Starting phenix.real_space_refine on Sun Aug 9 13:57:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1p_66466/08_2026/9x1p_66466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1p_66466/08_2026/9x1p_66466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9x1p_66466/08_2026/9x1p_66466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1p_66466/08_2026/9x1p_66466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9x1p_66466/08_2026/9x1p_66466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1p_66466/08_2026/9x1p_66466.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 5 7.51 5 P 41 5.49 5 S 99 5.16 5 C 21604 2.51 5 N 5961 2.21 5 O 6570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34280 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "B" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "C" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "D" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "E" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "F" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4529 Classifications: {'peptide': 578} Link IDs: {'PTRANS': 18, 'TRANS': 559} Chain: "G" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3197 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain breaks: 1 Chain: "H" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3197 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 14, 'TRANS': 380} Chain breaks: 1 Chain: "I" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "J" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 260 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 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: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.69, per 1000 atoms: 0.22 Number of scatterers: 34280 At special positions: 0 Unit cell: (135.36, 154.912, 184.24, 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) Mn 5 24.99 S 99 16.00 P 41 15.00 O 6570 8.00 N 5961 7.00 C 21604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7724 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 23 sheets defined 46.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 84 through 95 Processing helix chain 'A' and resid 95 through 102 removed outlier: 3.528A pdb=" N GLU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASN A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 190 through 207 removed outlier: 3.687A pdb=" N LEU A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.655A pdb=" N ALA A 243 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 320 through 341 Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.521A pdb=" N LEU A 352 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 348 through 353' Processing helix chain 'A' and resid 367 through 401 Processing helix chain 'A' and resid 407 through 428 removed outlier: 3.760A pdb=" N ASP A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.551A pdb=" N PHE A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 469 removed outlier: 5.430A pdb=" N ARG A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LYS A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 512 through 521 removed outlier: 4.332A pdb=" N GLU A 517 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP A 521 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 578 Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 84 through 96 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 141 through 149 Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 191 through 204 Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 259 through 277 Processing helix chain 'B' and resid 282 through 300 removed outlier: 3.641A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 340 Processing helix chain 'B' and resid 367 through 402 removed outlier: 3.775A pdb=" N LEU B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.693A pdb=" N ILE B 407 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 428 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.557A pdb=" N ALA B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 433' Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.098A pdb=" N PHE B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 469 removed outlier: 6.292A pdb=" N ARG B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N LYS B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 483 through 488 Processing helix chain 'B' and resid 500 through 511 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 547 through 552 Processing helix chain 'B' and resid 561 through 578 removed outlier: 3.986A pdb=" N LYS B 577 " --> pdb=" O GLU B 573 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 96 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.495A pdb=" N GLY C 100 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 149 Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 192 through 205 Processing helix chain 'C' and resid 240 through 244 removed outlier: 4.206A pdb=" N ALA C 243 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET C 244 " --> pdb=" O PRO C 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 244' Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.665A pdb=" N LEU C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 277 Processing helix chain 'C' and resid 281 through 299 removed outlier: 3.836A pdb=" N ALA C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 340 Processing helix chain 'C' and resid 348 through 353 removed outlier: 3.702A pdb=" N LEU C 352 " --> pdb=" O ASP C 348 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 353 " --> pdb=" O ILE C 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 348 through 353' Processing helix chain 'C' and resid 367 through 402 Processing helix chain 'C' and resid 410 through 428 removed outlier: 3.687A pdb=" N ILE C 414 " --> pdb=" O VAL C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 433 removed outlier: 3.915A pdb=" N GLU C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.867A pdb=" N PHE C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 465 removed outlier: 3.996A pdb=" N ILE C 457 " --> pdb=" O GLY C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 490 removed outlier: 3.973A pdb=" N THR C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 514 through 524 removed outlier: 4.878A pdb=" N SER C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA C 523 " --> pdb=" O MET C 519 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY C 524 " --> pdb=" O SER C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 552 Processing helix chain 'C' and resid 562 through 578 Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.598A pdb=" N ARG D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 49 through 54' Processing helix chain 'D' and resid 84 through 95 Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 141 through 149 Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 245 through 253 Processing helix chain 'D' and resid 259 through 277 Processing helix chain 'D' and resid 282 through 299 removed outlier: 4.098A pdb=" N VAL D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 339 removed outlier: 4.023A pdb=" N GLU D 324 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 344 removed outlier: 3.548A pdb=" N LEU D 344 " --> pdb=" O GLY D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 403 Processing helix chain 'D' and resid 410 through 428 Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.208A pdb=" N PHE D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 465 Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 483 through 488 Processing helix chain 'D' and resid 500 through 511 Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.605A pdb=" N ASP D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA D 523 " --> pdb=" O MET D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 552 Processing helix chain 'D' and resid 561 through 578 removed outlier: 3.619A pdb=" N ARG D 565 " --> pdb=" O GLY D 561 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.839A pdb=" N TRP E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.921A pdb=" N GLU E 80 " --> pdb=" O TRP E 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 80' Processing helix chain 'E' and resid 84 through 96 Processing helix chain 'E' and resid 141 through 149 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 190 through 203 removed outlier: 3.935A pdb=" N VAL E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 253 Processing helix chain 'E' and resid 259 through 277 Processing helix chain 'E' and resid 282 through 300 removed outlier: 3.800A pdb=" N VAL E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 341 removed outlier: 4.006A pdb=" N TYR E 340 " --> pdb=" O PHE E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 399 Processing helix chain 'E' and resid 406 through 409 Processing helix chain 'E' and resid 410 through 428 removed outlier: 3.991A pdb=" N ILE E 414 " --> pdb=" O VAL E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.780A pdb=" N PHE E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 469 removed outlier: 4.070A pdb=" N ARG E 456 " --> pdb=" O GLY E 452 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE E 457 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS E 467 " --> pdb=" O ARG E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 483 through 490 Processing helix chain 'E' and resid 500 through 511 Processing helix chain 'E' and resid 515 through 523 Processing helix chain 'E' and resid 548 through 552 Processing helix chain 'E' and resid 561 through 578 removed outlier: 3.789A pdb=" N ARG E 565 " --> pdb=" O GLY E 561 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 55 removed outlier: 3.592A pdb=" N TRP