Starting phenix.real_space_refine on Fri Mar 6 23:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x1p_66466/03_2026/9x1p_66466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x1p_66466/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9x1p_66466/03_2026/9x1p_66466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x1p_66466/03_2026/9x1p_66466.map" model { file = "/net/cci-nas-00/data/ceres_data/9x1p_66466/03_2026/9x1p_66466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x1p_66466/03_2026/9x1p_66466.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 6.88, per 1000 atoms: 0.20 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: 2.49 Conformation dependent library (CDL) restraints added in 1.0 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: 0.94 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: 6.79 Time building geometry restraints manager: 3.31 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=" C TYR H 135 " pdb=" N PRO H 136 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.20e-02 6.94e+03 2.91e+00 bond pdb=" CA ALA B 351 " pdb=" C ALA B 351 " ideal model delta sigma weight residual 1.523 1.507 0.015 1.41e-02 5.03e+03 1.20e+00 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" C4 ADP D 601 " pdb=" C5 ADP D 601 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 34923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 46838 1.90 - 3.81: 418 3.81 - 5.71: 51 5.71 - 7.61: 9 7.61 - 9.51: 2 Bond angle restraints: 47318 Sorted by residual: angle pdb=" N ILE G 90 " pdb=" CA ILE G 90 " pdb=" C ILE G 90 " ideal model delta sigma weight residual 111.91 108.70 3.21 8.90e-01 1.26e+00 1.30e+01 angle pdb=" N VAL C 499 " pdb=" CA VAL C 499 " pdb=" C VAL C 499 " ideal model delta sigma weight residual 112.96 109.52 3.44 1.00e+00 1.00e+00 1.18e+01 angle pdb=" N VAL A 486 " pdb=" CA VAL A 486 " pdb=" C VAL A 486 " ideal model delta sigma weight residual 112.96 109.53 3.43 1.00e+00 1.00e+00 1.18e+01 angle pdb=" CA GLY B 524 " pdb=" C GLY B 524 " pdb=" N LEU B 525 " ideal model delta sigma weight residual 118.95 115.70 3.25 1.06e+00 8.90e-01 9.42e+00 angle pdb=" N THR B 220 " pdb=" CA THR B 220 " pdb=" C THR B 220 " ideal model delta sigma weight residual 110.24 114.21 -3.97 1.30e+00 5.92e-01 9.33e+00 ... (remaining 47313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 20447 27.07 - 54.13: 541 54.13 - 81.20: 44 81.20 - 108.27: 4 108.27 - 135.34: 3 Dihedral angle restraints: 21039 sinusoidal: 8889 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 68.91 -53.00 121.91 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 21036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3408 0.031 - 0.062: 1201 0.062 - 0.092: 370 0.092 - 0.123: 268 0.123 - 0.154: 21 Chirality restraints: 5268 Sorted by residual: chirality pdb=" CA ILE B 522 " pdb=" N ILE B 522 " pdb=" C ILE B 522 " pdb=" CB ILE B 522 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE C 494 " pdb=" N ILE C 494 " pdb=" C ILE C 494 " pdb=" CB ILE C 494 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL D 533 " pdb=" N VAL D 533 " pdb=" C VAL D 533 " pdb=" CB VAL D 533 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 5265 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: 4.970 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: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.590 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.002 0.037 34928 Z= 0.118 Angle : 0.490 9.514 47318 Z= 0.261 Chirality : 0.041 0.154 5268 Planarity : 0.003 0.052 6004 Dihedral : 11.839 135.336 13315 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 covalent geometry : bond 0.00249 (34928) covalent geometry : angle 0.48964 (47318) hydrogen bonds : bond 0.14781 ( 1604) hydrogen bonds : angle 6.41202 ( 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 : 1.157 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: 0.2419 time to fit residues: 318.8802 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 : 1.312 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.146122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119703 restraints weight = 83576.922| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 3.30 r_work: 0.3600 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 34928 Z= 0.253 Angle : 0.679 10.365 47318 Z= 0.351 Chirality : 0.046 0.226 5268 Planarity : 0.005 0.067 6004 Dihedral : 10.481 137.505 5195 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.22 % Allowed : 12.96 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.13), residues: 4238 helix: 1.19 (0.13), residues: 1763 sheet: -0.98 (0.21), residues: 638 loop : -1.53 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 456 TYR 0.019 0.002 TYR E 389 PHE 0.032 0.003 PHE C 378 TRP 0.016 0.001 TRP D 305 HIS 0.014 0.002 HIS C 443 Details of bonding type rmsd covalent geometry : bond 0.00584 (34928) covalent geometry : angle 0.67882 (47318) hydrogen bonds : bond 0.04754 ( 1604) hydrogen bonds : angle 5.40791 ( 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 605 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 454 time to evaluate : 1.270 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: 0.7320 (OUTLIER) cc_final: 0.6821 (pp) REVERT: B 178 SER cc_start: 0.8703 (m) cc_final: 0.8464 (p) REVERT: B 231 TYR cc_start: 0.4953 (m-10) cc_final: 0.4642 (m-10) REVERT: B 244 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8213 (mtp) REVERT: B 327 MET cc_start: 0.9160 (mmm) cc_final: 0.8685 (mmm) REVERT: B 353 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6885 (tp) REVERT: B 456 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8290 (ptm-80) REVERT: C 79 SER cc_start: 0.8895 (t) cc_final: 0.8433 (p) REVERT: C 123 GLU cc_start: 0.8325 (mm-30) cc_final: 0.7940 (tm-30) REVERT: C 139 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6553 (tt) REVERT: C 311 GLN cc_start: 0.8812 (mm110) cc_final: 0.8605 (mm110) REVERT: C 389 TYR cc_start: 0.7674 (t80) cc_final: 0.7328 (t80) REVERT: C 451 LYS cc_start: 0.7920 (mttt) cc_final: 0.7335 (mttm) REVERT: C 467 LYS cc_start: 0.8247 (mttt) cc_final: 0.7685 (ptpp) REVERT: C 513 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.7015 (mp10) REVERT: D 179 ARG cc_start: 0.8220 (mmt90) cc_final: 0.8011 (mmt-90) REVERT: D 262 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7543 (tp-100) REVERT: D 315 LEU cc_start: 0.7625 (tp) cc_final: 0.7278 (tp) REVERT: D 327 MET cc_start: 0.7352 (mmt) cc_final: 0.7111 (mmt) REVERT: D 396 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7619 (tt) REVERT: D 420 PHE cc_start: 0.8595 (t80) cc_final: 0.8257 (t80) REVERT: D 426 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7845 (mmmt) REVERT: D 571 ARG cc_start: 0.7357 (ptt90) cc_final: 0.6871 (ttp80) REVERT: E 278 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7194 (mm-40) REVERT: E 472 LEU cc_start: 0.8656 (tp) cc_final: 0.8380 (tt) REVERT: F 74 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8918 (pp) REVERT: F 219 TYR cc_start: 0.7424 (OUTLIER) cc_final: 0.7123 (t80) REVERT: F 349 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7554 (mt) REVERT: G 16 LEU cc_start: 0.7455 (tp) cc_final: 0.7115 (mp) REVERT: G 140 LYS cc_start: 0.8867 (mttt) cc_final: 0.8608 (mptt) REVERT: G 153 LYS cc_start: 0.7906 (mttt) cc_final: 0.7640 (pttm) REVERT: G 159 LYS cc_start: 0.9196 (tttt) cc_final: 0.8983 (tptm) REVERT: G 160 LYS cc_start: 0.8632 (ptmt) cc_final: 0.8305 (pttm) REVERT: G 166 ASP cc_start: 0.8215 (m-30) cc_final: 0.7924 (m-30) REVERT: G 401 ARG cc_start: 0.8039 (tpt170) cc_final: 0.7835 (mmt180) REVERT: H 19 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7132 (mpt180) REVERT: H 193 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5609 (tp) REVERT: H 314 ARG cc_start: 0.8089 (ttt180) cc_final: 0.7452 (tpt90) REVERT: H 436 LYS cc_start: 0.7849 (tttt) cc_final: 0.7617 (tppt) outliers start: 151 outliers final: 86 residues processed: 574 average time/residue: 0.2163 time to fit residues: 198.8003 Evaluate side-chains 490 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 394 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 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 184 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 244 MET 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 194 THR 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 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 74 ILE 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 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 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 494 ILE 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 79 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 193 LEU 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: 0.0020 chunk 211 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 413 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 249 optimal weight: 0.8980 overall best weight: 4.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 HIS A 505 GLN B 193 ASN B 256 GLN B 415 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN D 174 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** E 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.147340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120498 restraints weight = 83163.285| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.30 r_work: 0.3579 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 34928 Z= 0.255 Angle : 0.668 10.383 47318 Z= 0.346 Chirality : 0.046 0.239 5268 Planarity : 0.005 0.074 6004 Dihedral : 10.508 137.157 5169 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.44 % Allowed : 14.39 % Favored : 81.17 % 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: -0.61 (0.13), residues: 4238 helix: 1.05 (0.13), residues: 1760 sheet: -1.09 (0.21), residues: 612 loop : -1.60 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 240 TYR 0.019 0.002 TYR E 340 PHE 0.031 0.003 PHE F 378 TRP 0.016 0.001 TRP D 305 HIS 0.008 0.002 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00589 (34928) covalent geometry : angle 0.66821 (47318) hydrogen bonds : bond 0.04632 ( 1604) hydrogen bonds : angle 5.35460 ( 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 563 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 404 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 206 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6786 (pp) REVERT: A 244 MET cc_start: 0.7001 (ttm) cc_final: 0.6615 (ttm) REVERT: A 248 GLU cc_start: 0.7324 (tp30) cc_final: 0.6872 (tp30) REVERT: A 327 MET cc_start: 0.9224 (ttp) cc_final: 0.8915 (ppp) REVERT: A 506 TYR cc_start: 0.6081 (m-10) cc_final: 0.5822 (m-10) REVERT: B 178 SER cc_start: 0.8735 (m) cc_final: 0.8498 (p) REVERT: B 231 TYR cc_start: 0.5124 (m-10) cc_final: 0.4764 (m-10) REVERT: B 244 MET cc_start: 0.8428 (mtp) cc_final: 0.8208 (mtp) REVERT: B 327 MET cc_start: 0.9183 (mmm) cc_final: 0.8808 (mmm) REVERT: B 354 GLU cc_start: 0.5801 (OUTLIER) cc_final: 0.5559 (pm20) REVERT: B 456 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8275 (ptm-80) REVERT: C 79 SER cc_start: 0.8897 (t) cc_final: 0.8441 (p) REVERT: C 123 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7871 (tm-30) REVERT: C 139 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6591 (tt) REVERT: C 389 TYR cc_start: 0.7744 (t80) cc_final: 0.7452 (t80) REVERT: C 451 LYS cc_start: 0.7955 (mttt) cc_final: 0.7464 (mttm) REVERT: C 467 LYS cc_start: 0.8225 (mttt) cc_final: 0.7936 (ptmt) REVERT: C 513 GLN cc_start: 0.7598 (mp10) cc_final: 0.7143 (mp10) REVERT: C 527 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6026 (tptp) REVERT: D 179 ARG cc_start: 0.8222 (mmt90) cc_final: 0.7962 (mmt-90) REVERT: D 315 LEU cc_start: 0.7528 (tp) cc_final: 0.7171 (tp) REVERT: D 420 PHE cc_start: 0.8610 (t80) cc_final: 0.8290 (t80) REVERT: D 426 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7849 (mmmt) REVERT: E 383 PHE cc_start: 0.8365 (t80) cc_final: 0.7912 (t80) REVERT: E 472 LEU cc_start: 0.8674 (tp) cc_final: 0.8370 (tt) REVERT: F 1 MET cc_start: 0.7922 (ttt) cc_final: 0.7555 (ttt) REVERT: F 74 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8909 (pp) REVERT: F 219 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.7093 (t80) REVERT: G 16 LEU cc_start: 0.7464 (tp) cc_final: 0.7074 (mp) REVERT: G 140 LYS cc_start: 0.8907 (mttt) cc_final: 0.8617 (mptt) REVERT: G 