG b 145 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG b 145 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG b 145 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG b 145 " 0.010 2.00e-02 2.50e+03 ... (remaining 6701 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 192 2.50 - 3.10: 28918 3.10 - 3.70: 57092 3.70 - 4.30: 87470 4.30 - 4.90: 143106 Nonbonded interactions: 316778 Sorted by model distance: nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 1.900 2.170 nonbonded pdb=" OG1 THR D 178 " pdb="MG MG D 601 " model vdw 1.966 2.170 nonbonded pdb=" OG1 THR C 179 " pdb="MG MG C 601 " model vdw 1.987 2.170 nonbonded pdb=" OG1 THR A 179 " pdb="MG MG A 601 " model vdw 2.004 2.170 nonbonded pdb=" OG1 THR F 178 " pdb="MG MG F 601 " model vdw 2.026 2.170 ... (remaining 316773 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' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' } 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 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)) } 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: 8.790 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 33.220 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 0.101 37821 Z= 0.317 Angle : 0.801 18.658 51304 Z= 0.501 Chirality : 0.049 0.270 5967 Planarity : 0.006 0.129 6704 Dihedral : 13.765 118.804 13897 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.05 % Allowed : 2.59 % Favored : 97.36 % 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: -2.64 (0.11), residues: 4839 helix: -1.55 (0.09), residues: 2604 sheet: -1.23 (0.20), residues: 578 loop : -1.95 (0.14), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 215 TYR 0.021 0.001 TYR a 143 PHE 0.024 0.002 PHE b 31 TRP 0.019 0.001 TRP a 216 HIS 0.011 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00604 (37821) covalent geometry : angle 0.80142 (51304) hydrogen bonds : bond 0.13658 ( 2259) hydrogen bonds : angle 7.13798 ( 6555) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 729 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: symmetry clash revert: symmetry clash REVERT: A 499 LYS cc_start: 0.8127 (tttp) cc_final: 0.7904 (ttmt) REVERT: B 36 ASP cc_start: 0.7926 (m-30) cc_final: 0.7663 (m-30) REVERT: B 70 ASP cc_start: 0.7868 (t0) cc_final: 0.7621 (t0) REVERT: B 384 LYS cc_start: 0.7619 (tttt) cc_final: 0.7155 (tttm) REVERT: B 449 PHE cc_start: 0.7338 (t80) cc_final: 0.6767 (t80) REVERT: B 462 GLU cc_start: 0.7830 (pp20) cc_final: 0.7601 (pp20) REVERT: C 192 ASN cc_start: 0.8614 (m-40) cc_final: 0.8345 (m-40) REVERT: C 199 LYS cc_start: 0.8630 (mttt) cc_final: 0.8173 (tmtt) REVERT: C 200 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8200 (mtpp) REVERT: C 221 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7814 (ttm-80) REVERT: C 224 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7790 (mt-10) REVERT: C 437 GLN cc_start: 0.8456 (tt0) cc_final: 0.8219 (mt0) REVERT: C 491 LYS cc_start: 0.8255 (mttt) cc_final: 0.7867 (mtmm) REVERT: C 525 VAL cc_start: 0.8047 (t) cc_final: 0.7817 (p) REVERT: D 22 ARG cc_start: 0.7661 (ttp-110) cc_final: 0.7236 (tpp-160) REVERT: D 95 ARG cc_start: 0.7627 (ptt-90) cc_final: 0.7206 (ptt90) REVERT: D 346 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7937 (ttt90) REVERT: D 391 LYS cc_start: 0.8438 (ttmt) cc_final: 0.7988 (tttm) REVERT: D 464 GLN cc_start: 0.7783 (mm-40) cc_final: 0.6852 (mp10) REVERT: D 477 LYS cc_start: 0.8534 (mptt) cc_final: 0.8274 (mptp) REVERT: E 272 GLN cc_start: 0.7474 (tt0) cc_final: 0.7049 (tt0) REVERT: E 309 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7792 (mtt180) REVERT: E 368 ASP cc_start: 0.7060 (t70) cc_final: 0.6660 (p0) REVERT: E 399 ILE cc_start: 0.7738 (mp) cc_final: 0.7192 (mp) REVERT: F 103 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7822 (tp30) REVERT: F 125 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8039 (pmtt) REVERT: F 256 GLN cc_start: 0.8361 (tt0) cc_final: 0.7768 (tt0) REVERT: F 258 GLN cc_start: 0.7053 (tt0) cc_final: 0.6537 (pm20) REVERT: F 417 ARG cc_start: 0.7192 (mtt90) cc_final: 0.6815 (mmm160) REVERT: G 9 ARG cc_start: 0.7263 (mmt90) cc_final: 0.6812 (mmt180) REVERT: G 117 TYR cc_start: 0.8653 (m-80) cc_final: 0.8403 (m-80) REVERT: G 193 LEU cc_start: 0.7328 (mp) cc_final: 0.7062 (tm) REVERT: G 198 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7305 (mm-30) REVERT: G 205 MET cc_start: 0.8716 (mtt) cc_final: 0.8424 (mtt) REVERT: a 64 PHE cc_start: 0.8232 (m-10) cc_final: 0.8023 (m-80) REVERT: a 69 ILE cc_start: 0.8823 (pt) cc_final: 0.8516 (pp) REVERT: b 77 GLN cc_start: 0.8575 (tt0) cc_final: 0.8259 (tt0) outliers start: 2 outliers final: 0 residues processed: 730 average time/residue: 0.8350 time to fit residues: 712.8603 Evaluate side-chains 485 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 305 HIS B 141 HIS B 192 ASN B 258 GLN B 437 GLN C 141 HIS D 45 ASN D 71 ASN D 128 HIS D 132 HIS D 209 ASN D 388 GLN D 432 GLN D 436 GLN ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN F 186 ASN F 272 GLN ** F 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN G 286 GLN H 38 HIS ** 2 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 42 GLN 6 67 ASN ** 8 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 16 HIS d 123 HIS d 197 GLN d 356 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110338 restraints weight = 50151.144| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.10 r_work: 0.3214 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37821 Z= 0.135 Angle : 0.598 10.044 51304 Z= 0.305 Chirality : 0.043 0.164 5967 Planarity : 0.005 0.066 6704 Dihedral : 6.121 133.372 5368 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.38 % Allowed : 12.06 % Favored : 85.56 % 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: -0.37 (0.12), residues: 4839 helix: 0.50 (0.10), residues: 2629 sheet: -0.90 (0.21), residues: 541 loop : -1.07 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG b 60 TYR 0.023 0.001 TYR a 143 PHE 0.032 0.001 PHE a 63 TRP 0.010 0.001 TRP a 216 HIS 0.010 0.001 HIS d 123 Details of bonding type rmsd covalent geometry : bond 0.00290 (37821) covalent geometry : angle 0.59813 (51304) hydrogen bonds : bond 0.04603 ( 2259) hydrogen bonds : angle 4.66500 ( 6555) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 619 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8175 (m-30) cc_final: 0.7707 (t70) REVERT: A 12 GLN cc_start: 0.8642 (pp30) cc_final: 0.8340 (pp30) REVERT: A 121 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8126 (ttm-80) REVERT: A 395 LEU cc_start: 0.7154 (tt) cc_final: 0.6917 (tm) REVERT: A 473 ASP cc_start: 0.8296 (t0) cc_final: 0.8043 (m-30) REVERT: A 484 THR cc_start: 0.7959 (m) cc_final: 0.7492 (p) REVERT: A 495 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7143 (tm-30) REVERT: A 499 LYS cc_start: 0.7835 (tttp) cc_final: 0.7614 (ttmt) REVERT: B 57 GLU cc_start: 0.8621 (tt0) cc_final: 0.8352 (tt0) REVERT: B 71 GLU cc_start: 0.8330 (pt0) cc_final: 0.7870 (pm20) REVERT: B 273 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7739 (t0) REVERT: B 449 PHE cc_start: 0.7104 (t80) cc_final: 0.6521 (t80) REVERT: C 199 LYS cc_start: 0.8506 (mttt) cc_final: 0.7639 (tmtt) REVERT: C 200 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7778 (mtmm) REVERT: C 221 ARG cc_start: 0.7735 (ttp-170) cc_final: 0.7245 (ttm-80) REVERT: C 224 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7813 (mt-10) REVERT: C 273 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7228 (t0) REVERT: C 429 GLU cc_start: 0.7605 (mp0) cc_final: 0.6816 (mp0) REVERT: C 502 GLU cc_start: 0.7336 (pp20) cc_final: 0.6345 (mm-30) REVERT: C 525 VAL cc_start: 0.7597 (t) cc_final: 0.7348 (p) REVERT: D 22 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.6726 (tpp-160) REVERT: D 95 ARG cc_start: 0.8155 (ptt-90) cc_final: 0.7262 (ptt90) REVERT: D 239 MET cc_start: 0.8459 (mtm) cc_final: 0.8236 (mtp) REVERT: D 391 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7614 (tttm) REVERT: D 428 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7225 (mtp) REVERT: D 464 GLN cc_start: 0.7570 (mm-40) cc_final: 0.6394 (mp10) REVERT: E 125 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8178 (ptpp) REVERT: E 272 GLN cc_start: 0.7341 (tt0) cc_final: 0.6905 (tt0) REVERT: E 309 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7829 (mtt180) REVERT: E 339 ASP cc_start: 0.8993 (m-30) cc_final: 0.8736 (m-30) REVERT: E 346 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.7046 (ttm-80) REVERT: E 368 ASP cc_start: 0.7162 (t70) cc_final: 0.6398 (p0) REVERT: E 399 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6841 (mp) REVERT: E 410 LYS cc_start: 0.6302 (mtpt) cc_final: 0.6092 (mtpt) REVERT: F 103 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8115 (tp30) REVERT: F 125 LYS cc_start: 0.8651 (mmtt) cc_final: 0.7746 (pmtt) REVERT: F 256 GLN cc_start: 0.8349 (tt0) cc_final: 0.7993 (tt0) REVERT: F 258 GLN cc_start: 0.7225 (tt0) cc_final: 0.6197 (pm20) REVERT: F 417 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6317 (mmm160) REVERT: F 448 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: F 474 ASP cc_start: 0.8029 (m-30) cc_final: 0.7654 (m-30) REVERT: G 9 ARG cc_start: 0.7073 (mmt90) cc_final: 0.6563 (mmt180) REVERT: G 44 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.6964 (ttm-80) REVERT: G 60 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7955 (tm-30) REVERT: G 76 ARG cc_start: 0.6727 (mtm-85) cc_final: 0.6060 (mtm-85) REVERT: G 198 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7335 (mm-30) REVERT: G 200 HIS cc_start: 0.7648 (m-70) cc_final: 0.7374 (m-70) REVERT: G 205 MET cc_start: 0.8543 (mtt) cc_final: 0.8173 (mtp) REVERT: H 109 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7095 (ttp80) REVERT: 1 1 MET cc_start: 0.5161 (OUTLIER) cc_final: 0.4045 (tmm) REVERT: 1 17 MET cc_start: 0.8748 (mmm) cc_final: 0.8536 (mmt) REVERT: 1 71 MET cc_start: 0.8858 (tmm) cc_final: 0.8607 (tmm) REVERT: 4 1 MET cc_start: 0.5778 (ttp) cc_final: 0.5533 (tpp) REVERT: 5 41 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6276 (ttm-80) REVERT: a 11 GLU cc_start: 0.6649 (pp20) cc_final: 0.6012 (tm-30) REVERT: a 23 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6484 (mtt) REVERT: a 72 ARG cc_start: 0.9226 (ttp-110) cc_final: 0.9011 (ttp-110) REVERT: a 227 GLN cc_start: 0.8564 (tp40) cc_final: 0.8150 (tp40) REVERT: b 77 GLN cc_start: 0.8540 (tt0) cc_final: 0.8221 (tt0) REVERT: b 86 ASP cc_start: 0.9165 (m-30) cc_final: 0.8901 (m-30) REVERT: b 87 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8079 (tm-30) REVERT: b 108 ARG cc_start: 0.8706 (tmm160) cc_final: 0.8445 (tmm160) REVERT: b 124 SER cc_start: 0.8883 (p) cc_final: 0.8439 (t) REVERT: b 128 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8844 (p) REVERT: b 131 GLU cc_start: 0.9108 (tt0) cc_final: 0.8287 (tt0) REVERT: b 132 GLN cc_start: 0.8847 (mp10) cc_final: 0.8305 (pm20) REVERT: b 134 LYS cc_start: 0.8733 (tptp) cc_final: 0.8523 (tptp) REVERT: b 137 ARG cc_start: 0.8980 (tpt90) cc_final: 0.8451 (tpt90) REVERT: d 186 TRP cc_start: 0.8845 (t-100) cc_final: 0.8607 (t-100) REVERT: d 273 HIS cc_start: 0.8580 (t-90) cc_final: 0.7850 (t-90) REVERT: d 308 ARG cc_start: 0.8455 (pmt170) cc_final: 0.7791 (ppp-140) outliers start: 92 outliers final: 21 residues processed: 662 average time/residue: 0.8038 time to fit residues: 630.8752 Evaluate side-chains 542 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 510 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 273 ASP Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 165 VAL Chi-restraints excluded: chain b residue 128 THR Chi-restraints excluded: chain b residue 150 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 358 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 453 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 302 optimal weight: 4.9990 chunk 386 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 415 optimal weight: 0.9990 chunk 458 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS B 90 GLN B 192 ASN B 437 GLN C 90 GLN C 141 HIS C 344 ASN C 399 GLN D 71 ASN E 71 ASN F 376 HIS G 125 ASN G 286 GLN 1 67 ASN 3 42 GLN 3 46 GLN 5 67 ASN 6 42 GLN 6 67 ASN a 16 HIS ** a 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 190 ASN b 95 GLN d 40 GLN d 123 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104518 restraints weight = 50622.539| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.96 r_work: 0.3116 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 37821 Z= 0.258 Angle : 0.650 8.207 51304 Z= 0.333 Chirality : 0.047 0.257 5967 Planarity : 0.005 0.077 6704 Dihedral : 6.355 125.528 5368 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.02 % Favored : 96.96 % Rotamer: Outliers : 3.29 % Allowed : 14.36 % Favored : 82.35 % 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: 0.13 (0.12), residues: 4839 helix: 0.92 (0.10), residues: 2643 sheet: -0.88 (0.21), residues: 584 loop : -0.80 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 211 TYR 0.021 0.002 TYR a 143 PHE 0.027 0.002 PHE d 297 TRP 0.012 0.001 TRP a 216 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00625 (37821) covalent geometry : angle 0.65016 (51304) hydrogen bonds : bond 0.05326 ( 2259) hydrogen bonds : angle 4.69879 ( 6555) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 535 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8288 (m-30) cc_final: 0.7916 (t70) REVERT: A 121 ARG cc_start: 0.8521 (mtp85) cc_final: 0.8123 (ttm-80) REVERT: A 356 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: A 414 ASP cc_start: 0.6999 (t0) cc_final: 0.6670 (t0) REVERT: A 495 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7246 (tm-30) REVERT: A 499 LYS cc_start: 0.7782 (tttp) cc_final: 0.7579 (ttpt) REVERT: B 71 GLU cc_start: 0.8371 (pt0) cc_final: 0.8008 (pm20) REVERT: B 72 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7607 (p90) REVERT: B 199 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7650 (tptt) REVERT: B 384 LYS cc_start: 0.7215 (tttt) cc_final: 0.6581 (tttm) REVERT: B 449 PHE cc_start: 0.7047 (t80) cc_final: 0.6577 (t80) REVERT: B 505 LYS cc_start: 0.6411 (pptt) cc_final: 0.6173 (mmmm) REVERT: C 199 LYS cc_start: 0.8630 (mttt) cc_final: 0.7754 (tmtt) REVERT: C 200 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7856 (mtmm) REVERT: C 221 ARG cc_start: 0.7782 (ttp-170) cc_final: 0.7342 (ttm-80) REVERT: C 224 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 358 ASP cc_start: 0.8103 (m-30) cc_final: 0.7820 (m-30) REVERT: C 414 ASP cc_start: 0.6773 (t70) cc_final: 0.6444 (t0) REVERT: C 488 ASP cc_start: 0.7860 (m-30) cc_final: 0.7270 (m-30) REVERT: C 502 GLU cc_start: 0.7320 (pp20) cc_final: 0.6345 (mm-30) REVERT: C 525 VAL cc_start: 0.7730 (t) cc_final: 0.7462 (p) REVERT: D 22 ARG cc_start: 0.7886 (ttp-110) cc_final: 0.6768 (tpp-160) REVERT: D 95 ARG cc_start: 0.8089 (ptt-90) cc_final: 0.7155 (ptt90) REVERT: D 391 LYS cc_start: 0.8191 (ttmt) cc_final: 0.7584 (tttm) REVERT: D 464 GLN cc_start: 0.7723 (mm-40) cc_final: 0.6467 (mp10) REVERT: E 272 GLN cc_start: 0.7371 (tt0) cc_final: 0.6970 (tt0) REVERT: E 309 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7845 (mtt180) REVERT: E 346 ARG cc_start: 0.7591 (ttm-80) cc_final: 0.7265 (ttm-80) REVERT: E 374 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6201 (m-30) REVERT: E 399 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.6940 (mp) REVERT: F 103 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8026 (tp30) REVERT: F 125 LYS cc_start: 0.8657 (mmtt) cc_final: 0.7748 (pmtt) REVERT: F 256 GLN cc_start: 0.8474 (tt0) cc_final: 0.8079 (tt0) REVERT: F 258 GLN cc_start: 0.7351 (tt0) cc_final: 0.6240 (pm20) REVERT: F 391 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7429 (ttmt) REVERT: F 417 ARG cc_start: 0.7217 (mtt90) cc_final: 0.6410 (mmm160) REVERT: F 448 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: F 474 ASP cc_start: 0.7998 (m-30) cc_final: 0.7582 (m-30) REVERT: G 9 ARG cc_start: 0.7238 (mmt90) cc_final: 0.6740 (mmt180) REVERT: G 60 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7870 (tm-30) REVERT: G 117 TYR cc_start: 0.8410 (m-80) cc_final: 0.8151 (m-80) REVERT: G 198 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7341 (mm-30) REVERT: G 205 MET cc_start: 0.8530 (mtt) cc_final: 0.8155 (mtp) REVERT: H 58 GLU cc_start: 0.7848 (mp0) cc_final: 0.7464 (mp0) REVERT: 1 1 MET cc_start: 0.5283 (OUTLIER) cc_final: 0.4142 (tpt) REVERT: 1 17 MET cc_start: 0.8953 (mmm) cc_final: 0.8521 (mmt) REVERT: 1 61 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: 1 68 LEU cc_start: 0.9043 (tm) cc_final: 0.8723 (tp) REVERT: 1 71 MET cc_start: 0.8941 (tmm) cc_final: 0.8532 (tmm) REVERT: 4 1 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5904 (tpp) REVERT: 4 48 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7835 (ttm170) REVERT: a 11 GLU cc_start: 0.6773 (pp20) cc_final: 0.6232 (tm-30) REVERT: a 72 ARG cc_start: 0.9250 (ttp-110) cc_final: 0.8991 (ttp-110) REVERT: a 197 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8070 (mp) REVERT: b 76 GLU cc_start: 0.8639 (pt0) cc_final: 0.8430 (pt0) REVERT: b 87 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8135 (tm-30) REVERT: b 95 GLN cc_start: 0.9094 (tt0) cc_final: 0.8819 (tp-100) REVERT: b 109 LYS cc_start: 0.9500 (ttmm) cc_final: 0.9054 (ptmm) REVERT: b 121 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8299 (pp30) REVERT: b 132 GLN cc_start: 0.8832 (mt0) cc_final: 0.8628 (mp10) REVERT: b 135 ARG cc_start: 0.8675 (mtm110) cc_final: 0.8385 (mtm-85) REVERT: b 137 ARG cc_start: 0.8941 (tpt90) cc_final: 0.8635 (tpt90) REVERT: b 141 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8458 (tm-30) REVERT: d 186 TRP cc_start: 0.8905 (t-100) cc_final: 0.8680 (t-100) REVERT: d 308 ARG cc_start: 0.8458 (pmt170) cc_final: 0.7770 (ppp-140) REVERT: d 372 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8104 (tpp80) outliers start: 127 outliers final: 49 residues processed: 608 average time/residue: 0.7853 time to fit residues: 567.9437 Evaluate side-chains 540 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 479 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 165 VAL 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 50 VAL Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 106 ASP Chi-restraints excluded: chain b residue 130 HIS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 174 SER Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 363 LEU Chi-restraints excluded: chain d residue 372 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 412 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 301 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 361 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 394 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN B 437 GLN C 141 HIS E 71 ASN