F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 84 through 96 Processing helix chain 'F' and resid 96 through 102 removed outlier: 4.395A pdb=" N GLY F 100 " --> pdb=" O GLY F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 149 Processing helix chain 'F' and resid 173 through 179 Processing helix chain 'F' and resid 190 through 206 removed outlier: 4.067A pdb=" N THR F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 253 Processing helix chain 'F' and resid 260 through 277 Processing helix chain 'F' and resid 281 through 300 removed outlier: 3.545A pdb=" N VAL F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 340 Processing helix chain 'F' and resid 367 through 403 Processing helix chain 'F' and resid 406 through 409 removed outlier: 3.588A pdb=" N ALA F 409 " --> pdb=" O ASN F 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 406 through 409' Processing helix chain 'F' and resid 410 through 428 Processing helix chain 'F' and resid 441 through 446 removed outlier: 4.145A pdb=" N PHE F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 469 removed outlier: 5.437A pdb=" N ARG F 466 " --> pdb=" O ALA F 462 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LYS F 467 " --> pdb=" O ARG F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 488 Processing helix chain 'F' and resid 500 through 511 removed outlier: 3.505A pdb=" N SER F 511 " --> pdb=" O VAL F 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 520 removed outlier: 3.608A pdb=" N SER F 520 " --> pdb=" O GLY F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 578 Processing helix chain 'G' and resid 6 through 27 removed outlier: 3.901A pdb=" N ARG G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 90 through 113 removed outlier: 3.677A pdb=" N LEU G 106 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 131 Processing helix chain 'G' and resid 134 through 148 removed outlier: 3.692A pdb=" N VAL G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS G 140 " --> pdb=" O PRO G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 179 removed outlier: 3.760A pdb=" N GLU G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.934A pdb=" N GLU G 191 " --> pdb=" O ILE G 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 187 through 192' Processing helix chain 'G' and resid 193 through 196 Processing helix chain 'G' and resid 197 through 202 Processing helix chain 'G' and resid 258 through 277 removed outlier: 3.536A pdb=" N VAL G 262 " --> pdb=" O ALA G 258 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 318 removed outlier: 3.594A pdb=" N TYR G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA G 311 " --> pdb=" O PRO G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 343 removed outlier: 4.119A pdb=" N LEU G 342 " --> pdb=" O PRO G 339 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G 343 " --> pdb=" O LYS G 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 339 through 343' Processing helix chain 'G' and resid 346 through 356 removed outlier: 3.821A pdb=" N GLU G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 388 Processing helix chain 'G' and resid 396 through 406 Processing helix chain 'G' and resid 409 through 428 Processing helix chain 'H' and resid 6 through 26 removed outlier: 3.965A pdb=" N ILE H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 113 removed outlier: 4.285A pdb=" N LEU H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 130 removed outlier: 3.785A pdb=" N THR H 130 " --> pdb=" O THR H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 149 Processing helix chain 'H' and resid 150 through 179 removed outlier: 4.534A pdb=" N LYS H 155 " --> pdb=" O LYS H 151 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU H 157 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL H 158 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS H 159 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS H 160 " --> pdb=" O GLU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 201 removed outlier: 5.263A pdb=" N GLU H 198 " --> pdb=" O GLU H 195 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS H 201 " --> pdb=" O GLU H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 279 Processing helix chain 'H' and resid 293 through 300 removed outlier: 4.374A pdb=" N LYS H 298 " --> pdb=" O LYS H 294 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 317 removed outlier: 3.523A pdb=" N TYR H 308 " --> pdb=" O VAL H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 345 Processing helix chain 'H' and resid 346 through 356 removed outlier: 3.696A pdb=" N GLU H 350 " --> pdb=" O PHE H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 388 Processing helix chain 'H' and resid 397 through 406 Processing helix chain 'H' and resid 409 through 428 removed outlier: 3.782A pdb=" N ALA H 415 " --> pdb=" O LYS H 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15 removed outlier: 4.379A pdb=" N GLN A 24 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 13 through 15 removed outlier: 4.379A pdb=" N GLN A 24 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 104 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ASN A 73 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE A 106 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 71 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 108 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE A 65 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 168 through 172 removed outlier: 6.919A pdb=" N VAL A 169 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A 182 " --> pdb=" O THR A 492 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE A 181 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER A 476 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE A 183 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 435 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLY A 473 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 437 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL A 475 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET A 436 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 210 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE A 361 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 212 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 360 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.019A pdb=" N ILE B 65 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 108 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 75 removed outlier: 5.144A pdb=" N LEU B 105 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN B 24 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 172 removed outlier: 6.580A pdb=" N VAL B 169 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 184 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE B 181 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER B 476 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILE B 183 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AA9, first strand: chain 'B' and resid 302 through 305 removed outlier: 6.657A pdb=" N GLY B 302 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 125 removed outlier: 6.845A pdb=" N ALA C 104 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN C 73 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE C 106 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 71 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N THR C 108 " --> pdb=" O ARG C 69 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE C 65 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN C 24 " --> pdb=" O THR C 15 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU C 17 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER C 22 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE C 23 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU C 105 " --> pdb=" O ALA C 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 168 through 172 removed outlier: 6.906A pdb=" N VAL C 169 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 160 " --> pdb=" O LYS C 544 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 495 " --> pdb=" O VAL C 531 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA C 182 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C 181 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER C 476 " --> pdb=" O PHE C 181 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE C 183 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU C 440 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL C 210 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 361 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 212 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 360 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 235 " --> pdb=" O VAL C 360 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 125 removed outlier: 6.239A pdb=" N HIS D 110 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE D 68 " --> pdb=" O HIS D 110 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU D 112 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY D 66 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS D 114 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL D 64 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 39 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG D 42 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 136 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY D 12 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN D 24 " --> pdb=" O THR D 15 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU D 105 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 168 through 172 removed outlier: 3.820A pdb=" N GLY D 159 