153 LYS cc_start: 0.7958 (mttt) cc_final: 0.7542 (ptpp) REVERT: G 159 LYS cc_start: 0.9175 (tttt) cc_final: 0.8950 (tptp) REVERT: G 160 LYS cc_start: 0.8628 (ptmt) cc_final: 0.8206 (pttm) REVERT: G 166 ASP cc_start: 0.8145 (m-30) cc_final: 0.7862 (m-30) REVERT: G 190 ASP cc_start: 0.7912 (m-30) cc_final: 0.7137 (p0) REVERT: H 19 ARG cc_start: 0.8371 (ttt180) cc_final: 0.7160 (mpt180) outliers start: 159 outliers final: 106 residues processed: 532 average time/residue: 0.2058 time to fit residues: 178.0316 Evaluate side-chains 487 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 374 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 144 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 505 GLN Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 546 TYR 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 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 203 VAL 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 354 GLU 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 131 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 194 THR 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 439 VAL 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 527 LYS 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 112 LEU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 156 ILE Chi-restraints excluded: chain D residue 162 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 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 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 247 GLU 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 326 ILE 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 F residue 433 GLU Chi-restraints excluded: chain F residue 435 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 79 VAL 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 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 387 ILE Chi-restraints excluded: chain H residue 424 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 45 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 285 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 427 ASN B 491 ASN D 174 ASN D 427 ASN E 256 GLN E 278 GLN ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 504 GLN G 403 HIS H 98 GLN H 168 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.148823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.121657 restraints weight = 82447.420| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 3.44 r_work: 0.3608 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34928 Z= 0.148 Angle : 0.582 9.710 47318 Z= 0.299 Chirality : 0.043 0.234 5268 Planarity : 0.004 0.050 6004 Dihedral : 10.212 136.744 5159 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.69 % Allowed : 16.23 % Favored : 80.08 % 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: -0.40 (0.13), residues: 4238 helix: 1.30 (0.13), residues: 1747 sheet: -1.03 (0.20), residues: 632 loop : -1.51 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 509 TYR 0.016 0.001 TYR B 219 PHE 0.033 0.002 PHE F 378 TRP 0.014 0.001 TRP A 305 HIS 0.020 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00336 (34928) covalent geometry : angle 0.58155 (47318) hydrogen bonds : bond 0.03858 ( 1604) hydrogen bonds : angle 5.09691 ( 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 540 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 408 time to evaluate : 1.349 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: A 206 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6413 (pp) REVERT: A 244 MET cc_start: 0.7077 (ttm) cc_final: 0.6743 (ttm) REVERT: A 506 TYR cc_start: 0.5806 (m-10) cc_final: 0.5600 (m-10) REVERT: B 178 SER cc_start: 0.8646 (m) cc_final: 0.8389 (p) REVERT: B 231 TYR cc_start: 0.5048 (m-10) cc_final: 0.4785 (m-10) REVERT: B 327 MET cc_start: 0.9238 (mmm) cc_final: 0.8872 (mmm) REVERT: B 354 GLU cc_start: 0.6005 (OUTLIER) cc_final: 0.5709 (pm20) REVERT: B 383 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6349 (t80) REVERT: B 482 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7344 (tp) REVERT: C 79 SER cc_start: 0.8902 (t) cc_final: 0.8398 (p) REVERT: C 123 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7749 (tm-30) REVERT: C 389 TYR cc_start: 0.7757 (t80) cc_final: 0.7413 (t80) REVERT: C 451 LYS cc_start: 0.7869 (mttt) cc_final: 0.7260 (mttm) REVERT: C 467 LYS cc_start: 0.8224 (mttt) cc_final: 0.7923 (ptmt) REVERT: C 513 GLN cc_start: 0.7432 (mp10) cc_final: 0.7005 (mp-120) REVERT: C 522 ILE cc_start: 0.7125 (mt) cc_final: 0.6797 (pt) REVERT: C 527 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6196 (tptp) REVERT: D 179 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7891 (mmt-90) REVERT: D 219 TYR cc_start: 0.8353 (m-80) cc_final: 0.8139 (m-80) REVERT: D 315 LEU cc_start: 0.7576 (tp) cc_final: 0.7201 (tp) REVERT: D 327 MET cc_start: 0.7246 (mmt) cc_final: 0.7012 (mmm) REVERT: D 335 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7023 (tmm160) REVERT: D 420 PHE cc_start: 0.8715 (t80) cc_final: 0.8331 (t80) REVERT: D 426 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7764 (mmmt) REVERT: E 7 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8921 (tp) REVERT: E 294 GLN cc_start: 0.8114 (mt0) cc_final: 0.7848 (mt0) REVERT: E 368 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7314 (mt-10) REVERT: E 472 LEU cc_start: 0.8731 (tp) cc_final: 0.8497 (tt) REVERT: F 1 MET cc_start: 0.7849 (ttt) cc_final: 0.7494 (ttt) REVERT: F 74 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8822 (pp) REVERT: F 219 TYR cc_start: 0.7355 (OUTLIER) cc_final: 0.6919 (t80) REVERT: G 16 LEU cc_start: 0.7285 (tp) cc_final: 0.6898 (mp) REVERT: G 140 LYS cc_start: 0.8860 (mttt) cc_final: 0.8573 (mptt) REVERT: G 153 LYS cc_start: 0.7827 (mttt) cc_final: 0.7404 (ptpp) REVERT: G 159 LYS cc_start: 0.9199 (tttt) cc_final: 0.8948 (tptp) REVERT: G 160 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8241 (pttm) REVERT: G 166 ASP cc_start: 0.8171 (m-30) cc_final: 0.7899 (m-30) REVERT: G 190 ASP cc_start: 0.7916 (m-30) cc_final: 0.7029 (p0) REVERT: H 19 ARG cc_start: 0.8375 (ttt180) cc_final: 0.7052 (mpt180) REVERT: H 168 HIS cc_start: 0.7740 (t70) cc_final: 0.7476 (t-170) REVERT: H 193 LEU cc_start: 0.5518 (OUTLIER) cc_final: 0.5273 (tp) REVERT: H 314 ARG cc_start: 0.7902 (ttt180) cc_final: 0.7242 (tpt90) outliers start: 132 outliers final: 83 residues processed: 513 average time/residue: 0.2033 time to fit residues: 170.5074 Evaluate side-chains 467 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 375 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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 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 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 354 GLU Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 129 VAL 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 483 SER Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 527 LYS 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 267 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 371 MET 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 514 VAL 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 234 LEU Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 358 VAL 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 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 373 LEU Chi-restraints excluded: chain F residue 433 GLU 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 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 Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 435 LEU 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: 7.9990 chunk 181 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 272 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN B 193 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 HIS C 504 GLN D 174 ASN E 256 GLN ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 504 GLN G 87 ASN G 403 HIS H 168 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.148862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121644 restraints weight = 83098.358| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.45 r_work: 0.3601 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34928 Z= 0.147 Angle : 0.572 9.798 47318 Z= 0.293 Chirality : 0.043 0.226 5268 Planarity : 0.004 0.051 6004 Dihedral : 10.091 138.704 5153 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.94 % Allowed : 16.59 % Favored : 79.47 % 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: -0.34 (0.13), residues: 4238 helix: 1.35 (0.13), residues: 1764 sheet: -0.98 (0.20), residues: 635 loop : -1.52 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 509 TYR 0.028 0.001 TYR B 219 PHE 0.025 0.002 PHE C 378 TRP 0.015 0.001 TRP A 305 HIS 0.017 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00335 (34928) covalent geometry : angle 0.57220 (47318) hydrogen bonds : bond 0.03705 ( 1604) hydrogen bonds : angle 4.98272 ( 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 524 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 383 time to evaluate : 1.283 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: 0.6932 (OUTLIER) cc_final: 0.6438 (pp) REVERT: A 244 MET cc_start: 0.7016 (ttm) cc_final: 0.6699 (ttm) REVERT: A 248 GLU cc_start: 0.7242 (tp30) cc_final: 0.6952 (tp30) REVERT: A 327 MET cc_start: 0.9113 (ttp) cc_final: 0.8840 (ppp) REVERT: A 506 TYR cc_start: 0.5911 (m-10) cc_final: 0.5667 (m-10) REVERT: B 178 SER cc_start: 0.8637 (m) cc_final: 0.8372 (p) REVERT: B 231 TYR cc_start: 0.5189 (m-10) cc_final: 0.4779 (m-10) REVERT: B 327 MET cc_start: 0.9195 (mmm) cc_final: 0.8908 (mmm) REVERT: B 354 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: B 383 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.6411 (t80) REVERT: B 482 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7356 (tp) REVERT: C 56 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.5073 (pm20) REVERT: C 79 SER cc_start: 0.8896 (t) cc_final: 0.8395 (p) REVERT: C 110 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7784 (t-170) REVERT: C 123 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7784 (tm-30) REVERT: C 139 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6504 (tt) REVERT: C 311 GLN cc_start: 0.8817 (mm110) cc_final: 0.8578 (mm110) REVERT: C 389 TYR cc_start: 0.7736 (t80) cc_final: 0.7366 (t80) REVERT: C 436 MET cc_start: 0.7742 (mmt) cc_final: 0.7275 (mmt) REVERT: C 451 LYS cc_start: 0.7867 (mttt) cc_final: 0.7375 (mttm) REVERT: C 467 LYS cc_start: 0.8110 (mttt) cc_final: 0.7881 (ptmt) REVERT: C 513 GLN cc_start: 0.7413 (mp10) cc_final: 0.7005 (mp-120) REVERT: C 527 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6188 (tptp) REVERT: D 179 ARG cc_start: 0.8247 (mmt90) cc_final: 0.7892 (mmt-90) REVERT: D 262 GLN cc_start: 0.7796 (tp40) cc_final: 0.7407 (tp-100) REVERT: D 315 LEU cc_start: 0.7587 (tp) cc_final: 0.7078 (tt) REVERT: D 327 MET cc_start: 0.7263 (mmt) cc_final: 0.6866 (mtp) REVERT: D 335 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7023 (tmm160) REVERT: D 420 PHE cc_start: 0.8737 (t80) cc_final: 0.8384 (t80) REVERT: D 426 LYS cc_start: 0.8067 (mmpt) cc_final: 0.7705 (mmmt) REVERT: D 571 ARG cc_start: 0.7220 (ptt90) cc_final: 0.6771 (ttp80) REVERT: E 7 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8932 (tp) REVERT: E 284 GLU cc_start: 0.8777 (mp0) cc_final: 0.8408 (mp0) REVERT: E 368 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7426 (mt-10) REVERT: E 461 ILE cc_start: 0.8896 (mt) cc_final: 0.8685 (mt) REVERT: F 1 MET cc_start: 0.7835 (ttt) cc_final: 0.7477 (ttt) REVERT: F 74 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8814 (pp) REVERT: F 219 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6939 (t80) REVERT: G 16 LEU cc_start: 0.7303 (tp) cc_final: 0.6927 (mp) REVERT: G 140 LYS cc_start: 0.8862 (mttt) cc_final: 0.8583 (mptt) REVERT: G 153 LYS cc_start: 0.7866 (mttt) cc_final: 0.7489 (ptpp) REVERT: G 159 LYS cc_start: 0.9168 (tttt) cc_final: 0.8909 (tptp) REVERT: G 166 ASP cc_start: 0.8179 (m-30) cc_final: 0.7896 (m-30) REVERT: G 190 ASP cc_start: 0.7916 (m-30) cc_final: 0.7044 (p0) REVERT: G 351 HIS cc_start: 0.7738 (m-70) cc_final: 0.7537 (m-70) REVERT: H 19 ARG cc_start: 0.8354 (ttt180) cc_final: 0.7037 (mpt180) REVERT: H 193 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5070 (tp) REVERT: H 314 ARG cc_start: 0.7909 (ttt180) cc_final: 0.7297 (tpt90) outliers start: 141 outliers final: 89 residues processed: 501 average time/residue: 0.2099 time to fit residues: 171.5608 Evaluate side-chains 469 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 368 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 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 505 GLN 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 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 239 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 110 HIS 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 439 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL 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 106 ILE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 371 MET 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 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 247 GLU 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 433 GLU 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 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 Chi-restraints excluded: chain H residue 424 ILE Chi-restraints excluded: chain H residue 435 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 131 optimal weight: 6.9990 chunk 232 optimal weight: 0.0670 chunk 237 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 134 optimal weight: 0.6980 chunk 365 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 overall best weight: 3.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 427 ASN ** B 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN F 275 HIS G 403 HIS H 168 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.147987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120716 restraints weight = 82605.084| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.42 r_work: 0.3594 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34928 Z= 0.185 Angle : 0.594 10.058 47318 Z= 0.305 Chirality : 0.044 0.226 5268 Planarity : 0.004 0.050 6004 Dihedral : 10.165 139.986 5151 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.27 % Allowed : 16.82 % Favored : 78.91 % 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: 1.29 (0.13), residues: 1771 sheet: -1.00 (0.20), residues: 639 loop : -1.55 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.016 0.001 TYR G 371 PHE 0.029 0.002 PHE A 181 TRP 0.016 0.001 TRP A 305 HIS 0.015 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00428 (34928) covalent geometry : angle 0.59419 (47318) hydrogen bonds : bond 0.03876 ( 1604) hydrogen bonds : angle 5.02247 ( 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 521 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 368 time to evaluate : 1.148 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 176 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7221 (tt) REVERT: A 206 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6410 (pp) REVERT: A 230 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 244 MET cc_start: 0.7066 (ttm) cc_final: 0.6684 (ttm) REVERT: A 305 TRP cc_start: 0.8080 (t-100) cc_final: 0.7866 (t-100) REVERT: A 506 TYR cc_start: 0.5839 (m-10) cc_final: 0.5569 (m-10) REVERT: B 178 SER cc_start: 0.8652 (m) cc_final: 0.8388 (p) REVERT: B 231 TYR cc_start: 0.5190 (m-10) cc_final: 0.4792 (m-10) REVERT: B 327 MET cc_start: 0.9213 (mmm) cc_final: 0.8900 (mmm) REVERT: B 482 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7314 (tp) REVERT: C 56 GLU cc_start: 0.5318 (OUTLIER) cc_final: 0.5087 (pm20) REVERT: C 79 SER cc_start: 0.8909 (t) cc_final: 0.8411 (p) REVERT: C 97 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7791 (tm-30) REVERT: C 110 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7855 (t-170) REVERT: C 123 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7807 (tm-30) REVERT: C 139 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6513 (tt) REVERT: C 150 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7554 (p90) REVERT: C 389 TYR cc_start: 0.7729 (t80) cc_final: 0.7348 (t80) REVERT: C 436 MET cc_start: 0.7746 (mmt) cc_final: 0.7306 (mmt) REVERT: C 451 LYS cc_start: 0.7878 (mttt) cc_final: 0.7380 (mttm) REVERT: C 513 GLN cc_start: 0.7424 (mp10) cc_final: 0.6996 (mp-120) REVERT: C 527 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6186 (tptp) REVERT: D 179 ARG cc_start: 0.8263 (mmt90) cc_final: 0.7932 (mmt-90) REVERT: D 315 LEU cc_start: 0.7570 (tp) cc_final: 0.7182 (tp) REVERT: D 335 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7025 (tmm160) REVERT: D 380 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8707 (tt0) REVERT: D 420 PHE cc_start: 0.8734 (t80) cc_final: 0.8383 (t80) REVERT: D 426 LYS cc_start: 0.8060 (mmpt) cc_final: 0.7710 (mmmt) REVERT: E 7 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8956 (tp) REVERT: E 284 GLU cc_start: 0.8792 (mp0) cc_final: 0.8421 (mp0) REVERT: E 368 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7375 (mt-10) REVERT: E 387 MET cc_start: 0.8348 (ptm) cc_final: 0.8088 (tmm) REVERT: E 461 ILE cc_start: 0.8890 (mt) cc_final: 0.8678 (mt) REVERT: F 1 MET cc_start: 0.7889 (ttt) cc_final: 0.7525 (ttt) REVERT: F 74 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8838 (pp) REVERT: F 219 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6925 (t80) REVERT: F 387 MET cc_start: 0.8099 (ttp) cc_final: 0.7857 (ttp) REVERT: G 16 LEU cc_start: 0.7307 (tp) cc_final: 0.6900 (mp) REVERT: G 140 LYS cc_start: 0.8892 (mttt) cc_final: 0.8601 (mptt) REVERT: G 146 GLU cc_start: 0.8983 (pt0) cc_final: 0.8743 (pp20) REVERT: G 153 LYS cc_start: 0.7889 (mttt) cc_final: 0.7511 (ptpp) REVERT: G 159 LYS cc_start: 0.9180 (tttt) cc_final: 0.8922 (tptp) REVERT: G 166 ASP cc_start: 0.8189 (m-30) cc_final: 0.7908 (m-30) REVERT: G 168 HIS cc_start: 0.6854 (t-170) cc_final: 0.6627 (t-170) REVERT: G 190 ASP cc_start: 0.8005 (m-30) cc_final: 0.7088 (p0) REVERT: G 351 HIS cc_start: 0.7762 (m-70) cc_final: 0.7532 (m-70) REVERT: H 19 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7049 (mpt180) REVERT: H 168 HIS cc_start: 0.7741 (t70) cc_final: 0.7503 (t-170) REVERT: H 193 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5389 (tp) REVERT: H 314 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7310 (tpt90) outliers start: 153 outliers final: 102 residues processed: 500 average time/residue: 0.2011 time to fit residues: 165.6632 Evaluate side-chains 471 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 357 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 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 349 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 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 239 ILE 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 482 LEU Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 56 GLU 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 114 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 TYR 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 439 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL 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 290 HIS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 371 MET 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 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 247 GLU 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 115 VAL 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 433 GLU 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 187 ILE Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 387 ILE 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 98 GLN Chi-restraints excluded: chain H residue 130 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 150 optimal weight: 7.9990 chunk 346 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 201 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 280 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN 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 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.146440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.119081 restraints weight = 83053.117| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.42 r_work: 0.3561 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 34928 Z= 0.255 Angle : 0.662 10.742 47318 Z= 0.342 Chirality : 0.046 0.232 5268 Planarity : 0.004 0.049 6004 Dihedral : 10.398 139.319 5151 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.19 % Allowed : 17.37 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 4238 helix: 1.10 (0.12), residues: 1763 sheet: -1.16 (0.20), residues: 614 loop : -1.62 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 328 TYR 0.021 0.002 TYR A 150 PHE 0.032 0.002 PHE C 378 TRP 0.014 0.001 TRP D 305 HIS 0.012 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00590 (34928) covalent geometry : angle 0.66238 (47318) hydrogen bonds : bond 0.04378 ( 1604) hydrogen bonds : angle 5.20208 ( 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 514 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 364 time to evaluate : 1.252 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: 0.7691 (OUTLIER) cc_final: 0.7432 (tt) REVERT: A 206 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6444 (pp) REVERT: A 230 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 178 SER cc_start: 0.8629 (m) cc_final: 0.8369 (p) REVERT: B 231 TYR cc_start: 0.5168 (m-10) cc_final: 0.4754 (m-10) REVERT: B 456 ARG cc_start: 0.8494 (mtt180) cc_final: 0.8140 (ptm-80) REVERT: B 482 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7425 (tp) REVERT: C 79 SER cc_start: 0.8958 (t) cc_final: 0.8458 (p) REVERT: C 97 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7893 (tm-30) REVERT: C 110 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7770 (t-170) REVERT: C 123 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7890 (tm-30) REVERT: C 139 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6458 (tt) REVERT: C 150 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8149 (p90) REVERT: C 191 LYS cc_start: 0.6705 (OUTLIER) cc_final: 0.6334 (tttt) REVERT: C 389 TYR cc_start: 0.7832 (t80) cc_final: 0.7408 (t80) REVERT: C 436 MET cc_start: 0.7795 (mmt) cc_final: 0.7363 (mmt) REVERT: C 451 LYS cc_start: 0.7876 (mttt) cc_final: 0.7364 (mttm) REVERT: C 527 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6206 (tptp) REVERT: D 179 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7934 (mmt-90) REVERT: D 262 GLN cc_start: 0.8278 (tp-100) cc_final: 0.7873 (tp-100) REVERT: D 315 LEU cc_start: 0.7562 (tp) cc_final: 0.7191 (tp) REVERT: D 327 MET cc_start: 0.7529 (mmt) cc_final: 0.7242 (mtp) REVERT: D 420 PHE cc_start: 0.8769 (t80) cc_final: 0.8415 (t80) REVERT: D 426 LYS cc_start: 0.8125 (mmpt) cc_final: 0.7757 (mmmt) REVERT: E 7 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8993 (tp) REVERT: E 387 MET cc_start: 0.8430 (ptm) cc_final: 0.8072 (tmm) REVERT: F 1 MET cc_start: 0.7939 (ttt) cc_final: 0.7587 (ttt) REVERT: F 74 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8828 (pp) REVERT: F 219 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6900 (t80) REVERT: F 422 ARG cc_start: 0.8323 (mtt90) cc_final: 0.7767 (mpt90) REVERT: G 16 LEU cc_start: 0.7311 (tp) cc_final: 0.6903 (mp) REVERT: G 140 LYS cc_start: 0.8902 (mttt) cc_final: 0.8606 (mptt) REVERT: G 146 GLU cc_start: 0.8985 (pt0) cc_final: 0.8731 (pp20) REVERT: G 153 LYS cc_start: 0.7925 (mttt) cc_final: 0.7506 (ptpp) REVERT: G 159 LYS cc_start: 0.9207 (tttt) cc_final: 0.8951 (tptp) REVERT: G 160 LYS cc_start: 0.8710 (ptmt) cc_final: 0.8281 (pttm) REVERT: G 166 ASP cc_start: 0.8256 (m-30) cc_final: 0.7960 (m-30) REVERT: G 168 HIS cc_start: 0.7102 (t-170) cc_final: 0.6896 (t-170) REVERT: G 312 TYR cc_start: 0.7506 (t80) cc_final: 0.7035 (t80) REVERT: G 351 HIS cc_start: 0.7790 (m-70) cc_final: 0.7530 (m-70) REVERT: H 19 ARG cc_start: 0.8372 (ttt180) cc_final: 0.7036 (mpt180) REVERT: H 314 ARG cc_start: 0.7926 (ttt180) cc_final: 0.7296 (tpt90) outliers start: 150 outliers final: 115 residues processed: 491 average time/residue: 0.2009 time to fit residues: 161.9316 Evaluate side-chains 481 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 355 time to evaluate : 1.283 ------------------------------------------------------------------------------- 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 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 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 183 