F 186 ASN G 125 ASN G 286 GLN 1 42 GLN 1 67 ASN 3 42 GLN 3 46 GLN ** 7 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 46 GLN a 16 HIS a 102 ASN b 127 GLN d 123 HIS d 288 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.109263 restraints weight = 50485.312| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.98 r_work: 0.3180 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37821 Z= 0.128 Angle : 0.565 8.849 51304 Z= 0.284 Chirality : 0.042 0.203 5967 Planarity : 0.004 0.072 6704 Dihedral : 5.790 125.677 5368 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 2.74 % Allowed : 16.35 % Favored : 80.91 % 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: 0.83 (0.12), residues: 4839 helix: 1.58 (0.10), residues: 2612 sheet: -0.65 (0.22), residues: 561 loop : -0.60 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d 211 TYR 0.023 0.001 TYR a 143 PHE 0.027 0.001 PHE d 297 TRP 0.010 0.001 TRP a 210 HIS 0.009 0.001 HIS d 123 Details of bonding type rmsd covalent geometry : bond 0.00277 (37821) covalent geometry : angle 0.56465 (51304) hydrogen bonds : bond 0.04296 ( 2259) hydrogen bonds : angle 4.31754 ( 6555) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 566 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8313 (m-30) cc_final: 0.7699 (t0) REVERT: A 121 ARG cc_start: 0.8474 (mtp85) cc_final: 0.8115 (ttm-80) REVERT: A 414 ASP cc_start: 0.6922 (t0) cc_final: 0.6583 (t0) REVERT: A 473 ASP cc_start: 0.8335 (t0) cc_final: 0.8010 (m-30) REVERT: A 484 THR cc_start: 0.7970 (m) cc_final: 0.7488 (p) REVERT: A 485 GLU cc_start: 0.7646 (pt0) cc_final: 0.7444 (mp0) REVERT: A 495 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 70 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.7754 (t0) REVERT: B 71 GLU cc_start: 0.8342 (pt0) cc_final: 0.7875 (pm20) REVERT: B 72 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7487 (p90) REVERT: B 199 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7706 (tptt) REVERT: B 245 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8056 (m-10) REVERT: B 449 PHE cc_start: 0.7182 (t80) cc_final: 0.6637 (t80) REVERT: B 505 LYS cc_start: 0.6656 (pptt) cc_final: 0.6397 (mtmm) REVERT: C 199 LYS cc_start: 0.8586 (mttt) cc_final: 0.7727 (tmtt) REVERT: C 200 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7806 (mtpt) REVERT: C 221 ARG cc_start: 0.7741 (ttp-170) cc_final: 0.7306 (ttm-80) REVERT: C 358 ASP cc_start: 0.8094 (m-30) cc_final: 0.7840 (m-30) REVERT: C 414 ASP cc_start: 0.6681 (t70) cc_final: 0.6342 (t0) REVERT: C 525 VAL cc_start: 0.7588 (t) cc_final: 0.7323 (m) REVERT: D 20 SER cc_start: 0.9084 (p) cc_final: 0.8765 (m) REVERT: D 22 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.6827 (tpp-160) REVERT: D 95 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7129 (ppt170) REVERT: D 191 ASN cc_start: 0.8149 (m-40) cc_final: 0.7680 (p0) REVERT: D 239 MET cc_start: 0.8387 (mtm) cc_final: 0.8118 (mtp) REVERT: D 391 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7615 (tttm) REVERT: D 464 GLN cc_start: 0.7607 (mm-40) cc_final: 0.6372 (mp10) REVERT: E 125 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8236 (ptpp) REVERT: E 272 GLN cc_start: 0.7405 (tt0) cc_final: 0.6998 (tt0) REVERT: E 309 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.7813 (mtt180) REVERT: E 346 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7339 (ttm-80) REVERT: E 368 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6386 (p0) REVERT: E 399 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.6908 (mp) REVERT: E 410 LYS cc_start: 0.6163 (mtpt) cc_final: 0.5764 (mtmt) REVERT: F 103 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8004 (tp30) REVERT: F 125 LYS cc_start: 0.8653 (mmtt) cc_final: 0.7759 (pmtt) REVERT: F 256 GLN cc_start: 0.8273 (tt0) cc_final: 0.7897 (tt0) REVERT: F 258 GLN cc_start: 0.7282 (tt0) cc_final: 0.6226 (pm20) REVERT: F 417 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6336 (mmm160) REVERT: F 474 ASP cc_start: 0.8017 (m-30) cc_final: 0.7571 (m-30) REVERT: G 9 ARG cc_start: 0.7061 (mmt90) cc_final: 0.6550 (mmt180) REVERT: G 13 ARG cc_start: 0.7081 (ttp-110) cc_final: 0.6348 (ptt90) REVERT: G 44 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7076 (ttm-80) REVERT: G 136 GLU cc_start: 0.7958 (tt0) cc_final: 0.7526 (tp30) REVERT: G 198 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7387 (mm-30) REVERT: G 205 MET cc_start: 0.8426 (mtt) cc_final: 0.8145 (mtp) REVERT: G 234 LEU cc_start: 0.8565 (mt) cc_final: 0.8137 (tt) REVERT: H 58 GLU cc_start: 0.7844 (mp0) cc_final: 0.7441 (mp0) REVERT: H 109 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7111 (ttp80) REVERT: 1 61 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: 1 71 MET cc_start: 0.8927 (tmm) cc_final: 0.8540 (tmm) REVERT: 4 1 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5899 (tpp) REVERT: 4 48 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7664 (ttm170) REVERT: a 11 GLU cc_start: 0.6695 (pp20) cc_final: 0.6147 (tm-30) REVERT: a 23 MET cc_start: 0.6462 (OUTLIER) cc_final: 0.5941 (mpm) REVERT: a 70 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: a 72 ARG cc_start: 0.9212 (ttp-110) cc_final: 0.8948 (ttp-110) REVERT: a 197 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7903 (mp) REVERT: a 223 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8363 (p) REVERT: b 76 GLU cc_start: 0.8643 (pt0) cc_final: 0.8404 (pt0) REVERT: b 77 GLN cc_start: 0.8663 (tt0) cc_final: 0.8260 (tt0) REVERT: b 87 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8126 (tm-30) REVERT: b 95 GLN cc_start: 0.9126 (tt0) cc_final: 0.8790 (tp-100) REVERT: b 109 LYS cc_start: 0.9443 (ttmm) cc_final: 0.9190 (ptmm) REVERT: b 121 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8203 (pp30) REVERT: b 128 THR cc_start: 0.9307 (p) cc_final: 0.8969 (t) REVERT: b 132 GLN cc_start: 0.8928 (mt0) cc_final: 0.8555 (mp10) REVERT: b 138 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.8853 (p0) REVERT: b 141 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8245 (tm-30) REVERT: d 186 TRP cc_start: 0.8878 (t-100) cc_final: 0.8657 (t-100) REVERT: d 205 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7562 (mm-30) REVERT: d 260 ARG cc_start: 0.8402 (ttm-80) cc_final: 0.8068 (ttm-80) REVERT: d 308 ARG cc_start: 0.8382 (pmt170) cc_final: 0.7655 (ppp-140) REVERT: d 372 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7954 (tpp80) outliers start: 106 outliers final: 36 residues processed: 617 average time/residue: 0.8406 time to fit residues: 619.5548 Evaluate side-chains 566 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 513 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 124 SER Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain a residue 223 VAL Chi-restraints excluded: chain b residue 26 ILE Chi-restraints excluded: chain b residue 50 VAL Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 130 HIS Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 372 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 446 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 192 optimal weight: 0.7980 chunk 373 optimal weight: 0.5980 chunk 269 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 465 optimal weight: 1.9990 chunk 292 optimal weight: 5.9990 chunk 383 optimal weight: 0.1980 chunk 193 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN B 437 GLN C 141 HIS D 71 ASN D 256 GLN F 186 ASN G 286 GLN 1 42 GLN 1 67 ASN 6 42 GLN ** 7 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 46 GLN a 102 ASN a 190 ASN b 102 ASN b 127 GLN ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109660 restraints weight = 49966.159| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.97 r_work: 0.3199 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37821 Z= 0.127 Angle : 0.567 14.628 51304 Z= 0.283 Chirality : 0.042 0.195 5967 Planarity : 0.004 0.072 6704 Dihedral : 5.564 119.447 5368 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 2.90 % Allowed : 17.15 % Favored : 79.95 % 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: 1.16 (0.12), residues: 4839 helix: 1.82 (0.10), residues: 2616 sheet: -0.56 (0.21), residues: 577 loop : -0.38 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG d 211 TYR 0.022 0.001 TYR a 143 PHE 0.025 0.001 PHE d 187 TRP 0.011 0.001 TRP a 210 HIS 0.005 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00282 (37821) covalent geometry : angle 0.56652 (51304) hydrogen bonds : bond 0.04214 ( 2259) hydrogen bonds : angle 4.19330 ( 6555) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 550 time to evaluate : 1.185 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 9 ASP cc_start: 0.8125 (m-30) cc_final: 0.7727 (t0) REVERT: A 121 ARG cc_start: 0.8434 (mtp85) cc_final: 0.8078 (ttm-80) REVERT: A 356 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8254 (mt-10) REVERT: A 395 LEU cc_start: 0.7262 (mt) cc_final: 0.6814 (pp) REVERT: A 404 GLU cc_start: 0.7620 (tt0) cc_final: 0.7288 (tt0) REVERT: A 414 ASP cc_start: 0.6873 (t0) cc_final: 0.6556 (t0) REVERT: A 484 THR cc_start: 0.8027 (m) cc_final: 0.7544 (p) REVERT: A 495 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 71 GLU cc_start: 0.8335 (pt0) cc_final: 0.7972 (pm20) REVERT: B 72 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7587 (p90) REVERT: B 128 THR cc_start: 0.8265 (m) cc_final: 0.8051 (m) REVERT: B 159 MET cc_start: 0.8680 (mmm) cc_final: 0.8317 (mmm) REVERT: B 199 