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 171 " --> pdb=" O GLU D 157 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU D 157 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 435 " --> pdb=" O GLY D 471 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLY D 473 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 437 " --> pdb=" O GLY D 473 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL D 475 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 439 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR D 209 " --> pdb=" O MET D 436 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE D 438 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 211 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLU D 440 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU D 213 " --> pdb=" O GLU D 440 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL D 210 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE D 361 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL D 212 " --> pdb=" O ILE D 361 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AB6, first strand: chain 'E' and resid 12 through 15 removed outlier: 4.215A pdb=" N GLN E 24 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 27 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU E 105 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 12 through 15 removed outlier: 4.215A pdb=" N GLN E 24 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA E 27 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU E 105 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY E 70 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS E 110 " --> pdb=" O ILE E 68 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE E 68 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU E 112 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY E 66 " --> pdb=" O LEU E 112 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS E 114 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL E 64 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 18 through 19 removed outlier: 3.668A pdb=" N ALA E 18 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN F 73 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN F 24 " --> pdb=" O THR F 15 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU F 105 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 18 through 19 removed outlier: 3.668A pdb=" N ALA E 18 " --> pdb=" O ASN F 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN F 73 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 64 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS F 114 " --> pdb=" O VAL F 64 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY F 66 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU F 112 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE F 68 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS F 110 " --> pdb=" O ILE F 68 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY F 70 " --> pdb=" O THR F 108 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 168 through 172 removed outlier: 3.912A pdb=" N GLY E 159 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU E 171 " --> pdb=" O GLU E 157 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU E 157 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA E 182 " --> pdb=" O ILE E 494 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE E 181 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N SER E 476 " --> pdb=" O PHE E 181 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE E 183 " --> pdb=" O SER E 476 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL E 435 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N GLY E 473 " --> pdb=" O VAL E 435 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL E 437 " --> pdb=" O GLY E 473 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL E 475 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 439 " --> pdb=" O VAL E 475 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE E 211 " --> pdb=" O ILE E 438 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU E 440 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU E 213 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 168 through 172 removed outlier: 7.192A pdb=" N VAL F 169 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA F 541 " --> pdb=" O ILE F 532 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 532 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA F 182 " --> pdb=" O ILE F 494 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE F 181 " --> pdb=" O LEU F 474 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N SER F 476 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE F 183 " --> pdb=" O SER F 476 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL F 437 " --> pdb=" O GLY F 471 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE F 211 " --> pdb=" O ILE F 438 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N GLU F 440 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU F 213 " --> pdb=" O GLU F 440 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 210 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE F 361 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL F 212 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU F 363 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP F 214 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 76 through 84 removed outlier: 4.731A pdb=" N ASP G 122 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY G 50 " --> pdb=" O ASP G 122 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL G 286 " --> pdb=" O MET G 121 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET G 359 " --> pdb=" O ILE G 327 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE G 327 " --> pdb=" O MET G 359 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY G 323 " --> pdb=" O ARG G 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 181 through 183 removed outlier: 6.134A pdb=" N ARG H 77 " --> pdb=" O ILE H 182 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR H 46 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ASP H 122 " --> pdb=" O TYR H 46 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N VAL H 48 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL H 119 " --> pdb=" O VAL H 284 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL H 286 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET H 121 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR H 361 " --> pdb=" O ILE H 326 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE H 326 " --> pdb=" O TYR H 361 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ARG H 363 " --> pdb=" O TYR H 324 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TYR H 324 " --> pdb=" O ARG H 363 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 391 through 392 1624 hydrogen bonds defined for protein. 4665 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: 5.78 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 11559 1.36 - 1.51: 8930 1.51 - 1.66: 14256 1.66 - 1.80: 133 1.80 - 1.95: 50 Bond restraints: 34928 Sorted by residual: bond pdb=" O3B AGS A 601 " pdb=" PB AGS A 601 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O3B AGS F 601 " pdb=" PB AGS F 601 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O3B AGS B 601 " pdb=" PB AGS B 601 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3A AGS B 601 " pdb=" PA AGS B 601 " ideal model delta sigma weight residual 1.664 1.576 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" O3A AGS A 601 " pdb=" PA AGS A 601 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 34923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 46875 2.18 - 4.36: 371 4.36 - 6.54: 47 6.54 - 8.73: 15 8.73 - 10.91: 10 Bond angle restraints: 47318 Sorted by residual: angle pdb=" N3 DT J 8 " pdb=" C4 DT J 8 " pdb=" O4 DT J 8 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT J 11 " pdb=" C4 DT J 11 " pdb=" O4 DT J 11 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT J 4 " pdb=" C4 DT J 4 " pdb=" O4 DT J 4 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT J 10 " pdb=" C4 DT J 10 " pdb=" O4 DT J 10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT J 13 " pdb=" C4 DT J 13 " pdb=" O4 DT J 13 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 47313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 20752 33.69 - 67.38: 328 67.38 - 101.07: 10 101.07 - 134.76: 1 134.76 - 168.45: 2 Dihedral angle restraints: 21093 sinusoidal: 8943 harmonic: 12150 Sorted by residual: dihedral pdb=" O2A ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PA ADP D 601 " pdb=" PB ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 43.96 -103.96 1 2.00e+01 2.50e-03 2.98e+01 dihedral pdb=" O1B ADP D 601 " pdb=" O3A ADP D 601 " pdb=" PB ADP D 601 " pdb=" PA ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 26.46 -86.46 1 2.00e+01 2.50e-03 2.25e+01 dihedral pdb=" O1B AGS A 601 " pdb=" O3B AGS A 601 " pdb=" PB AGS A 601 " pdb=" PG AGS A 601 " ideal model delta sinusoidal sigma weight residual 138.55 -53.00 -168.45 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 21090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4394 0.053 - 0.107: 733 0.107 - 0.160: 132 0.160 - 0.214: 0 0.214 - 0.267: 3 Chirality restraints: 5262 Sorted by residual: chirality pdb=" C3' AGS F 601 " pdb=" C2' AGS F 601 " pdb=" C4' AGS F 601 " pdb=" O3' AGS F 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C3' AGS A 601 " pdb=" C2' AGS A 601 " pdb=" C4' AGS A 601 " pdb=" O3' AGS A 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' AGS B 601 " pdb=" C2' AGS B 601 " pdb=" C4' AGS B 601 " pdb=" O3' AGS B 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 