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 THR 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 218 ASP 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 383 PHE Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 482 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 105 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 TYR 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 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 527 LYS Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL 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 127 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 349 ILE 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 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 229 ARG Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 247 GLU 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 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 115 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 433 GLU 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 48 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 387 ILE 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 98 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 154 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 326 optimal weight: 5.9990 chunk 182 optimal weight: 0.0050 chunk 218 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 274 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 348 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 287 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 491 ASN F 275 HIS G 263 HIS ** G 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.149478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122464 restraints weight = 82528.213| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.43 r_work: 0.3613 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 34928 Z= 0.115 Angle : 0.569 9.666 47318 Z= 0.290 Chirality : 0.042 0.242 5268 Planarity : 0.003 0.049 6004 Dihedral : 10.044 138.089 5151 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.13 % Allowed : 18.80 % Favored : 78.07 % 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: -0.27 (0.13), residues: 4238 helix: 1.41 (0.13), residues: 1753 sheet: -0.91 (0.20), residues: 641 loop : -1.50 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 497 TYR 0.019 0.001 TYR B 219 PHE 0.025 0.002 PHE A 181 TRP 0.023 0.001 TRP A 305 HIS 0.013 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00255 (34928) covalent geometry : angle 0.56907 (47318) hydrogen bonds : bond 0.03466 ( 1604) hydrogen bonds : angle 4.92517 ( 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 497 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 385 time to evaluate : 1.020 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: 0.7384 (OUTLIER) cc_final: 0.7176 (tt) REVERT: A 206 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6477 (pp) REVERT: A 230 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7818 (tm-30) REVERT: A 327 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8864 (tmm) REVERT: B 178 SER cc_start: 0.8603 (m) cc_final: 0.8343 (p) REVERT: B 327 MET cc_start: 0.9148 (mmm) cc_final: 0.8787 (mmm) REVERT: C 64 VAL cc_start: 0.6752 (t) cc_final: 0.6414 (m) REVERT: C 79 SER cc_start: 0.8846 (t) cc_final: 0.8338 (p) REVERT: C 97 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7747 (tm-30) REVERT: C 110 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7803 (t-170) REVERT: C 116 GLN cc_start: 0.7800 (tt0) cc_final: 0.7575 (pt0) REVERT: C 123 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7833 (tm-30) REVERT: C 139 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6520 (tt) REVERT: C 150 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7418 (p90) REVERT: C 436 MET cc_start: 0.7663 (mmt) cc_final: 0.7256 (mmt) REVERT: C 451 LYS cc_start: 0.7807 (mttt) cc_final: 0.7315 (mttm) REVERT: C 478 ARG cc_start: 0.6264 (tpm170) cc_final: 0.5892 (tpp-160) REVERT: C 513 GLN cc_start: 0.7450 (mp10) cc_final: 0.7088 (mp-120) REVERT: C 527 LYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6231 (tptp) REVERT: D 179 ARG cc_start: 0.8221 (mmt90) cc_final: 0.7869 (mmt-90) REVERT: D 262 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7445 (tp-100) REVERT: D 315 LEU cc_start: 0.7555 (tp) cc_final: 0.7053 (tt) REVERT: D 327 MET cc_start: 0.7488 (mmt) cc_final: 0.7209 (mtp) REVERT: D 335 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7034 (tmm160) REVERT: D 380 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8654 (tt0) REVERT: D 420 PHE cc_start: 0.8729 (t80) cc_final: 0.8362 (t80) REVERT: D 422 ARG cc_start: 0.8559 (mmt-90) cc_final: 0.8178 (mmp80) REVERT: D 426 LYS cc_start: 0.8042 (mmpt) cc_final: 0.7664 (mmmt) REVERT: D 571 ARG cc_start: 0.7247 (ptt90) cc_final: 0.6942 (ttp80) REVERT: E 7 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8949 (tp) REVERT: E 331 MET cc_start: 0.7104 (tpt) cc_final: 0.6895 (tpt) REVERT: E 461 ILE cc_start: 0.8840 (mt) cc_final: 0.8609 (mt) REVERT: F 1 MET cc_start: 0.7879 (ttt) cc_final: 0.7497 (ttt) REVERT: F 74 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8747 (pp) REVERT: F 219 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6808 (t80) REVERT: F 349 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7439 (mt) REVERT: F 422 ARG cc_start: 0.8323 (mtt90) cc_final: 0.7778 (mpt90) REVERT: G 16 LEU cc_start: 0.7253 (tp) cc_final: 0.6847 (mp) REVERT: G 140 LYS cc_start: 0.8878 (mttt) cc_final: 0.8587 (mptt) REVERT: G 146 GLU cc_start: 0.8970 (pt0) cc_final: 0.8727 (pp20) REVERT: G 153 LYS cc_start: 0.7718 (mttt) cc_final: 0.7275 (ptpp) REVERT: G 159 LYS cc_start: 0.9163 (tttt) cc_final: 0.8819 (ptpt) REVERT: G 160 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8335 (pttm) REVERT: G 166 ASP cc_start: 0.8217 (m-30) cc_final: 0.7935 (m-30) REVERT: G 168 HIS cc_start: 0.6897 (t-170) cc_final: 0.6566 (t-170) REVERT: G 351 HIS cc_start: 0.7800 (m-70) cc_final: 0.7547 (m-70) REVERT: H 19 ARG cc_start: 0.8318 (ttt180) cc_final: 0.6965 (mpt180) REVERT: H 314 ARG cc_start: 0.7930 (ttt180) cc_final: 0.7324 (tpt90) REVERT: H 430 GLU cc_start: 0.8589 (pt0) cc_final: 