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7649 (tptt) REVERT: B 245 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8033 (m-10) REVERT: B 449 PHE cc_start: 0.7241 (t80) cc_final: 0.6702 (t80) REVERT: B 505 LYS cc_start: 0.6693 (pptt) cc_final: 0.6397 (mtpt) REVERT: C 199 LYS cc_start: 0.8413 (mttt) cc_final: 0.7544 (tmtt) REVERT: C 200 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7673 (mtmm) REVERT: C 221 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7316 (ttm-80) REVERT: C 273 ASP cc_start: 0.7904 (m-30) cc_final: 0.7276 (t0) REVERT: C 358 ASP cc_start: 0.8134 (m-30) cc_final: 0.7883 (m-30) REVERT: C 414 ASP cc_start: 0.6681 (t70) cc_final: 0.6352 (t0) REVERT: C 525 VAL cc_start: 0.7639 (t) cc_final: 0.7369 (m) REVERT: D 20 SER cc_start: 0.9081 (p) cc_final: 0.8777 (m) REVERT: D 22 ARG cc_start: 0.7900 (ttp-110) cc_final: 0.6822 (tpp-160) REVERT: D 95 ARG cc_start: 0.8118 (ptt-90) cc_final: 0.7232 (ptt90) REVERT: D 140 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: D 191 ASN cc_start: 0.8125 (m-40) cc_final: 0.7666 (p0) REVERT: D 239 MET cc_start: 0.8322 (mtm) cc_final: 0.8079 (mtp) REVERT: D 391 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7631 (tttm) REVERT: D 464 GLN cc_start: 0.7584 (mm-40) cc_final: 0.6353 (mp10) REVERT: E 103 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7754 (tp30) REVERT: E 125 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8285 (ptpp) REVERT: E 159 THR cc_start: 0.7637 (m) cc_final: 0.7378 (p) REVERT: E 272 GLN cc_start: 0.7456 (tt0) cc_final: 0.7052 (tt0) REVERT: E 309 ARG cc_start: 0.8328 (mtm-85) cc_final: 0.7811 (mtt180) REVERT: E 346 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7417 (ttm-80) REVERT: E 368 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6388 (p0) REVERT: E 399 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6823 (mp) REVERT: F 103 GLU cc_start: 0.8676 (mm-30) cc_final: 0.7993 (tp30) REVERT: F 111 ASN cc_start: 0.7625 (m-40) cc_final: 0.7291 (m-40) REVERT: F 125 LYS cc_start: 0.8638 (mmtt) cc_final: 0.7775 (pmtt) REVERT: F 258 GLN cc_start: 0.7249 (tt0) cc_final: 0.6182 (pm20) REVERT: F 296 ASP cc_start: 0.7782 (m-30) cc_final: 0.7548 (m-30) REVERT: F 448 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: F 474 ASP cc_start: 0.8012 (m-30) cc_final: 0.7540 (m-30) REVERT: G 9 ARG cc_start: 0.7084 (mmt90) cc_final: 0.6572 (mmt180) REVERT: G 13 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6386 (ptt90) REVERT: G 49 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: G 136 GLU cc_start: 0.7946 (tt0) cc_final: 0.7643 (tp30) REVERT: G 205 MET cc_start: 0.8373 (mtt) cc_final: 0.8105 (mtp) REVERT: H 58 GLU cc_start: 0.7788 (mp0) cc_final: 0.7302 (mp0) REVERT: 1 1 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.4240 (tpt) REVERT: 1 17 MET cc_start: 0.8965 (mmm) cc_final: 0.8611 (mmt) REVERT: 1 61 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: 1 71 MET cc_start: 0.8922 (tmm) cc_final: 0.8576 (tmm) REVERT: 4 1 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5962 (tpp) REVERT: 4 48 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7660 (ttm170) REVERT: 5 1 MET cc_start: 0.7321 (ttt) cc_final: 0.6852 (ttm) REVERT: 5 41 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6525 (ttm-80) REVERT: a 11 GLU cc_start: 0.6731 (pp20) cc_final: 0.6220 (tm-30) REVERT: a 23 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5827 (mpm) REVERT: a 72 ARG cc_start: 0.9190 (ttp-110) cc_final: 0.8916 (ttp-110) REVERT: a 197 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7919 (mp) REVERT: a 223 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8292 (p) REVERT: b 76 GLU cc_start: 0.8650 (pt0) cc_final: 0.8350 (pt0) REVERT: b 87 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8121 (tm-30) REVERT: b 115 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8917 (ttp80) REVERT: b 138 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.8800 (p0) REVERT: b 141 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8314 (tm-30) REVERT: d 118 ARG cc_start: 0.8687 (ttt180) cc_final: 0.8436 (tpt-90) REVERT: d 123 HIS cc_start: 0.8643 (t70) cc_final: 0.8440 (t-170) REVERT: d 186 TRP cc_start: 0.8858 (t-100) cc_final: 0.8635 (t-100) REVERT: d 205 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7632 (mm-30) REVERT: d 260 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8087 (ttm-80) REVERT: d 308 ARG cc_start: 0.8416 (pmt170) cc_final: 0.7617 (ppp-140) REVERT: d 372 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7929 (tpp80) outliers start: 112 outliers final: 40 residues processed: 608 average time/residue: 0.7203 time to fit residues: 525.1223 Evaluate side-chains 568 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 506 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 165 VAL Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain a residue 223 VAL Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 363 LEU Chi-restraints excluded: chain d residue 372 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 437 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 477 optimal weight: 9.9990 chunk 421 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 337 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN B 437 GLN C 141 HIS C 361 ASN D 71 ASN D 256 GLN F 388 GLN G 286 GLN 1 42 GLN 1 67 ASN ** 7 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 213 ASN ** b 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.105021 restraints weight = 51248.244| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.02 r_work: 0.3144 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 37821 Z= 0.198 Angle : 0.615 9.796 51304 Z= 0.310 Chirality : 0.045 0.205 5967 Planarity : 0.005 0.071 6704 Dihedral : 5.819 121.144 5368 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.33 % Rotamer: Outliers : 3.16 % Allowed : 17.93 % Favored : 78.91 % 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: 1.06 (0.12), residues: 4839 helix: 1.71 (0.10), residues: 2617 sheet: -0.66 (0.21), residues: 592 loop : -0.33 (0.16), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG d 211 TYR 0.020 0.001 TYR a 143 PHE 0.029 0.002 PHE d 187 TRP 0.011 0.001 TRP a 210 HIS 0.004 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00475 (37821) covalent geometry : angle 0.61550 (51304) hydrogen bonds : bond 0.04730 ( 2259) hydrogen bonds : angle 4.36386 ( 6555) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 519 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8011 (m-30) cc_final: 0.7592 (t70) REVERT: A 121 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8090 (ttm-80) REVERT: A 356 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 395 LEU cc_start: 0.7246 (mt) cc_final: 0.6770 (pp) REVERT: A 404 GLU cc_start: 0.7633 (tt0) cc_final: 0.7320 (tt0) REVERT: A 414 ASP cc_start: 0.6882 (t0) cc_final: 0.6550 (t0) REVERT: A 476 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7959 (ttp-170) REVERT: A 484 THR cc_start: 0.7951 (m) cc_final: 0.7488 (p) REVERT: A 495 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 71 GLU cc_start: 0.8364 (pt0) cc_final: 0.7975 (pm20) REVERT: B 72 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7619 (p90) REVERT: B 199 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7715 (tptt) REVERT: B 245 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: B 449 PHE cc_start: 0.7159 (t80) cc_final: 0.6667 (t80) REVERT: C 199 LYS cc_start: 0.8569 (mttt) cc_final: 0.7693 (tmtt) REVERT: C 200 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7777 (mtmm) REVERT: C 221 ARG cc_start: 0.7751 (ttp-170) cc_final: 0.7305 (ttm-80) REVERT: C 273 ASP cc_start: 0.8108 (m-30) cc_final: 0.7416 (t0) REVERT: C 358 ASP cc_start: 0.8085 (m-30) cc_final: 0.7825 (m-30) REVERT: C 414 ASP cc_start: 0.6799 (t70) cc_final: 0.6464 (t0) REVERT: C 466 ARG cc_start: 0.7670 (ttp80) cc_final: 0.7451 (ttp80) REVERT: C 525 VAL cc_start: 0.7717 (t) cc_final: 0.7425 (m) REVERT: D 20 SER cc_start: 0.9114 (p) cc_final: 0.8803 (m) REVERT: D 22 ARG cc_start: 0.7847 (ttp-110) cc_final: 0.6753 (tpp-160) REVERT: D 95 ARG cc_start: 0.8067 (ptt-90) cc_final: 0.7153 (ptt90) REVERT: D 191 ASN cc_start: 0.8121 (m-40) cc_final: 0.7647 (p0) REVERT: D 239 MET cc_start: 0.8448 (mtm) cc_final: 0.8223 (mtp) REVERT: D 391 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7573 (tttm) REVERT: D 428 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7425 (mtp) REVERT: D 463 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8354 (tt0) REVERT: D 464 GLN cc_start: 0.7620 (mm-40) cc_final: 0.6404 (mp10) REVERT: E 272 GLN cc_start: 0.7397 (tt0) cc_final: 0.6817 (tt0) REVERT: E 309 ARG cc_start: 0.8300 (mtm-85) cc_final: 0.7842 (mtt180) REVERT: E 316 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: E 346 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7513 (ttm-80) REVERT: E 368 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6390 (p0) REVERT: E 374 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6383 (m-30) REVERT: E 399 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.6907 (mp) REVERT: F 125 LYS cc_start: 0.8653 (mmtt) cc_final: 0.7765 (pmtt) REVERT: F 256 GLN cc_start: 0.8359 (tt0) cc_final: 0.8130 (tt0) REVERT: F 258 GLN cc_start: 0.7252 (tt0) cc_final: 0.6136 (pm20) REVERT: F 296 ASP cc_start: 0.7803 (m-30) cc_final: 0.7585 (m-30) REVERT: F 417 ARG cc_start: 0.7189 (mtt90) cc_final: 0.6428 (mmm160) REVERT: F 448 