5259 not shown) Planarity restraints: 6004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 192 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.80e+00 pdb=" C SER C 192 " 0.048 2.00e-02 2.50e+03 pdb=" O SER C 192 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN C 193 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET G 338 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO G 339 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 339 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 339 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 461 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C ILE C 461 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE C 461 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA C 462 " 0.012 2.00e-02 2.50e+03 ... (remaining 6001 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 123 2.40 - 3.03: 20276 3.03 - 3.65: 49057 3.65 - 4.28: 74158 4.28 - 4.90: 125342 Nonbonded interactions: 268956 Sorted by model distance: nonbonded pdb=" O3G AGS F 601 " pdb="MN MN F 602 " model vdw 1.780 2.320 nonbonded pdb=" O1B ADP D 601 " pdb="MN MN D 602 " model vdw 1.802 2.320 nonbonded pdb=" OG SER D 192 " pdb="MN MN D 602 " model vdw 1.828 2.320 nonbonded pdb=" O2B AGS B 601 " pdb="MN MN B 602 " model vdw 1.837 2.320 nonbonded pdb=" OG SER E 192 " pdb="MN MN E 602 " model vdw 1.845 2.320 ... (remaining 268951 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 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) selection = (chain 'D' and resid 1 through 578) selection = (chain 'E' and resid 1 through 578) selection = (chain 'F' and resid 1 through 578) } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 6.060 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: 0.050 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.210 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 34928 Z= 0.165 Angle : 0.542 10.908 47318 Z= 0.296 Chirality : 0.041 0.267 5262 Planarity : 0.003 0.052 6004 Dihedral : 11.967 168.453 13369 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.16 % Allowed : 6.96 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 4238 helix: 1.51 (0.13), residues: 1700 sheet: -0.75 (0.21), residues: 647 loop : -1.44 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 338 TYR 0.011 0.001 TYR H 46 PHE 0.015 0.001 PHE C 378 TRP 0.007 0.001 TRP E 200 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (34928) covalent geometry : angle 0.54229 / 0.30 (47318) hydrogen bonds : bond 0.14781 / 9.96 ( 1604) hydrogen bonds : angle 6.41202 / 4.53 ( 4665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 768 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6942 (pp) REVERT: A 505 GLN cc_start: 0.7400 (mt0) cc_final: 0.7196 (pt0) REVERT: B 34 LYS cc_start: 0.8404 (mttt) cc_final: 0.8105 (mmtt) REVERT: B 178 SER cc_start: 0.8390 (m) cc_final: 0.8098 (p) REVERT: B 231 TYR cc_start: 0.4902 (m-10) cc_final: 0.4626 (m-10) REVERT: B 277 ASN cc_start: 0.8045 (m-40) cc_final: 0.7621 (m110) REVERT: B 353 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6390 (tp) REVERT: B 456 ARG cc_start: 0.8410 (mtt180) cc_final: 0.8004 (ptm-80) REVERT: B 458 LEU cc_start: 0.7911 (mt) cc_final: 0.7701 (mt) REVERT: C 79 SER cc_start: 0.8739 (t) cc_final: 0.8145 (p) REVERT: C 139 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6028 (tt) REVERT: C 150 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7186 (p90) REVERT: C 389 TYR cc_start: 0.7515 (t80) cc_final: 0.7000 (t80) REVERT: C 463 ARG cc_start: 0.7397 (mtm180) cc_final: 0.7155 (mtt-85) REVERT: C 467 LYS cc_start: 0.8050 (mttt) cc_final: 0.7765 (ptmm) REVERT: C 478 ARG cc_start: 0.7572 (mtt180) cc_final: 0.6920 (tpp-160) REVERT: C 522 ILE cc_start: 0.6751 (mt) cc_final: 0.6433 (pt) REVERT: D 28 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7732 (t-90) REVERT: D 196 SER cc_start: 0.8590 (t) cc_final: 0.8380 (m) REVERT: D 270 TRP cc_start: 0.8704 (t-100) cc_final: 0.8404 (t-100) REVERT: D 315 LEU cc_start: 0.7628 (tp) cc_final: 0.7095 (tt) REVERT: D 420 PHE cc_start: 0.9009 (t80) cc_final: 0.8660 (t80) REVERT: D 426 LYS cc_start: 0.7927 (mmpt) cc_final: 0.7618 (mmmt) REVERT: D 448 HIS cc_start: 0.9089 (t-90) cc_final: 0.8038 (t-90) REVERT: D 460 ARG cc_start: 0.8405 (ttt180) cc_final: 0.8003 (mtp85) REVERT: D 518 LEU cc_start: 0.8668 (mt) cc_final: 0.8244 (mt) REVERT: E 121 LYS cc_start: 0.8193 (tttt) cc_final: 0.7746 (tptt) REVERT: E 383 PHE cc_start: 0.8177 (t80) cc_final: 0.7577 (t80) REVERT: E 444 ILE cc_start: 0.8653 (mt) cc_final: 0.8438 (mp) REVERT: E 461 ILE cc_start: 0.8637 (mt) cc_final: 0.8398 (mt) REVERT: E 517 GLU cc_start: 0.7411 (pt0) cc_final: 0.7070 (pt0) REVERT: F 74 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8772 (pp) REVERT: F 219 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6868 (t80) REVERT: F 349 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7667 (mt) REVERT: F 387 MET cc_start: 0.7948 (ttp) cc_final: 0.7731 (ttp) REVERT: G 16 LEU cc_start: 0.7068 (tp) cc_final: 0.6866 (mp) REVERT: G 140 LYS cc_start: 0.8849 (mttt) cc_final: 0.8580 (mptt) REVERT: G 157 LEU cc_start: 0.8345 (tp) cc_final: 0.7891 (tp) REVERT: G 159 LYS cc_start: 0.9198 (tttt) cc_final: 0.8908 (ptpt) REVERT: G 301 ILE cc_start: 0.4614 (OUTLIER) cc_final: 0.4346 (mt) REVERT: G 312 TYR cc_start: 0.7354 (t80) cc_final: 0.6713 (t80) REVERT: H 19 ARG cc_start: 0.8221 (ttt180) cc_final: 0.6914 (mpt180) REVERT: H 314 ARG cc_start: 0.7852 (ttt180) cc_final: 0.7289 (tpt90) REVERT: H 436 LYS cc_start: 0.7665 (tttt) cc_final: 0.7457 (tppt) outliers start: 113 outliers final: 43 residues processed: 864 average time/residue: 0.2455 time to fit residues: 325.6212 Evaluate side-chains 488 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 436 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 491 ASN Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 301 ILE Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS B 277 ASN B 427 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 477 GLN C 504 GLN ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 256 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 ASN E 256 GLN ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN F 275 HIS F 443 HIS G 351 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 HIS H 260 ASN H 400 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.146189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.119824 restraints weight = 83182.749| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.29 r_work: 0.3606 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 34928 Z= 0.251 Angle : 0.679 10.364 47318 Z= 0.352 Chirality : 0.046 0.239 5262 Planarity : 0.005 0.091 6004 Dihedral : 10.675 150.658 5249 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.94 % Allowed : 13.04 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 4238 helix: 1.27 (0.13), residues: 1741 sheet: -0.96 (0.20), residues: 663 loop : -1.50 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 456 TYR 0.020 0.002 TYR H 200 PHE 0.029 0.003 PHE H 62 TRP 0.019 0.001 TRP D 305 HIS 0.014 0.002 HIS C 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (34928) covalent geometry : angle 0.67896 / 0.35 (47318) hydrogen bonds : bond 0.04930 / 3.36 ( 1604) hydrogen bonds : angle 5.47370 / 3.88 ( 4665) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 459 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6822 (pp) REVERT: B 178 SER cc_start: 0.8723 (m) cc_final: 0.8476 (p) REVERT: B 231 TYR cc_start: 0.4919 (m-10) cc_final: 0.4636 (m-10) REVERT: B 244 MET cc_start: 0.8418 (mtp) cc_final: 0.8131 (mtp) REVERT: B 327 MET cc_start: 0.9156 (mmm) cc_final: 0.8697 (mmm) REVERT: B 353 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6862 (tp) REVERT: B 456 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8293 (ptm-80) REVERT: C 79 SER cc_start: 0.8885 (t) cc_final: 0.8433 (p) REVERT: C 123 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7950 (tm-30) REVERT: C 139 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6550 (tt) REVERT: C 389 TYR cc_start: 0.7642 (t80) cc_final: 0.7281 (t80) REVERT: C 417 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8030 (tt) REVERT: C 451 LYS cc_start: 0.7901 (mttt) cc_final: 0.7322 (mttm) REVERT: C 467 LYS cc_start: 0.8241 (mttt) cc_final: 0.7698 (ptpp) REVERT: C 513 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: D 179 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7996 (mmt-90) REVERT: D 262 GLN cc_start: 0.7849 (tp-100) cc_final: 0.7518 (tp-100) REVERT: D 315 LEU cc_start: 0.7665 (tp) cc_final: 0.7217 (tt) REVERT: D 327 MET cc_start: 0.7367 (mmt) cc_final: 0.7138 (mmt) REVERT: D 396 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7629 (tt) REVERT: D 420 PHE cc_start: 0.8576 (t80) cc_final: 0.8245 (t80) REVERT: D 426 LYS cc_start: 0.8116 (mmpt) cc_final: 0.7812 (mmmt) REVERT: D 571 ARG cc_start: 0.7368 (ptt90) cc_final: 0.6886 (ttp80) REVERT: E 278 GLN cc_start: 0.7347 (mm-40) cc_final: 0.7110 (mm-40) REVERT: E 350 VAL cc_start: 0.6177 (m) cc_final: 0.5918 (p) REVERT: E 461 ILE cc_start: 0.8943 (mt) cc_final: 0.8720 (mt) REVERT: E 472 LEU cc_start: 0.8682 (tp) cc_final: 0.8429 (tt) REVERT: F 74 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8933 (pp) REVERT: F 219 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.7124 (t80) REVERT: F 227 THR cc_start: 0.7664 (t) cc_final: 0.7347 (m) REVERT: F 349 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7545 (mt) REVERT: G 16 LEU cc_start: 0.7451 (tp) cc_final: 0.7136 (mp) REVERT: G 140 LYS cc_start: 0.8891 (mttt) cc_final: 0.8641 (mptt) REVERT: G 153 LYS cc_start: 0.7909 (mttt) cc_final: 0.7643 (pttm) REVERT: G 159 LYS cc_start: 0.9170 (tttt) cc_final: 0.8959 (tptm) REVERT: G 160 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8340 (pttm) REVERT: G 166 ASP cc_start: 0.8150 (m-30) cc_final: 0.7852 (m-30) REVERT: H 19 ARG cc_start: 0.8365 (ttt180) cc_final: 0.7134 (mpt180) REVERT: H 314 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7438 (tpt90) REVERT: H 436 LYS cc_start: 0.7874 (tttt) cc_final: 0.7645 (tppt) outliers start: 141 outliers final: 83 residues processed: 568 average time/residue: 0.2294 time to fit residues: 209.7672 Evaluate side-chains 483 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 391 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 311 GLN Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain E residue 520 SER Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 424 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 409 optimal weight: 0.0050 chunk 211 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 413 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 0.0060 chunk 87 optimal weight: 7.9990 chunk 372 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 overall best weight: 2.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 GLN B 256 GLN B 415 ASN B 491 ASN C 513 GLN D 174 ASN D 427 ASN E 57 ASN ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.149122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.121917 restraints weight = 83085.218| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.47 r_work: 0.3607 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34928 Z= 0.170 Angle : 0.609 9.930 47318 Z= 0.316 Chirality : 0.044 0.323 5262 Planarity : 0.004 0.057 6004 Dihedral : 10.446 142.837 5223 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.74 % Allowed : 14.41 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 4238 helix: 1.28 (0.13), residues: 1759 sheet: -0.98 (0.20), residues: 613 loop : -1.44 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 481 TYR 0.018 0.001 TYR H 46 PHE 0.031 0.002 PHE F 378 TRP 0.014 0.001 TRP D 305 HIS 0.019 0.002 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (34928) covalent geometry : angle 0.60867 / 0.32 (47318) hydrogen bonds : bond 0.04226 / 2.87 ( 1604) hydrogen bonds : angle 5.21970 / 3.70 ( 4665) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 413 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6684 (pp) REVERT: A 248 GLU cc_start: 0.7344 (tp30) cc_final: 0.7069 (tp30) REVERT: A 327 MET cc_start: 0.9222 (ttp) cc_final: 0.8887 (tmm) REVERT: A 506 TYR cc_start: 0.6005 (m-10) cc_final: 0.5786 (m-10) REVERT: B 178 SER cc_start: 0.8739 (m) cc_final: 0.8495 (p) REVERT: B 231 TYR cc_start: 0.4909 (m-10) cc_final: 0.4642 (m-10) REVERT: B 327 MET cc_start: 0.9193 (mmm) cc_final: 0.8802 (mmm) REVERT: B 456 ARG cc_start: 0.8547 (mtt180) cc_final: 0.8243 (ptm-80) REVERT: C 79 SER cc_start: 0.8878 (t) cc_final: 0.8410 (p) REVERT: C 139 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6557 (tt) REVERT: C 389 TYR cc_start: 0.7641 (t80) cc_final: 0.7300 (t80) REVERT: C 451 LYS cc_start: 0.7903 (mttt) cc_final: 0.7327 (mttm) REVERT: C 467 LYS cc_start: 0.8219 (mttt) cc_final: 0.7903 (ptmt) REVERT: C 513 GLN cc_start: 0.7533 (mp10) cc_final: 0.7137 (mp10) REVERT: C 522 ILE cc_start: 0.7304 (mt) cc_final: 0.6987 (pt) REVERT: D 179 ARG cc_start: 0.8217 (mmt90) cc_final: 0.7965 (mmt-90) REVERT: D 262 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7292 (tp-100) REVERT: D 315 LEU cc_start: 0.7638 (tp) cc_final: 0.7184 (tt) REVERT: D 335 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7031 (tmm160) REVERT: D 420 PHE cc_start: 0.8647 (t80) cc_final: 0.8311 (t80) REVERT: D 426 LYS cc_start: 0.8186 (mmpt) cc_final: 0.7812 (mmmt) REVERT: D 484 GLU cc_start: 0.8659 (mp0) cc_final: 0.8209 (mp0) REVERT: D 571 ARG cc_start: 0.7272 (ptt90) cc_final: 0.6790 (ttp80) REVERT: E 284 GLU cc_start: 0.8821 (mp0) cc_final: 0.8440 (mp0) REVERT: E 472 LEU cc_start: 0.8714 (tp) cc_final: 0.8480 (tt) REVERT: F 74 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8921 (pp) REVERT: F 219 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.7003 (t80) REVERT: F 253 MET cc_start: 0.7367 (mtp) cc_final: 0.6941 (mtt) REVERT: F 349 ILE cc_start: 0.7953 (OUTLIER) cc_final: 0.7513 (mt) REVERT: G 16 LEU cc_start: 0.7394 (tp) cc_final: 0.7049 (mp) REVERT: G 140 LYS cc_start: 0.8861 (mttt) cc_final: 0.8589 (mptt) REVERT: G 153 LYS cc_start: 0.7821 (mttt) cc_final: 0.7332 (pttp) REVERT: G 159 LYS cc_start: 0.9180 (tttt) cc_final: 0.8888 (ptpt) REVERT: G 160 LYS cc_start: 0.8633 (ptmt) cc_final: 0.8253 (pttm) REVERT: G 166 ASP cc_start: 0.8118 (m-30) cc_final: 0.7835 (m-30) REVERT: H 19 ARG cc_start: 0.8357 (ttt180) cc_final: 0.7111 (mpt180) REVERT: H 193 LEU cc_start: 0.5804 (OUTLIER) cc_final: 0.5539 (tp) REVERT: H 314 ARG cc_start: 0.8068 (ttt180) cc_final: 0.7446 (tpt90) REVERT: H 436 LYS cc_start: 0.7858 (tttt) cc_final: 0.7634 (tppt) outliers start: 134 outliers final: 85 residues processed: 522 average time/residue: 0.2213 time to fit residues: 188.6305 Evaluate side-chains 468 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 377 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 73 ASN Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 474 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 144 THR Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 387 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 45 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 6 optimal weight: 0.0870 chunk 411 optimal weight: 9.9990 chunk 289 optimal weight: 0.0980 chunk 196 optimal weight: 7.9990 chunk 293 optimal weight: 0.8980 chunk 291 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 427 ASN B 491 ASN C 504 GLN D 174 ASN D 290 HIS E 278 GLN F 275 HIS G 87 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.150897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.123933 restraints weight = 82456.056| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.46 r_work: 0.3634 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34928 Z= 0.113 Angle : 0.555 9.639 47318 Z= 0.287 Chirality : 0.043 0.301 5262 Planarity : 0.004 0.052 6004 Dihedral : 10.210 138.328 5216 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.13 % Allowed : 15.42 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.13), residues: 4238 helix: 1.51 (0.13), residues: 1743 sheet: -0.87 (0.20), residues: 647 loop : -1.40 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.022 0.001 TYR B 219 PHE 0.031 0.002 PHE F 378 TRP 0.011 0.001 TRP B 270 HIS 0.019 0.001 HIS G 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (34928) covalent geometry : angle 0.55464 / 0.29 (47318) hydrogen bonds : bond 0.03627 / 2.46 ( 1604) hydrogen bonds : angle 4.99777 / 3.54 ( 4665) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 417 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: A 206 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6707 (pp) REVERT: A 244 MET cc_start: 0.6982 (ttm) cc_final: 0.6514 (ttm) REVERT: A 506 TYR cc_start: 0.6065 (m-10) cc_final: 0.5836 (m-10) REVERT: B 178 SER cc_start: 0.8711 (m) cc_final: 0.8497 (p) REVERT: B 231 TYR cc_start: 0.4806 (m-10) cc_final: 0.4586 (m-10) REVERT: B 327 MET cc_start: 0.9114 (mmm) cc_final: 0.8840 (mmm) REVERT: B 353 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6943 (tp) REVERT: C 79 SER cc_start: 0.8804 (t) cc_final: 0.8333 (p) REVERT: C 123 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7780 (tm-30) REVERT: C 139 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6626 (tt) REVERT: C 389 TYR cc_start: 0.7578 (t80) cc_final: 0.7279 (t80) REVERT: C 451 LYS cc_start: 0.7902 (mttt) cc_final: 0.7340 (mttm) REVERT: C 467 LYS cc_start: 0.8131 (mttt) cc_final: 0.7908 (ptmt) REVERT: C 478 ARG cc_start: 0.5748 (tpm170) cc_final: 0.3745 (tpp80) REVERT: C 513 GLN cc_start: 0.7444 (mp10) cc_final: 0.7049 (mp10) REVERT: D 179 ARG cc_start: 0.8177 (mmt90) cc_final: 0.7935 (mmt-90) REVERT: D 262 GLN cc_start: 0.7712 (tp-100) cc_final: 0.7266 (tp-100) REVERT: D 315 LEU cc_start: 0.7677 (tp) cc_final: 0.7200 (tt) REVERT: D 327 MET cc_start: 0.7280 (mmt) cc_final: 0.7062 (mmm) REVERT: D 335 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7052 (tmm160) REVERT: D 420 PHE cc_start: 0.8609 (t80) cc_final: 0.8282 (t80) REVERT: D 426 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7740 (mmmt) REVERT: D 571 ARG cc_start: 0.7256 (ptt90) cc_final: 0.6931 (ttp80) REVERT: E 284 GLU cc_start: 0.8807 (mp0) cc_final: 0.8383 (mp0) REVERT: F 1 MET cc_start: 0.7863 (ttt) cc_final: 0.7491 (ttt) REVERT: F 74 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8858 (pp) REVERT: F 80 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7087 (mm-30) REVERT: F 219 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6905 (t80) REVERT: F 349 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7491 (mt) REVERT: G 16 LEU cc_start: 0.7370 (tp) cc_final: 0.7023 (mp) REVERT: G 140 LYS cc_start: 0.8840 (mttt) cc_final: 0.8581 (mptt) REVERT: G 153 LYS cc_start: 0.7792 (mttt) cc_final: 0.7373 (ptpp) REVERT: G 159 LYS cc_start: 0.9121 (tttt) cc_final: 0.8847 (ptpt) REVERT: G 160 LYS cc_start: 0.8632 (ptmt) cc_final: 0.8257 (pttm) REVERT: G 166 ASP cc_start: 0.8122 (m-30) cc_final: 0.7829 (m-30) REVERT: H 19 ARG cc_start: 0.8365 (ttt180) cc_final: 0.7074 (mpt180) REVERT: H 193 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5434 (tp) REVERT: H 314 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7423 (tpt90) outliers start: 112 outliers final: 68 residues processed: 507 average time/residue: 0.2253 time to fit residues: 185.4334 Evaluate side-chains 454 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 378 