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: F 474 ASP cc_start: 0.8040 (m-30) cc_final: 0.7588 (m-30) REVERT: G 9 ARG cc_start: 0.7110 (mmt90) cc_final: 0.6617 (mmt180) REVERT: G 44 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.6963 (ttm-80) REVERT: G 49 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: G 136 GLU cc_start: 0.7846 (tt0) cc_final: 0.7541 (tp30) REVERT: G 192 MET cc_start: 0.8214 (tpp) cc_final: 0.7715 (tpt) REVERT: G 198 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7251 (mm-30) REVERT: G 205 MET cc_start: 0.8412 (mtt) cc_final: 0.8128 (mtp) REVERT: H 58 GLU cc_start: 0.7817 (mp0) cc_final: 0.7313 (mp0) REVERT: H 100 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: H 109 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7207 (ttp80) REVERT: 1 1 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.4504 (tpt) REVERT: 1 17 MET cc_start: 0.8997 (mmm) cc_final: 0.8686 (mmt) REVERT: 1 61 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: 1 71 MET cc_start: 0.8921 (tmm) cc_final: 0.8549 (tmm) REVERT: 4 1 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.6097 (tpp) REVERT: 4 48 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7754 (ttm170) REVERT: 5 41 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6504 (ttm-80) REVERT: 8 1 MET cc_start: 0.7827 (tpt) cc_final: 0.6473 (ttt) REVERT: a 11 GLU cc_start: 0.6746 (pp20) cc_final: 0.6351 (tm-30) REVERT: a 21 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7386 (tt) REVERT: a 23 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.5800 (mpm) REVERT: a 197 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8001 (mp) REVERT: a 223 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8480 (p) REVERT: b 76 GLU cc_start: 0.8671 (pt0) cc_final: 0.8369 (pt0) REVERT: b 77 GLN cc_start: 0.8648 (tt0) cc_final: 0.8320 (tt0) REVERT: b 87 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8158 (tm-30) REVERT: b 95 GLN cc_start: 0.9138 (tt0) cc_final: 0.8826 (tp-100) REVERT: b 138 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.8788 (p0) REVERT: b 141 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8137 (tm-30) REVERT: d 186 TRP cc_start: 0.8890 (t-100) cc_final: 0.8664 (t-100) REVERT: d 260 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.8034 (ttm-80) REVERT: d 372 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7978 (tpp80) outliers start: 122 outliers final: 51 residues processed: 587 average time/residue: 0.8134 time to fit residues: 568.8735 Evaluate side-chains 561 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 486 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 49 GLU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain 6 residue 42 GLN Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 21 LEU Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 165 VAL Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain a residue 223 VAL Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 196 HIS Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 372 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 239 optimal weight: 0.0970 chunk 164 optimal weight: 3.9990 chunk 448 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 469 optimal weight: 0.4980 chunk 275 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 432 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 358 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 191 GLN A 192 ASN B 192 ASN B 437 GLN C 90 GLN C 141 HIS D 71 ASN D 256 GLN F 186 ASN G 286 GLN 1 42 GLN 1 67 ASN ** 7 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN a 190 ASN b 28 ASN b 127 GLN ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.141941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108008 restraints weight = 51284.645| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.91 r_work: 0.3166 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37821 Z= 0.148 Angle : 0.595 9.830 51304 Z= 0.297 Chirality : 0.043 0.208 5967 Planarity : 0.004 0.067 6704 Dihedral : 5.613 120.557 5368 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 2.87 % Allowed : 18.71 % Favored : 78.42 % 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: 1.23 (0.12), residues: 4839 helix: 1.86 (0.10), residues: 2615 sheet: -0.56 (0.21), residues: 579 loop : -0.28 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG d 211 TYR 0.022 0.001 TYR a 143 PHE 0.028 0.001 PHE d 297 TRP 0.017 0.001 TRP d 261 HIS 0.004 0.001 HIS a 16 Details of bonding type rmsd covalent geometry : bond 0.00342 (37821) covalent geometry : angle 0.59546 (51304) hydrogen bonds : bond 0.04372 ( 2259) hydrogen bonds : angle 4.26180 ( 6555) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 535 time to evaluate : 1.626 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 9 ASP cc_start: 0.7908 (m-30) cc_final: 0.7600 (p0) REVERT: A 16 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8710 (tm-30) REVERT: A 121 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8071 (ttm-80) REVERT: A 356 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 395 LEU cc_start: 0.7173 (mt) cc_final: 0.6690 (pp) REVERT: A 404 GLU cc_start: 0.7601 (tt0) cc_final: 0.7356 (tt0) REVERT: A 414 ASP cc_start: 0.6794 (t0) cc_final: 0.6452 (t0) REVERT: A 484 THR cc_start: 0.7894 (m) cc_final: 0.7457 (p) REVERT: A 495 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7174 (tm-30) REVERT: B 71 GLU cc_start: 0.8341 (pt0) cc_final: 0.7977 (pm20) REVERT: B 72 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7575 (p90) REVERT: B 159 MET cc_start: 0.8617 (mmm) cc_final: 0.8281 (mmm) REVERT: B 199 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7689 (tptt) REVERT: B 245 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8139 (m-10) REVERT: B 449 PHE cc_start: 0.7145 (t80) cc_final: 0.6666 (t80) REVERT: B 462 GLU cc_start: 0.8495 (pp20) cc_final: 0.8200 (pp20) REVERT: B 480 GLU cc_start: 0.7711 (pt0) cc_final: 0.6911 (pt0) REVERT: C 33 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7739 (t) REVERT: C 199 LYS cc_start: 0.8554 (mttt) cc_final: 0.7669 (tmtt) REVERT: C 200 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7711 (mtmm) REVERT: C 221 ARG cc_start: 0.7763 (ttp-170) cc_final: 0.7269 (ttm-80) REVERT: C 273 ASP cc_start: 0.7893 (m-30) cc_final: 0.7208 (t0) REVERT: C 358 ASP cc_start: 0.8052 (m-30) cc_final: 0.7822 (m-30) REVERT: C 414 ASP cc_start: 0.6644 (t70) cc_final: 0.6335 (t0) REVERT: C 466 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7390 (ttp80) REVERT: C 525 VAL cc_start: 0.7634 (t) cc_final: 0.7355 (m) REVERT: D 20 SER cc_start: 0.9067 (p) cc_final: 0.8779 (m) REVERT: D 22 ARG cc_start: 0.7753 (ttp-110) cc_final: 0.6700 (tpp-160) REVERT: D 95 ARG cc_start: 0.8010 (ptt-90) cc_final: 0.7063 (ptt90) REVERT: D 140 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: D 191 ASN cc_start: 0.8090 (m-40) cc_final: 0.7628 (p0) REVERT: D 192 PHE cc_start: 0.7919 (t80) cc_final: 0.7570 (t80) REVERT: D 239 MET cc_start: 0.8359 (mtm) cc_final: 0.8080 (mtp) REVERT: D 391 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7523 (tttm) REVERT: D 428 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7395 (mtp) REVERT: D 464 GLN cc_start: 0.7571 (mm-40) cc_final: 0.6329 (mp10) REVERT: E 95 ARG cc_start: 0.8002 (ptt90) cc_final: 0.7774 (ptt-90) REVERT: E 103 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: E 272 GLN cc_start: 0.7379 (tt0) cc_final: 0.6785 (tt0) REVERT: E 309 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7814 (mtt180) REVERT: E 346 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7450 (ttm-80) REVERT: E 368 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6373 (p0) REVERT: E 374 ASP cc_start: 0.6805 (OUTLIER) cc_final: 0.6328 (m-30) REVERT: E 399 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.6900 (mp) REVERT: F 103 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8321 (mm-30) REVERT: F 111 ASN cc_start: 0.7699 (m-40) cc_final: 0.7402 (m-40) REVERT: F 125 LYS cc_start: 0.8637 (mmtt) cc_final: 0.7733 (pmtt) REVERT: F 258 GLN cc_start: 0.7246 (tt0) cc_final: 0.6053 (pm20) REVERT: F 296 ASP cc_start: 0.7797 (m-30) cc_final: 0.7564 (m-30) REVERT: F 417 ARG cc_start: 0.7010 (mtt90) cc_final: 0.6275 (mmm160) REVERT: F 448 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: F 474 ASP cc_start: 0.7972 (m-30) cc_final: 0.7531 (m-30) REVERT: G 9 ARG cc_start: 0.6996 (mmt90) cc_final: 0.6496 (mmt180) REVERT: G 13 ARG cc_start: 0.6984 (ttp-110) cc_final: 0.6228 (ptt90) REVERT: G 44 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.6891 (ttm-80) REVERT: G 136 GLU cc_start: 0.7785 (tt0) cc_final: 0.7538 (tp30) REVERT: G 192 MET cc_start: 0.8148 (tpp) cc_final: 0.7690 (tpt) REVERT: G 198 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7178 (mm-30) REVERT: G 205 MET cc_start: 0.8290 (mtt) cc_final: 0.8058 (mtp) REVERT: H 58 GLU cc_start: 0.7758 (mp0) cc_final: 0.7283 (mp0) REVERT: H 100 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: 1 1 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.4564 (tpt) REVERT: 1 17 MET cc_start: 0.8980 (mmm) cc_final: 0.8706 (mmt) REVERT: 1 61 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: 1 68 LEU cc_start: 0.9086 (tp) cc_final: 0.8809 (tp) REVERT: 1 71 MET cc_start: 0.8939 (tmm) cc_final: 0.8510 (tmm) REVERT: 4 48 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7662 (ttm170) REVERT: 5 41 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6509 (ttm-80) REVERT: 8 1 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.6489 (ttt) REVERT: a 11 GLU cc_start: 0.6763 (pp20) cc_final: 0.6348 (tm-30) REVERT: a 72 ARG cc_start: 0.9171 (ttp-110) cc_final: 0.8957 (ttp-110) REVERT: a 85 PRO cc_start: 0.9310 (Cg_endo) cc_final: 0.9103 (Cg_exo) REVERT: a 197 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7919 (mp) REVERT: a 223 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8417 (p) REVERT: b 76 GLU cc_start: 0.8699 (pt0) cc_final: 0.8417 (pt0) REVERT: b 77 GLN cc_start: 0.8669 (tt0) cc_final: 0.8407 (tt0) REVERT: b 87 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8121 (tm-30) REVERT: b 95 GLN cc_start: 0.9145 (tt0) cc_final: 0.8815 (tp-100) REVERT: b 138 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8844 (p0) REVERT: b 141 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8139 (tm-30) REVERT: d 186 TRP cc_start: 0.8848 (t-100) cc_final: 0.8630 (t-100) REVERT: d 260 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.8076 (ttm-80) REVERT: d 308 ARG cc_start: 0.8450 (pmt170) cc_final: 0.7484 (ppp-140) REVERT: d 372 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7934 (tpp80) outliers start: 111 outliers final: 49 residues processed: 588 average time/residue: 0.7714 time to fit residues: 543.1269 Evaluate side-chains 582 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 510 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 165 VAL Chi-restraints excluded: chain a residue 176 GLU Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain a residue 223 VAL Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 196 HIS Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 372 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 306 optimal weight: 1.9990 chunk 401 optimal weight: 0.8980 chunk 349 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 377 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 464 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 191 GLN A 192 ASN B 192 ASN B 437 GLN C 141 HIS D 71 ASN D 256 GLN G 286 GLN 1 42 GLN 1 67 ASN ** 7 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107382 restraints weight = 51142.589| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.92 r_work: 0.3158 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37821 Z= 0.164 Angle : 0.615 12.686 51304 Z= 0.307 Chirality : 0.044 0.226 5967 Planarity : 0.005 0.065 6704 Dihedral : 5.639 119.286 5368 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 2.82 % Allowed : 19.28 % Favored : 77.90 % 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: 1.26 (0.12), residues: 4839 helix: 1.87 (0.10), residues: 2610 sheet: -0.51 (0.21), residues: 579 loop : -0.24 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG d 211 TYR 0.021 0.001 TYR a 143 PHE 0.027 0.001 PHE d 187 TRP 0.025 0.001 TRP d 261 HIS 0.004 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00384 (37821) covalent geometry : angle 0.61522 (51304) hydrogen bonds : bond 0.04489 ( 2259) hydrogen bonds : angle 4.29476 ( 6555) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 522 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: A 121 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8126 (ttm-80) REVERT: A 356 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: A 395 LEU cc_start: 0.7243 (mt) cc_final: 0.6740 (pt) REVERT: A 404 GLU cc_start: 0.7653 (tt0) cc_final: 0.7419 (tt0) REVERT: A 414 ASP cc_start: 0.6869 (t0) cc_final: 0.6492 (t0) REVERT: A 439 MET cc_start: 0.8811 (mtp) cc_final: 0.8426 (mtp) REVERT: A 484 THR cc_start: 0.7927 (m) cc_final: 0.7478 (p) REVERT: A 495 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 70 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7598 (t0) REVERT: B 71 GLU cc_start: 0.8305 (pt0) cc_final: 0.7746 (pm20) REVERT: B 72 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7427 (p90) REVERT: B 199 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7730 (tptt) REVERT: B 245 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: B 449 PHE cc_start: 0.7148 (t80) cc_final: 0.6653 (t80) REVERT: B 462 GLU cc_start: 0.8521 (pp20) cc_final: 0.8219 (pp20) REVERT: B 480 GLU cc_start: 0.7640 (pt0) cc_final: 0.6826 (pt0) REVERT: C 33 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7847 (t) REVERT: C 199 LYS cc_start: 0.8647 (mttt) cc_final: 0.7772 (tmtt) REVERT: C 200 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7765 (mtmm) REVERT: C 221 ARG cc_start: 0.7822 (ttp-170) cc_final: 0.7342 (ttm-80) REVERT: C 273 ASP cc_start: 0.7997 (m-30) cc_final: 0.7330 (t0) REVERT: C 358 ASP cc_start: 0.8054 (m-30) cc_final: 0.7802 (m-30) REVERT: C 414 ASP cc_start: 0.6745 (t70) cc_final: 0.6428 (t0) REVERT: C 495 GLU cc_start: 0.6386 (pt0) cc_final: 0.6102 (pt0) REVERT: C 525 VAL cc_start: 0.7654 (t) cc_final: 0.7383 (m) REVERT: D 20 SER cc_start: 0.9089 (p) cc_final: 0.8818 (m) REVERT: D 22 ARG cc_start: 0.7796 (ttp-110) cc_final: 0.6771 (tpp-160) REVERT: D 95 ARG cc_start: 0.8030 (ptt-90) cc_final: 0.7096 (ptt90) REVERT: D 140 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: D 191 ASN cc_start: 0.8152 (m-40) cc_final: 0.7686 (p0) REVERT: D 192 PHE cc_start: 0.8003 (t80) cc_final: 0.7672 (t80) REVERT: D 239 MET cc_start: 0.8383 (mtm) cc_final: 0.8122 (mtp) REVERT: D 391 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7607 (tttm) REVERT: D 428 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7400 (mtp) REVERT: D 464 GLN cc_start: 0.7621 (mm-40) cc_final: 0.6388 (mp10) REVERT: E 54 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7386 (mp0) REVERT: E 103 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: E 272 GLN cc_start: 0.7379 (tt0) cc_final: 0.6779 (tt0) REVERT: E 309 ARG cc_start: 0.8322 (mtm-85) cc_final: 0.7869 (mtt180) REVERT: E 316 MET cc_start: 0.8874 (mtp) cc_final: 0.8553 (mtp) REVERT: E 346 ARG cc_start: 0.7712 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: E 368 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6423 (p0) REVERT: E 374 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6373 (m-30) REVERT: E 399 ILE cc_start: 0.7548 (OUTLIER) cc_final: 0.6963 (mp) REVERT: F 95 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7682 (ptp-110) REVERT: F 103 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8319 (mm-30) REVERT: F 111 ASN cc_start: 0.7716 (m-40) cc_final: 0.7437 (m-40) REVERT: F 125 LYS cc_start: 0.8628 (mmtt) cc_final: 0.7758 (pmtt) REVERT: F 190 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7464 (ttm170) REVERT: F 258 GLN cc_start: 0.7255 (tt0) cc_final: 0.6179 (pm20) REVERT: F 296 ASP cc_start: 0.7813 (m-30) cc_final: 0.7593 (m-30) REVERT: F 417 ARG cc_start: 0.7135 (mtt90) cc_final: 0.6425 (mmm160) REVERT: F 448 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: F 474 ASP cc_start: 0.8076 (m-30) cc_final: 0.7645 (m-30) REVERT: G 9 ARG cc_start: 0.7040 (mmt90) cc_final: 0.6538 (mmt180) REVERT: G 13 ARG cc_start: 0.7010 (ttp-110) cc_final: 0.6279 (ptt90) REVERT: G 44 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7023 (ttm-80) REVERT: G 192 MET cc_start: 0.8031 (tpp) cc_final: 0.7691 (tpt) REVERT: G 205 MET cc_start: 0.8322 (mtt) cc_final: 0.8087 (mtp) REVERT: H 58 GLU cc_start: 0.7804 (mp0) cc_final: 0.7323 (mp0) REVERT: H 100 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7826 (mt-10) REVERT: 1 17 MET cc_start: 0.9003 (mmm) cc_final: 0.8732 (mmt) REVERT: 1 61 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: 1 68 LEU cc_start: 0.9057 (tp) cc_final: 0.8752 (tp) REVERT: 1 71 MET cc_start: 0.8944 (tmm) cc_final: 0.8506 (tmm) REVERT: 4 1 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.6069 (tpp) REVERT: 4 48 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7740 (ttm170) REVERT: 5 1 MET cc_start: 0.7555 (ttt) cc_final: 0.7125 (ttm) REVERT: 5 41 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6530 (ttm-80) REVERT: 8 1 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.6499 (ttt) REVERT: a 11 GLU cc_start: 0.6702 (pp20) cc_final: 0.6270 (tm-30) REVERT: a 23 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5766 (mpm) REVERT: a 72 ARG cc_start: 0.9157 (ttp-110) cc_final: 0.8923 (ttp-110) REVERT: a 85 PRO cc_start: 0.9297 (Cg_endo) cc_final: 0.9089 (Cg_exo) REVERT: a 197 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (mp) REVERT: a 223 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8471 (p) REVERT: b 76 GLU cc_start: 0.8696 (pt0) cc_final: 0.8427 (pt0) REVERT: b 87 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8131 (tm-30) REVERT: b 95 GLN cc_start: 0.9143 (tt0) cc_final: 0.8655 (tp40) REVERT: b 138 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8822 (p0) REVERT: b 141 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8134 (tm-30) REVERT: b 151 MET cc_start: 0.8536 (tpt) cc_final: 0.8296 (mmp) REVERT: d 101 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8249 (tm130) REVERT: d 123 HIS cc_start: 0.8649 (t70) cc_final: 0.8382 (t-170) REVERT: d 260 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8133 (ttm-80) REVERT: d 372 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7967 (tpp80) REVERT: d 404 HIS cc_start: 0.8425 (m170) cc_final: 0.7921 (m90) outliers start: 109 outliers final: 54 residues processed: 577 average time/residue: 0.7420 time to fit residues: 512.4945 Evaluate side-chains 585 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 505 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 428 MET Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain a residue 223 VAL Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 101 GLN Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 363 LEU Chi-restraints excluded: chain d residue 372 ARG Chi-restraints excluded: chain d residue 406 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 360 optimal weight: 0.5980 chunk 447 optimal weight: 7.9990 chunk 305 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 372 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 384 optimal weight: 0.6980 chunk 313 optimal weight: 0.7980 chunk 357 optimal weight: 0.9980 chunk 418 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 192 ASN B 192 ASN B 437 GLN C 141 HIS D 71 ASN D 256 GLN G 286 GLN 1 67 ASN ** 9 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN b 132 GLN d 140 GLN ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.109252 restraints weight = 51040.397| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.95 r_work: 0.3189 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37821 Z= 0.126 Angle : 0.602 11.171 51304 Z= 0.298 Chirality : 0.042 0.269 5967 Planarity : 0.004 0.070 6704 Dihedral : 5.376 115.893 5368 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.23 % Favored : 97.73 % Rotamer: Outliers : 2.17 % Allowed : 19.95 % Favored : 77.88 % 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: 1.42 (0.12), residues: 4839 helix: 2.03 (0.10), residues: 2618 sheet: -0.51 (0.21), residues: 586 loop : -0.22 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG d 211 TYR 0.023 0.001 TYR a 143 PHE 0.036 0.001 PHE d 187 TRP 0.039 0.001 TRP d 186 HIS 0.004 0.001 HIS d 348 Details of bonding type rmsd covalent geometry : bond 0.00279 (37821) covalent geometry : angle 0.60196 (51304) hydrogen bonds : bond 0.04121 ( 2259) hydrogen bonds : angle 4.18069 ( 6555) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 556 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8060 (ttm-80) REVERT: A 395 LEU cc_start: 0.7172 (mt) cc_final: 0.6679 (pt) REVERT: A 404 GLU cc_start: 0.7568 (tt0) cc_final: 0.7342 (tt0) REVERT: A 414 ASP cc_start: 0.6796 (t0) cc_final: 0.6406 (t0) REVERT: A 439 MET cc_start: 0.8751 (mtp) cc_final: 0.8389 (mtp) REVERT: A 484 THR cc_start: 0.7896 (m) cc_final: 0.7462 (p) REVERT: A 495 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 71 GLU cc_start: 0.8291 (pt0) cc_final: 0.7933 (pm20) REVERT: B 72 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7565 (p90) REVERT: B 159 MET cc_start: 0.8626 (mmm) cc_final: 0.8323 (mmm) REVERT: B 199 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7667 (tptt) REVERT: B 245 PHE cc_start: 0.8906 (OUTLIER) cc_final: 0.8078 (m-10) REVERT: B 449 PHE cc_start: 0.7149 (t80) cc_final: 0.6665 (t80) REVERT: B 462 GLU cc_start: 0.8489 (pp20) cc_final: 0.8207 (pp20) REVERT: B 463 ASP cc_start: 0.8003 (m-30) cc_final: 0.7780 (m-30) REVERT: B 480 GLU cc_start: 0.7671 (pt0) cc_final: 0.6814 (pt0) REVERT: C 33 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7879 (t) REVERT: C 199 LYS cc_start: 0.8540 (mttt) cc_final: 0.7628 (tmtt) REVERT: C 200 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7668 (mtmm) REVERT: C 221 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7274 (ttm-80) REVERT: C 273 ASP cc_start: 0.7787 (m-30) cc_final: 0.7127 (t0) REVERT: C 317 ASP cc_start: 0.8244 (m-30) cc_final: 0.7974 (m-30) REVERT: C 358 ASP cc_start: 0.8041 (m-30) cc_final: 0.7776 (m-30) REVERT: C 414 ASP cc_start: 0.6597 (t70) cc_final: 0.6302 (t0) REVERT: C 525 VAL cc_start: 0.7612 (t) cc_final: 0.7352 (m) REVERT: D 20 SER cc_start: 0.9072 (p) cc_final: 0.8822 (m) REVERT: D 22 ARG cc_start: 0.7756 (ttp-110) cc_final: 0.6724 (tpp-160) REVERT: D 95 ARG cc_start: 0.8002 (ptt-90) cc_final: 0.7046 (ptt90) REVERT: D 191 ASN cc_start: 0.8077 (m-40) cc_final: 0.7613 (p0) REVERT: D 192 PHE cc_start: 0.7866 (t80) cc_final: 0.7518 (t80) REVERT: D 239 MET cc_start: 0.8265 (mtm) cc_final: 0.7951 (mtp) REVERT: D 368 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: D 391 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7521 (tttm) REVERT: D 464 GLN cc_start: 0.7469 (mm-40) cc_final: 0.6225 (mp10) REVERT: E 54 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7356 (mp0) REVERT: E 95 ARG cc_start: 0.7971 (ptt90) cc_final: 0.7747 (ptt-90) REVERT: E 103 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7674 (tp30) REVERT: E 272 GLN cc_start: 0.7310 (tt0) cc_final: 0.6904 (tt0) REVERT: E 309 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7758 (mtt180) REVERT: E 316 MET cc_start: 0.8823 (mtp) cc_final: 0.8493 (mtp) REVERT: E 346 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7363 (ttm-80) REVERT: E 368 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6402 (p0) REVERT: E 374 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6309 (m-30) REVERT: E 399 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.6919 (mp) REVERT: F 22 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7384 (ptm160) REVERT: F 27 THR cc_start: 0.7948 (m) cc_final: 0.7621 (t) REVERT: F 95 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7587 (ptp-110) REVERT: F 98 SER cc_start: 0.8939 (p) cc_final: 0.8719 (m) REVERT: F 103 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8326 (mm-30) REVERT: F 111 ASN cc_start: 0.7627 (m-40) cc_final: 0.7321 (m-40) REVERT: F 125 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7719 (pmtt) REVERT: F 190 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7404 (ttm170) REVERT: F 258 GLN cc_start: 0.7157 (tt0) cc_final: 0.6047 (pm20) REVERT: F 296 ASP cc_start: 0.7777 (m-30) cc_final: 0.7558 (m-30) REVERT: F 391 LYS cc_start: 0.7964 (ttpt) cc_final: 0.7329 (ttmt) REVERT: F 417 ARG cc_start: 0.6944 (mtt90) cc_final: 0.6194 (mmm160) REVERT: F 448 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: F 474 ASP cc_start: 0.7968 (m-30) cc_final: 0.7478 (m-30) REVERT: G 9 ARG cc_start: 0.6979 (mmt90) cc_final: 0.6485 (mmt180) REVERT: G 13 ARG cc_start: 0.6921 (ttp-110) cc_final: 0.6259 (ptt90) REVERT: G 44 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.6820 (ttm-80) REVERT: G 139 MET cc_start: 0.6961 (mmt) cc_final: 0.5220 (pmm) REVERT: G 192 MET cc_start: 0.7897 (tpp) cc_final: 0.7524 (tpt) REVERT: G 234 LEU cc_start: 0.8499 (mt) cc_final: 0.8105 (tt) REVERT: H 58 GLU cc_start: 0.7681 (mp0) cc_final: 0.7174 (mp0) REVERT: 1 17 MET cc_start: 0.8970 (mmm) cc_final: 0.8681 (mmt) REVERT: 1 61 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: 1 68 LEU cc_start: 0.9049 (tp) cc_final: 0.8768 (tp) REVERT: 1 71 MET cc_start: 0.8960 (tmm) cc_final: 0.8540 (tmm) REVERT: 4 1 MET cc_start: 0.6413 (ttp) cc_final: 0.6121 (tpp) REVERT: 4 48 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7657 (ttm170) REVERT: 5 17 MET cc_start: 0.8929 (mmm) cc_final: 0.8726 (mmt) REVERT: 5 41 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6403 (ttm-80) REVERT: 8 1 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.6499 (ttt) REVERT: a 11 GLU cc_start: 0.6818 (pp20) cc_final: 0.6342 (tm-30) REVERT: a 72 ARG cc_start: 0.9146 (ttp-110) cc_final: 0.8900 (ttp-110) REVERT: a 85 PRO cc_start: 0.9271 (Cg_endo) cc_final: 0.9070 (Cg_exo) REVERT: a 197 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7947 (mp) REVERT: b 76 GLU cc_start: 0.8692 (pt0) cc_final: 0.8348 (pt0) REVERT: b 77 GLN cc_start: 0.8669 (tt0) cc_final: 0.8415 (tt0) REVERT: b 87 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8149 (tm-30) REVERT: b 127 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8509 (pp30) REVERT: b 138 ASP cc_start: 0.9298 (OUTLIER) cc_final: 0.8818 (p0) REVERT: b 141 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8351 (tm-30) REVERT: d 123 HIS cc_start: 0.8668 (t70) cc_final: 0.8398 (t-170) REVERT: d 260 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.8103 (ttm-80) REVERT: d 308 ARG cc_start: 0.8377 (pmt170) cc_final: 0.7109 (ppp-140) REVERT: d 372 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7963 (tpp80) REVERT: d 404 HIS cc_start: 0.8393 (m170) cc_final: 0.7887 (m90) outliers start: 84 outliers final: 49 residues processed: 600 average time/residue: 0.7703 time to fit residues: 554.1835 Evaluate side-chains 579 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 512 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 5 residue 41 ARG Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 197 LEU Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 73 LYS Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 127 GLN Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 372 ARG Chi-restraints excluded: chain d residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 147 optimal weight: 0.4980 chunk 406 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 386 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 439 optimal weight: 6.9990 chunk 460 optimal weight: 2.