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 387 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 411 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 272 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 491 ASN C 504 GLN D 174 ASN D 290 HIS D 448 HIS F 275 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.149559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.122369 restraints weight = 83355.073| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.48 r_work: 0.3626 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34928 Z= 0.153 Angle : 0.576 9.641 47318 Z= 0.296 Chirality : 0.043 0.275 5262 Planarity : 0.004 0.052 6004 Dihedral : 10.129 136.431 5208 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.55 % Allowed : 15.67 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4238 helix: 1.51 (0.13), residues: 1746 sheet: -0.91 (0.20), residues: 655 loop : -1.42 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 509 TYR 0.017 0.001 TYR F 304 PHE 0.033 0.002 PHE C 468 TRP 0.010 0.001 TRP A 270 HIS 0.022 0.001 HIS G 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (34928) covalent geometry : angle 0.57579 / 0.30 (47318) hydrogen bonds : bond 0.03715 / 2.52 ( 1604) hydrogen bonds : angle 4.94859 / 3.51 ( 4665) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 384 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6626 (pp) REVERT: A 244 MET cc_start: 0.6883 (ttm) cc_final: 0.6625 (ttm) REVERT: A 305 TRP cc_start: 0.8024 (t-100) cc_final: 0.7730 (t-100) REVERT: A 506 TYR cc_start: 0.6113 (m-10) cc_final: 0.5823 (m-10) REVERT: B 178 SER cc_start: 0.8705 (m) cc_final: 0.8483 (p) REVERT: B 231 TYR cc_start: 0.4946 (m-10) cc_final: 0.4687 (m-10) REVERT: B 327 MET cc_start: 0.9175 (mmm) cc_final: 0.8958 (mmm) REVERT: B 383 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6337 (t80) REVERT: C 79 SER cc_start: 0.8852 (t) cc_final: 0.8373 (p) REVERT: C 123 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7730 (tm-30) REVERT: C 139 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6657 (tt) REVERT: C 311 GLN cc_start: 0.8770 (mm110) cc_final: 0.8506 (mp10) REVERT: C 389 TYR cc_start: 0.7569 (t80) cc_final: 0.7283 (t80) REVERT: C 451 LYS cc_start: 0.7914 (mttt) cc_final: 0.7341 (mttm) REVERT: C 467 LYS cc_start: 0.8164 (mttt) cc_final: 0.7942 (ptmt) REVERT: C 478 ARG cc_start: 0.5727 (tpm170) cc_final: 0.3662 (tpp80) REVERT: C 513 GLN cc_start: 0.7506 (mp10) cc_final: 0.7094 (mp-120) REVERT: C 570 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8278 (tppt) REVERT: D 179 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7993 (mmt-90) REVERT: D 315 LEU cc_start: 0.7630 (tp) cc_final: 0.7125 (tt) REVERT: D 327 MET cc_start: 0.7255 (mmt) cc_final: 0.6852 (mtp) REVERT: D 335 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7029 (tmm160) REVERT: D 420 PHE cc_start: 0.8648 (t80) cc_final: 0.8289 (t80) REVERT: D 426 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7691 (mmmt) REVERT: D 571 ARG cc_start: 0.7305 (ptt90) cc_final: 0.6830 (ttp80) REVERT: F 1 MET cc_start: 0.7848 (ttt) cc_final: 0.7490 (ttt) REVERT: F 74 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8864 (pp) REVERT: F 219 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6915 (t80) REVERT: F 349 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7520 (mt) REVERT: G 16 LEU cc_start: 0.7386 (tp) cc_final: 0.7004 (mp) REVERT: G 140 LYS cc_start: 0.8850 (mttt) cc_final: 0.8598 (mptt) REVERT: G 146 GLU cc_start: 0.8985 (pt0) cc_final: 0.8741 (pp20) REVERT: G 153 LYS cc_start: 0.7821 (mttt) cc_final: 0.7452 (ptpp) REVERT: G 159 LYS cc_start: 0.9134 (tttt) cc_final: 0.8828 (ptpt) REVERT: G 166 ASP cc_start: 0.8168 (m-30) cc_final: 0.7869 (m-30) REVERT: G 190 ASP cc_start: 0.7902 (m-30) cc_final: 0.7094 (p0) REVERT: H 19 ARG cc_start: 0.8345 (ttt180) cc_final: 0.7111 (mpt180) REVERT: H 193 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5535 (tp) REVERT: H 314 ARG cc_start: 0.8066 (ttt180) cc_final: 0.7409 (tpt90) outliers start: 127 outliers final: 80 residues processed: 487 average time/residue: 0.2194 time to fit residues: 175.0126 Evaluate side-chains 456 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 369 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 424 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 131 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 376 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 365 optimal weight: 6.9990 chunk 195 optimal weight: 7.9990 chunk 350 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 HIS B 193 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 HIS F 275 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.146242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118708 restraints weight = 83070.114| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.43 r_work: 0.3556 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 34928 Z= 0.318 Angle : 0.720 10.298 47318 Z= 0.372 Chirality : 0.048 0.289 5262 Planarity : 0.005 0.051 6004 Dihedral : 10.405 137.288 5205 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.16 % Allowed : 16.34 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4238 helix: 1.04 (0.12), residues: 1760 sheet: -1.20 (0.21), residues: 610 loop : -1.59 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 509 TYR 0.023 0.002 TYR E 389 PHE 0.035 0.003 PHE H 62 TRP 0.012 0.002 TRP A 200 HIS 0.029 0.002 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.32 (34928) covalent geometry : angle 0.71974 / 0.37 (47318) hydrogen bonds : bond 0.04708 / 3.19 ( 1604) hydrogen bonds : angle 5.28715 / 3.75 ( 4665) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 373 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6291 (pp) REVERT: A 244 MET cc_start: 0.6683 (ttm) cc_final: 0.6483 (ttm) REVERT: A 248 GLU cc_start: 0.7437 (tp30) cc_final: 0.7117 (tp30) REVERT: A 327 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8902 (tmm) REVERT: A 506 TYR cc_start: 0.5938 (m-10) cc_final: 0.5567 (m-10) REVERT: B 178 SER cc_start: 0.8615 (m) cc_final: 0.8342 (p) REVERT: B 231 TYR cc_start: 0.5107 (m-10) cc_final: 0.4810 (m-10) REVERT: B 371 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.8039 (ptt) REVERT: B 456 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8240 (ptm-80) REVERT: C 79 SER cc_start: 0.8955 (t) cc_final: 0.8465 (p) REVERT: C 97 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7871 (tm-30) REVERT: C 110 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7707 (t-170) REVERT: C 123 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7688 (tm-30) REVERT: C 191 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6233 (tttt) REVERT: C 389 TYR cc_start: 0.7820 (t80) cc_final: 0.7578 (t80) REVERT: C 451 LYS cc_start: 0.7931 (mttt) cc_final: 0.7428 (mttm) REVERT: C 467 LYS cc_start: 0.8219 (mttt) cc_final: 0.7936 (ptmt) REVERT: C 513 GLN cc_start: 0.7439 (mp10) cc_final: 0.6929 (mp-120) REVERT: D 179 ARG cc_start: 0.8311 (mmt90) cc_final: 0.7993 (mmt-90) REVERT: D 315 LEU cc_start: 0.7569 (tp) cc_final: 0.7187 (tp) REVERT: D 420 PHE cc_start: 0.8754 (t80) cc_final: 0.8431 (t80) REVERT: D 426 LYS cc_start: 0.8133 (mmpt) cc_final: 0.7759 (mmmt) REVERT: D 482 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9017 (tt) REVERT: E 283 ARG cc_start: 0.9015 (mtp180) cc_final: 0.8451 (ttt-90) REVERT: E 387 MET cc_start: 0.8357 (ptm) cc_final: 0.8083 (tmm) REVERT: F 1 MET cc_start: 0.7922 (ttt) cc_final: 0.7606 (ttt) REVERT: F 74 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8861 (pp) REVERT: F 219 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6996 (t80) REVERT: G 16 LEU cc_start: 0.7338 (tp) cc_final: 0.6931 (mp) REVERT: G 140 LYS cc_start: 0.8885 (mttt) cc_final: 0.8603 (mptt) REVERT: G 146 GLU cc_start: 0.9000 (pt0) cc_final: 0.8753 (pp20) REVERT: G 153 LYS cc_start: 0.7988 (mttt) cc_final: 0.7563 (ptpp) REVERT: G 159 LYS cc_start: 0.9221 (tttt) cc_final: 0.8968 (tptp) REVERT: G 160 LYS cc_start: 0.8701 (ptmt) cc_final: 0.8275 (pttm) REVERT: G 166 ASP cc_start: 0.8246 (m-30) cc_final: 0.7956 (m-30) REVERT: G 190 ASP cc_start: 0.7934 (m-30) cc_final: 0.7110 (p0) REVERT: H 19 ARG cc_start: 0.8423 (ttt180) cc_final: 0.7105 (mpt180) REVERT: H 193 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5316 (tp) REVERT: H 314 ARG cc_start: 0.8023 (ttt180) cc_final: 0.7309 (tpt90) outliers start: 149 outliers final: 108 residues processed: 493 average time/residue: 0.2171 time to fit residues: 175.9132 Evaluate side-chains 472 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 355 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 32 ASP Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 326 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 272 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 387 ILE Chi-restraints excluded: chain H residue 424 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 150 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 157 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 GLN B 193 ASN B 427 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 HIS F 275 HIS F 504 GLN G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120988 restraints weight = 82748.406| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.44 r_work: 0.3600 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34928 Z= 0.161 Angle : 0.605 10.205 47318 Z= 0.311 Chirality : 0.044 0.270 5262 Planarity : 0.004 0.052 6004 Dihedral : 10.224 135.928 5205 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.63 % Allowed : 17.54 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 4238 helix: 1.25 (0.13), residues: 1762 sheet: -1.01 (0.20), residues: 642 loop : -1.55 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 