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN B 437 GLN C 141 HIS C 143 GLN D 71 ASN G 125 ASN G 286 GLN ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 67 ASN 6 42 GLN ** 9 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.138983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.104967 restraints weight = 51339.296| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.89 r_work: 0.3121 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 37821 Z= 0.223 Angle : 0.667 11.980 51304 Z= 0.335 Chirality : 0.046 0.299 5967 Planarity : 0.005 0.087 6704 Dihedral : 5.822 118.496 5368 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.87 % Favored : 97.09 % Rotamer: Outliers : 2.20 % Allowed : 20.36 % Favored : 77.44 % 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: 1.15 (0.12), residues: 4839 helix: 1.73 (0.10), residues: 2621 sheet: -0.49 (0.22), residues: 570 loop : -0.25 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 1 48 TYR 0.019 0.002 TYR a 143 PHE 0.026 0.002 PHE d 297 TRP 0.035 0.002 TRP d 186 HIS 0.010 0.001 HIS d 348 Details of bonding type rmsd covalent geometry : bond 0.00540 (37821) covalent geometry : angle 0.66744 (51304) hydrogen bonds : bond 0.04885 ( 2259) hydrogen bonds : angle 4.42162 ( 6555) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 512 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLN cc_start: 0.8082 (pp30) cc_final: 0.7785 (pp30) REVERT: A 16 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8707 (tm-30) REVERT: A 121 ARG cc_start: 0.8481 (mtp85) cc_final: 0.8114 (ttm-80) REVERT: A 356 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: A 395 LEU cc_start: 0.7254 (mt) cc_final: 0.6715 (pt) REVERT: A 414 ASP cc_start: 0.6922 (t0) cc_final: 0.6572 (t0) REVERT: A 484 THR cc_start: 0.7924 (m) cc_final: 0.7472 (p) REVERT: A 495 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7261 (tm-30) REVERT: B 70 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7755 (t0) REVERT: B 71 GLU cc_start: 0.8301 (pt0) cc_final: 0.7944 (pt0) REVERT: B 72 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7454 (p90) REVERT: B 199 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7747 (tptt) REVERT: B 245 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8128 (m-10) REVERT: B 449 PHE cc_start: 0.7099 (t80) cc_final: 0.6634 (t80) REVERT: B 462 GLU cc_start: 0.8530 (pp20) cc_final: 0.8237 (pp20) REVERT: B 480 GLU cc_start: 0.7649 (pt0) cc_final: 0.6785 (pt0) REVERT: C 159 MET cc_start: 0.8843 (mtm) cc_final: 0.8629 (mmm) REVERT: C 199 LYS cc_start: 0.8602 (mttt) cc_final: 0.7718 (tmtt) REVERT: C 200 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7749 (mtmm) REVERT: C 221 ARG cc_start: 0.7832 (ttp-170) cc_final: 0.7353 (ttm-80) REVERT: C 358 ASP cc_start: 0.8065 (m-30) cc_final: 0.7844 (m-30) REVERT: C 414 ASP cc_start: 0.6826 (t70) cc_final: 0.6500 (t0) REVERT: C 525 VAL cc_start: 0.7721 (t) cc_final: 0.7478 (p) REVERT: D 20 SER cc_start: 0.9108 (p) cc_final: 0.8852 (m) REVERT: D 22 ARG cc_start: 0.7805 (ttp-110) cc_final: 0.6770 (tpp-160) REVERT: D 95 ARG cc_start: 0.8054 (ptt-90) cc_final: 0.7112 (ptt90) REVERT: D 191 ASN cc_start: 0.8157 (m-40) cc_final: 0.7679 (p0) REVERT: D 192 PHE cc_start: 0.7992 (t80) cc_final: 0.7685 (t80) REVERT: D 239 MET cc_start: 0.8458 (mtm) cc_final: 0.8239 (mtp) REVERT: D 391 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7595 (tttm) REVERT: D 464 GLN cc_start: 0.7605 (mm-40) cc_final: 0.6378 (mp10) REVERT: D 474 ASP cc_start: 0.8345 (m-30) cc_final: 0.8116 (m-30) REVERT: E 54 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7391 (mp0) REVERT: E 103 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: E 272 GLN cc_start: 0.7377 (tt0) cc_final: 0.6786 (tt0) REVERT: E 309 ARG cc_start: 0.8334 (mtm-85) cc_final: 0.7880 (mtt180) REVERT: E 346 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7462 (ttm-80) REVERT: E 368 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6401 (p0) REVERT: E 374 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6385 (m-30) REVERT: E 399 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.6999 (mp) REVERT: F 22 ARG cc_start: 0.8261 (ttp-110) cc_final: 0.7527 (ptm160) REVERT: F 103 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8275 (mm-30) REVERT: F 125 LYS cc_start: 0.8622 (mmtt) cc_final: 0.7752 (pmtt) REVERT: F 190 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7465 (ttm170) REVERT: F 258 GLN cc_start: 0.7317 (tt0) cc_final: 0.6217 (pm20) REVERT: F 296 ASP cc_start: 0.7825 (m-30) cc_final: 0.7606 (m-30) REVERT: F 417 ARG cc_start: 0.7155 (mtt90) cc_final: 0.6428 (mmm160) REVERT: F 448 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: F 474 ASP cc_start: 0.8072 (m-30) cc_final: 0.7637 (m-30) REVERT: G 9 ARG cc_start: 0.7134 (mmt90) cc_final: 0.6642 (mmt180) REVERT: G 192 MET cc_start: 0.7943 (tpp) cc_final: 0.7572 (tpt) REVERT: G 228 MET cc_start: 0.8111 (tpp) cc_final: 0.7696 (tpp) REVERT: H 58 GLU cc_start: 0.7803 (mp0) cc_final: 0.7219 (mp0) REVERT: 1 17 MET cc_start: 0.9008 (mmm) cc_final: 0.8749 (mmt) REVERT: 1 61 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: 1 68 LEU cc_start: 0.9061 (tp) cc_final: 0.8750 (tp) REVERT: 1 71 MET cc_start: 0.8933 (tmm) cc_final: 0.8536 (tmm) REVERT: 4 1 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6240 (tpp) REVERT: 4 48 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7796 (ttm170) REVERT: 5 1 MET cc_start: 0.7610 (ttt) cc_final: 0.7395 (tmm) REVERT: 8 1 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6526 (ttp) REVERT: a 72 ARG cc_start: 0.9168 (ttp-110) cc_final: 0.8929 (ttp-110) REVERT: a 85 PRO cc_start: 0.9276 (Cg_endo) cc_final: 0.9071 (Cg_exo) REVERT: b 76 GLU cc_start: 0.8688 (pt0) cc_final: 0.8333 (pt0) REVERT: b 77 GLN cc_start: 0.8668 (tt0) cc_final: 0.8387 (tt0) REVERT: b 87 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8215 (tm-30) REVERT: b 138 ASP cc_start: 0.9321 (OUTLIER) cc_final: 0.8803 (p0) REVERT: b 141 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8225 (tm-30) REVERT: b 152 SER cc_start: 0.8922 (m) cc_final: 0.7287 (m) REVERT: d 123 HIS cc_start: 0.8613 (t70) cc_final: 0.8347 (t-170) REVERT: d 128 GLN cc_start: 0.9035 (tp40) cc_final: 0.8669 (tt0) REVERT: d 186 TRP cc_start: 0.8767 (t-100) cc_final: 0.8513 (t-100) REVERT: d 187 PHE cc_start: 0.8868 (t80) cc_final: 0.8642 (t80) REVERT: d 260 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8161 (ttm-80) REVERT: d 372 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8051 (tpp80) REVERT: d 404 HIS cc_start: 0.8440 (m170) cc_final: 0.7930 (m90) outliers start: 85 outliers final: 50 residues processed: 555 average time/residue: 0.8279 time to fit residues: 549.3335 Evaluate side-chains 568 residues out of total 3866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 501 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 356 GLU Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 429 GLU Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 214 GLU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 480 GLU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 448 GLU Chi-restraints excluded: chain F residue 453 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 83 SER Chi-restraints excluded: chain 1 residue 61 GLU Chi-restraints excluded: chain 1 residue 78 THR Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 48 ARG Chi-restraints excluded: chain 5 residue 4 THR Chi-restraints excluded: chain 8 residue 1 MET Chi-restraints excluded: chain 9 residue 37 SER Chi-restraints excluded: chain a residue 38 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 HIS Chi-restraints excluded: chain a residue 184 SER Chi-restraints excluded: chain a residue 204 PHE Chi-restraints excluded: chain b residue 90 THR Chi-restraints excluded: chain b residue 97 SER Chi-restraints excluded: chain b residue 127 GLN Chi-restraints excluded: chain b residue 138 ASP Chi-restraints excluded: chain d residue 70 HIS Chi-restraints excluded: chain d residue 126 VAL Chi-restraints excluded: chain d residue 218 VAL Chi-restraints excluded: chain d residue 219 VAL Chi-restraints excluded: chain d residue 337 THR Chi-restraints excluded: chain d residue 372 ARG Chi-restraints excluded: chain d residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 32 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 422 optimal weight: 3.9990 chunk 282 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 355 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 447 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN B 192 ASN B 437 GLN C 141 HIS D 256 GLN G 125 ASN G 286 GLN 1 67 ASN 6 42 GLN ** 9 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 16 HIS ** a 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 127 GLN ** d 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.142521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108749 restraints weight = 51021.069| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.89 r_work: 0.3185 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37821 Z= 0.133 Angle : 0.624 11.512 51304 Z= 0.308 Chirality : 0.043 0.277 5967 Planarity : 0.005 0.090 6704 Dihedral : 5.477 117.965 5368 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.15 % Favored : 97.81 % Rotamer: Outliers : 1.97 % Allowed : 20.52 % Favored : 77.52 % 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: 1.38 (0.12), residues: 4839 helix: 1.98 (0.10), residues: 2616 sheet: -0.48 (0.21), residues: 575 loop : -0.23 (0.16), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG d 211 TYR 0.022 0.001 TYR a 143 PHE 0.022 0.001 PHE d 297 TRP 0.032 0.001 TRP d 186 HIS 0.013 0.001 HIS d 348 Details of bonding type rmsd covalent geometry : bond 0.00298 (37821) covalent geometry : angle 0.62359 (51304) hydrogen bonds : bond 0.04222 ( 2259) hydrogen bonds : angle 4.23376 ( 6555) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16348.34 seconds wall clock time: 278 minutes 11.01 seconds (16691.01 seconds total)