509 TYR 0.036 0.001 TYR B 219 PHE 0.026 0.002 PHE C 378 TRP 0.015 0.001 TRP D 305 HIS 0.023 0.001 HIS G 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (34928) covalent geometry : angle 0.60469 / 0.31 (47318) hydrogen bonds : bond 0.03902 / 2.64 ( 1604) hydrogen bonds : angle 5.07316 / 3.60 ( 4665) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 377 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6382 (pp) REVERT: A 244 MET cc_start: 0.6801 (ttm) cc_final: 0.6581 (ttm) REVERT: A 327 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8877 (tmm) REVERT: A 506 TYR cc_start: 0.5891 (m-10) cc_final: 0.5538 (m-10) REVERT: B 178 SER cc_start: 0.8655 (m) cc_final: 0.8392 (p) REVERT: B 231 TYR cc_start: 0.5228 (m-10) cc_final: 0.4871 (m-10) REVERT: B 327 MET cc_start: 0.9141 (mmm) cc_final: 0.8843 (mmm) REVERT: C 79 SER cc_start: 0.8941 (t) cc_final: 0.8448 (p) REVERT: C 123 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7721 (tm-30) REVERT: C 311 GLN cc_start: 0.8838 (mm110) cc_final: 0.8480 (mp10) REVERT: C 389 TYR cc_start: 0.7681 (t80) cc_final: 0.7457 (t80) REVERT: C 436 MET cc_start: 0.7786 (mmt) cc_final: 0.7315 (mmt) REVERT: C 451 LYS cc_start: 0.7881 (mttt) cc_final: 0.7384 (mttm) REVERT: C 467 LYS cc_start: 0.8195 (mttt) cc_final: 0.7963 (ptmm) REVERT: C 570 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8120 (tppt) REVERT: D 179 ARG cc_start: 0.8226 (mmt90) cc_final: 0.7922 (mmt-90) REVERT: D 315 LEU cc_start: 0.7540 (tp) cc_final: 0.7154 (tp) REVERT: D 335 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7026 (tmm160) REVERT: D 380 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8670 (tt0) REVERT: D 384 GLU cc_start: 0.8841 (tp30) cc_final: 0.8594 (tp30) REVERT: D 420 PHE cc_start: 0.8725 (t80) cc_final: 0.8363 (t80) REVERT: D 426 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7733 (mmmt) REVERT: D 482 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9019 (tt) REVERT: E 7 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8946 (tp) REVERT: E 283 ARG cc_start: 0.8978 (mtp180) cc_final: 0.8440 (ttt-90) REVERT: E 387 MET cc_start: 0.8329 (ptm) cc_final: 0.8053 (tmm) REVERT: F 1 MET cc_start: 0.7881 (ttt) cc_final: 0.7533 (ttt) REVERT: F 74 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8796 (pp) REVERT: F 219 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.6936 (t80) REVERT: G 16 LEU cc_start: 0.7292 (tp) cc_final: 0.6904 (mp) REVERT: G 140 LYS cc_start: 0.8876 (mttt) cc_final: 0.8586 (mptt) REVERT: G 146 GLU cc_start: 0.8984 (pt0) cc_final: 0.8732 (pp20) REVERT: G 153 LYS cc_start: 0.7859 (mttt) cc_final: 0.7434 (ptpp) REVERT: G 159 LYS cc_start: 0.9182 (tttt) cc_final: 0.8937 (tptp) REVERT: G 160 LYS cc_start: 0.8677 (ptmt) cc_final: 0.8240 (pttm) REVERT: G 166 ASP cc_start: 0.8219 (m-30) cc_final: 0.7940 (m-30) REVERT: G 190 ASP cc_start: 0.7902 (m-30) cc_final: 0.7023 (p0) REVERT: H 19 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7028 (mpt180) REVERT: H 193 LEU cc_start: 0.5622 (OUTLIER) cc_final: 0.5180 (tp) REVERT: H 314 ARG cc_start: 0.7987 (ttt180) cc_final: 0.7347 (tpt90) outliers start: 130 outliers final: 93 residues processed: 486 average time/residue: 0.2239 time to fit residues: 177.6020 Evaluate side-chains 460 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 359 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 331 MET Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 387 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 326 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 290 HIS D 448 HIS F 275 HIS F 504 GLN G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.148896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121649 restraints weight = 82625.346| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.43 r_work: 0.3604 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34928 Z= 0.149 Angle : 0.596 12.223 47318 Z= 0.305 Chirality : 0.043 0.264 5262 Planarity : 0.004 0.055 6004 Dihedral : 10.130 136.401 5205 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.44 % Allowed : 18.07 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.13), residues: 4238 helix: 1.30 (0.13), residues: 1768 sheet: -0.94 (0.20), residues: 651 loop : -1.52 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 509 TYR 0.028 0.001 TYR B 219 PHE 0.058 0.002 PHE B 468 TRP 0.016 0.001 TRP A 305 HIS 0.022 0.001 HIS G 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (34928) covalent geometry : angle 0.59622 / 0.31 (47318) hydrogen bonds : bond 0.03759 / 2.55 ( 1604) hydrogen bonds : angle 4.99450 / 3.54 ( 4665) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 363 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7133 (tt) REVERT: A 206 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6525 (pp) REVERT: A 327 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8900 (tmm) REVERT: B 178 SER cc_start: 0.8656 (m) cc_final: 0.8393 (p) REVERT: B 231 TYR cc_start: 0.5205 (m-10) cc_final: 0.4857 (m-10) REVERT: B 327 MET cc_start: 0.9129 (mmm) cc_final: 0.8770 (mmm) REVERT: C 79 SER cc_start: 0.8931 (t) cc_final: 0.8427 (p) REVERT: C 110 HIS cc_start: 0.8299 (OUTLIER) cc_final: 0.7785 (t-170) REVERT: C 123 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7736 (tm-30) REVERT: C 389 TYR cc_start: 0.7672 (t80) cc_final: 0.7452 (t80) REVERT: C 436 MET cc_start: 0.7772 (mmt) cc_final: 0.7329 (mmt) REVERT: C 451 LYS cc_start: 0.7881 (mttt) cc_final: 0.7385 (mttm) REVERT: C 467 LYS cc_start: 0.8181 (mttt) cc_final: 0.7972 (ptmm) REVERT: C 570 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8110 (tppt) REVERT: D 179 ARG cc_start: 0.8223 (mmt90) cc_final: 0.7891 (mmt-90) REVERT: D 315 LEU cc_start: 0.7536 (tp) cc_final: 0.7154 (tp) REVERT: D 327 MET cc_start: 0.7248 (mmm) cc_final: 0.6962 (mtp) REVERT: D 335 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7028 (tmm160) REVERT: D 420 PHE cc_start: 0.8707 (t80) cc_final: 0.8350 (t80) REVERT: D 426 LYS cc_start: 0.8063 (mmpt) cc_final: 0.7712 (mmmt) REVERT: D 482 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9038 (tt) REVERT: D 571 ARG cc_start: 0.7258 (ptt90) cc_final: 0.6954 (ttp80) REVERT: E 7 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8942 (tp) REVERT: E 283 ARG cc_start: 0.8980 (mtp180) cc_final: 0.8478 (ttt-90) REVERT: E 387 MET cc_start: 0.8364 (ptm) cc_final: 0.8067 (tmm) REVERT: F 1 MET cc_start: 0.7902 (ttt) cc_final: 0.7537 (ttt) REVERT: F 74 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8797 (pp) REVERT: F 219 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6863 (t80) REVERT: F 349 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7479 (mt) REVERT: G 16 LEU cc_start: 0.7317 (tp) cc_final: 0.6918 (mp) REVERT: G 140 LYS cc_start: 0.8881 (mttt) cc_final: 0.8591 (mptt) REVERT: G 146 GLU cc_start: 0.8976 (pt0) cc_final: 0.8731 (pp20) REVERT: G 153 LYS cc_start: 0.7865 (mttt) cc_final: 0.7476 (ptpp) REVERT: G 159 LYS cc_start: 0.9175 (tttt) cc_final: 0.8921 (tptp) REVERT: G 166 ASP cc_start: 0.8224 (m-30) cc_final: 0.7943 (m-30) REVERT: G 190 ASP cc_start: 0.7948 (m-30) cc_final: 0.7056 (p0) REVERT: H 19 ARG cc_start: 0.8370 (ttt180) cc_final: 0.7018 (mpt180) REVERT: H 193 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5425 (tp) REVERT: H 314 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7361 (tpt90) outliers start: 123 outliers final: 91 residues processed: 464 average time/residue: 0.2232 time to fit residues: 168.7725 Evaluate side-chains 455 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 353 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 398 TYR Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 435 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain G residue 403 HIS Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 387 ILE Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 435 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 216 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 chunk 269 optimal weight: 9.9990 chunk 185 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 387 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 288 optimal weight: 0.2980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 ASN B 491 ASN C 73 ASN D 174 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 HIS F 275 HIS F 504 GLN G 263 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.123050 restraints weight = 82190.359| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.49 r_work: 0.3621 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34928 Z= 0.112 Angle : 0.574 14.350 47318 Z= 0.293 Chirality : 0.042 0.253 5262 Planarity : 0.004 0.050 6004 Dihedral : 9.891 136.539 5199 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.74 % Allowed : 18.94 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 4238 helix: 1.48 (0.13), residues: 1755 sheet: -0.77 (0.20), residues: 680 loop : -1.46 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 509 TYR 0.027 0.001 TYR B 219 PHE 0.045 0.002 PHE B 468 TRP 0.024 0.001 TRP A 305 HIS 0.036 0.001 HIS G 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (34928) covalent geometry : angle 0.57432 / 0.29 (47318) hydrogen bonds : bond 0.03388 / 2.29 ( 1604) hydrogen bonds : angle 4.87297 / 3.45 ( 4665) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 379 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6459 (pp) REVERT: A 327 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8882 (tmm) REVERT: A 506 TYR cc_start: 0.5760 (m-10) cc_final: 0.5532 (m-10) REVERT: B 178 SER cc_start: 0.8567 (m) cc_final: 0.8325 (p) REVERT: B 231 TYR cc_start: 0.5037 (m-10) cc_final: 0.4757 (m-10) REVERT: B 327 MET cc_start: 0.9137 (mmm) cc_final: 0.8789 (mmm) REVERT: B 468 PHE cc_start: 0.6473 (OUTLIER) cc_final: 0.6231 (t80) REVERT: C 64 VAL cc_start: 0.6695 (t) cc_final: 0.6348 (m) REVERT: C 79 SER cc_start: 0.8917 (t) cc_final: 0.8426 (p) REVERT: C 110 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7818 (t-170) REVERT: C 123 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7707 (tm-30) REVERT: C 311 GLN cc_start: 0.8804 (mm110) cc_final: 0.8471 (mp10) REVERT: C 389 TYR cc_start: 0.7662 (t80) cc_final: 0.7438 (t80) REVERT: C 451 LYS cc_start: 0.7801 (mttt) cc_final: 0.7317 (mttm) REVERT: C 513 GLN cc_start: 0.7294 (mp10) cc_final: 0.6893 (mp-120) REVERT: C 570 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8173 (tppt) REVERT: D 179 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7929 (mmt-90) REVERT: D 315 LEU cc_start: 0.7608 (tp) cc_final: 0.7212 (tp) REVERT: D 327 MET cc_start: 0.7204 (mmm) cc_final: 0.6868 (mtp) REVERT: D 335 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7033 (tmm160) REVERT: D 380 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8652 (tt0) REVERT: D 420 PHE cc_start: 0.8726 (t80) cc_final: 0.8376 (t80) REVERT: D 422 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.8167 (mmp80) REVERT: D 426 LYS cc_start: 0.7981 (mmpt) cc_final: 0.7614 (mmmt) REVERT: D 482 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9045 (tt) REVERT: D 571 ARG cc_start: 0.7229 (ptt90) cc_final: 0.6927 (ttp80) REVERT: E 7 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8932 (tp) REVERT: E 283 ARG cc_start: 0.8985 (mtp180) cc_final: 0.8443 (ttt-90) REVERT: F 1 MET cc_start: 0.7879 (ttt) cc_final: 0.7518 (ttt) REVERT: F 74 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8735 (pp) REVERT: F 219 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6736 (t80) REVERT: F 349 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7452 (mt) REVERT: F 387 MET cc_start: 0.8075 (ttp) cc_final: 0.7813 (mtp) REVERT: G 16 LEU cc_start: 0.7330 (tp) cc_final: 0.6948 (mp) REVERT: G 140 LYS cc_start: 0.8843 (mttt) cc_final: 0.8572 (mptt) REVERT: G 146 GLU cc_start: 0.8981 (pt0) cc_final: 0.8739 (pp20) REVERT: G 153 LYS cc_start: 0.7708 (mttt) cc_final: 0.7297 (ptpp) REVERT: G 159 LYS cc_start: 0.9159 (tttt) cc_final: 0.8814 (ptpt) REVERT: G 166 ASP cc_start: 0.8238 (m-30) cc_final: 0.7955 (m-30) REVERT: H 19 ARG cc_start: 0.8338 (ttt180) cc_final: 0.6952 (mpt180) REVERT: H 193 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5117 (tp) REVERT: H 314 ARG cc_start: 0.8024 (ttt180) cc_final: 0.7342 (tpt90) outliers start: 98 outliers final: 74 residues processed: 459 average time/residue: 0.2195 time to fit residues: 164.0404 Evaluate side-chains 445 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 360 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 435 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 174 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 203 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 282 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 491 ASN D 174 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS D 448 HIS E 256 GLN F 275 HIS G 263 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.150346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.123190 restraints weight = 82593.666| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.49 r_work: 0.3627 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34928 Z= 0.119 Angle : 0.581 16.690 47318 Z= 0.295 Chirality : 0.043 0.251 5262 Planarity : 0.004 0.058 6004 Dihedral : 9.800 137.290 5199 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.54 % Allowed : 19.41 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4238 helix: 1.49 (0.13), residues: 1771 sheet: -0.73 (0.20), residues: 678 loop : -1.46 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 456 TYR 0.022 0.001 TYR E 340 PHE 0.033 0.002 PHE B 468 TRP 0.038 0.001 TRP A 305 HIS 0.023 0.001 HIS G 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (34928) covalent geometry : angle 0.58052 / 0.30 (47318) hydrogen bonds : bond 0.03363 / 2.28 ( 1604) hydrogen bonds : angle 4.82212 / 3.41 ( 4665) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8476 Ramachandran restraints generated. 4238 Oldfield, 0 Emsley, 4238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 373 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6639 (pp) REVERT: A 506 TYR cc_start: 0.5888 (m-10) cc_final: 0.5600 (m-10) REVERT: B 178 SER cc_start: 0.8608 (m) cc_final: 0.8398 (p) REVERT: B 231 TYR cc_start: 0.4963 (m-10) cc_final: 0.4698 (m-10) REVERT: B 327 MET cc_start: 0.9118 (mmm) cc_final: 0.8764 (mmm) REVERT: C 64 VAL cc_start: 0.6683 (t) cc_final: 0.6353 (m) REVERT: C 79 SER cc_start: 0.8900 (t) cc_final: 0.8417 (p) REVERT: C 110 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7792 (t-170) REVERT: C 123 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7613 (tm-30) REVERT: C 451 LYS cc_start: 0.7790 (mttt) cc_final: 0.7322 (mttm) REVERT: C 513 GLN cc_start: 0.7426 (mp10) cc_final: 0.7005 (mp-120) REVERT: C 570 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8120 (tppt) REVERT: D 179 ARG cc_start: 0.8220 (mmt90) cc_final: 0.7925 (mmt-90) REVERT: D 315 LEU cc_start: 0.7658 (tp) cc_final: 0.7168 (tt) REVERT: D 327 MET cc_start: 0.7240 (mmm) cc_final: 0.6963 (mtp) REVERT: D 335 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7062 (tmm160) REVERT: D 420 PHE cc_start: 0.8657 (t80) cc_final: 0.8304 (t80) REVERT: D 422 ARG cc_start: 0.8548 (mmt-90) cc_final: 0.8167 (mmp80) REVERT: D 426 LYS cc_start: 0.7968 (mmpt) cc_final: 0.7720 (mmmt) REVERT: D 482 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9088 (tt) REVERT: D 571 ARG cc_start: 0.7309 (ptt90) cc_final: 0.7007 (ttp80) REVERT: E 283 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8458 (ttt-90) REVERT: F 1 MET cc_start: 0.7831 (ttt) cc_final: 0.7437 (ttt) REVERT: F 74 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8776 (pp) REVERT: F 219 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6773 (t80) REVERT: F 349 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7479 (mt) REVERT: F 387 MET cc_start: 0.8120 (ttp) cc_final: 0.7859 (mtp) REVERT: G 16 LEU cc_start: 0.7434 (tp) cc_final: 0.7046 (mp) REVERT: G 140 LYS cc_start: 0.8853 (mttt) cc_final: 0.8596 (mptt) REVERT: G 146 GLU cc_start: 0.8959 (pt0) cc_final: 0.8711 (pp20) REVERT: G 153 LYS cc_start: 0.7784 (mttt) cc_final: 0.7355 (ptpp) REVERT: G 159 LYS cc_start: 0.9154 (tttt) cc_final: 0.8825 (ptpt) REVERT: G 166 ASP cc_start: 0.8233 (m-30) cc_final: 0.7951 (m-30) REVERT: G 190 ASP cc_start: 0.7907 (m-30) cc_final: 0.7020 (p0) REVERT: H 19 ARG cc_start: 0.8324 (ttt180) cc_final: 0.6994 (mpt180) REVERT: H 62 PHE cc_start: 0.5032 (t80) cc_final: 0.4765 (t80) REVERT: H 193 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5434 (tp) REVERT: H 263 HIS cc_start: 0.6712 (t-170) cc_final: 0.6147 (t-170) REVERT: H 314 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7411 (tpt90) REVERT: H 430 GLU cc_start: 0.8595 (pt0) cc_final: 0.7767 (tp30) outliers start: 91 outliers final: 75 residues processed: 445 average time/residue: 0.2253 time to fit residues: 163.0630 Evaluate side-chains 446 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 363 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 TRP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 180 HIS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 128 ARG Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 378 PHE Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 570 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 387 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 359 ASN Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain E residue 457 ILE Chi-restraints excluded: chain E residue 519 MET Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 219 TYR Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 349 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 45 VAL Chi-restraints excluded: chain G residue 46 TYR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 296 THR Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 21 TYR Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 193 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 216 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.0770 chunk 187 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 174 optimal weight: 5.9990 chunk 223 optimal weight: 0.0470 chunk 289 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN D 174 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS D 448 HIS F 275 HIS G 263 HIS G 403 HIS ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.151177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.124311 restraints weight = 82393.395| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.48 r_work: 0.3636 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 34928 Z= 0.112 Angle : 0.575 11.529 47318 Z= 0.293 Chirality : 0.042 0.248 5262 Planarity : 0.004 0.082 6004 Dihedral : 9.757 137.604 5198 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.46 % Allowed : 19.50 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4238 helix: 1.52 (0.13), residues: 1765 sheet: -0.68 (0.20), residues: 668 loop : -1.42 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 509 TYR 0.023 0.001 TYR A 150 PHE 0.060 0.002 PHE B 468 TRP 0.028 0.001 TRP A 305 HIS 0.024 0.001 HIS G 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (34928) covalent geometry : angle 0.57453 / 0.29 (47318) hydrogen bonds : bond 0.03260 / 2.21 ( 1604) hydrogen bonds : angle 4.78441 / 3.38 ( 4665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9161.88 seconds wall clock time: 157 minutes 32.26 seconds (9452.26 seconds total)