0.7817 (tp30) outliers start: 112 outliers final: 80 residues processed: 477 average time/residue: 0.2060 time to fit residues: 159.4885 Evaluate side-chains 453 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 362 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 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 546 TYR Chi-restraints excluded: chain B residue 1 MET 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 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 286 VAL 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 105 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 TYR 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 483 SER Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL 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 127 THR 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 484 GLU 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 229 ARG Chi-restraints excluded: chain E residue 234 LEU 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 115 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 439 VAL Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain G residue 5 ILE 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 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 130 THR Chi-restraints excluded: chain H residue 387 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: 2.9990 chunk 287 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 387 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 288 optimal weight: 0.0570 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 491 ASN D 174 ASN F 275 HIS G 263 HIS G 351 HIS H 98 GLN H 168 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.148994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.121823 restraints weight = 82110.873| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.42 r_work: 0.3605 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34928 Z= 0.141 Angle : 0.582 9.662 47318 Z= 0.298 Chirality : 0.043 0.228 5268 Planarity : 0.004 0.051 6004 Dihedral : 10.030 138.515 5149 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.13 % Allowed : 19.25 % Favored : 77.63 % 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: -0.23 (0.13), residues: 4238 helix: 1.46 (0.13), residues: 1749 sheet: -0.89 (0.20), residues: 650 loop : -1.48 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 509 TYR 0.020 0.001 TYR F 304 PHE 0.032 0.002 PHE A 181 TRP 0.014 0.001 TRP B 270 HIS 0.012 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00323 (34928) covalent geometry : angle 0.58197 (47318) hydrogen bonds : bond 0.03580 ( 1604) hydrogen bonds : angle 4.87308 ( 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 486 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 374 time to evaluate : 1.667 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: 0.7055 (OUTLIER) cc_final: 0.6429 (pp) REVERT: A 230 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 327 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8847 (tmm) REVERT: B 17 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6652 (pp20) REVERT: B 178 SER cc_start: 0.8608 (m) cc_final: 0.8360 (p) REVERT: B 231 TYR cc_start: 0.4945 (m-10) cc_final: 0.4597 (m-10) REVERT: B 327 MET cc_start: 0.9104 (mmm) cc_final: 0.8784 (mmm) REVERT: C 64 VAL cc_start: 0.6792 (t) cc_final: 0.6485 (m) REVERT: C 79 SER cc_start: 0.8855 (t) cc_final: 0.8353 (p) REVERT: C 97 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7757 (tm-30) REVERT: C 110 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7847 (t-170) REVERT: C 116 GLN cc_start: 0.7815 (tt0) cc_final: 0.7575 (pt0) REVERT: C 123 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7834 (tm-30) REVERT: C 139 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6557 (tt) REVERT: C 150 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7532 (p90) REVERT: C 311 GLN cc_start: 0.8807 (mm110) cc_final: 0.8450 (mp10) REVERT: C 436 MET cc_start: 0.7719 (mmt) cc_final: 0.7257 (mmt) REVERT: C 451 LYS cc_start: 0.7823 (mttt) cc_final: 0.7340 (mttm) REVERT: C 478 ARG cc_start: 0.6263 (tpm170) cc_final: 0.5847 (tpp-160) REVERT: C 513 GLN cc_start: 0.7412 (mp10) cc_final: 0.6957 (mp-120) REVERT: C 527 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6314 (tptp) REVERT: D 179 ARG cc_start: 0.8238 (mmt90) cc_final: 0.7911 (mmt-90) REVERT: D 262 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7445 (tp-100) REVERT: D 315 LEU cc_start: 0.7601 (tp) cc_final: 0.7080 (tt) REVERT: D 335 ARG cc_start: 0.7653 (ttm110) cc_final: 0.7030 (tmm160) REVERT: D 380 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8668 (tt0) REVERT: D 420 PHE cc_start: 0.8750 (t80) cc_final: 0.8365 (t80) REVERT: D 422 ARG cc_start: 0.8553 (mmt-90) cc_final: 0.8184 (mmp80) REVERT: D 426 LYS cc_start: 0.8011 (mmpt) cc_final: 0.7640 (mmmt) REVERT: D 571 ARG cc_start: 0.7266 (ptt90) cc_final: 0.6943 (ttp80) REVERT: E 461 ILE cc_start: 0.8816 (mt) cc_final: 0.8578 (mt) REVERT: F 1 MET cc_start: 0.7873 (ttt) cc_final: 0.7479 (ttt) REVERT: F 74 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8749 (pp) REVERT: F 219 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6728 (t80) REVERT: F 349 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7457 (mt) REVERT: F 422 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7823 (mpt90) REVERT: G 16 LEU cc_start: 0.7258 (tp) cc_final: 0.6858 (mp) REVERT: G 140 LYS cc_start: 0.8870 (mttt) cc_final: 0.8592 (mptt) REVERT: G 146 GLU cc_start: 0.8969 (pt0) cc_final: 0.8724 (pp20) REVERT: G 153 LYS cc_start: 0.7775 (mttt) cc_final: 0.7334 (ptpp) REVERT: G 159 LYS cc_start: 0.9169 (tttt) cc_final: 0.8819 (ptpt) REVERT: G 160 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8338 (pttm) REVERT: G 166 ASP cc_start: 0.8230 (m-30) cc_final: 0.7950 (m-30) REVERT: G 168 HIS cc_start: 0.6859 (t-170) cc_final: 0.6452 (t-170) REVERT: G 190 ASP cc_start: 0.7837 (m-30) cc_final: 0.7023 (p0) REVERT: H 19 ARG cc_start: 0.8320 (ttt180) cc_final: 0.6940 (mpt180) REVERT: H 193 LEU cc_start: 0.5646 (OUTLIER) cc_final: 0.5393 (tp) REVERT: H 314 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7308 (tpt90) REVERT: H 430 GLU cc_start: 0.8620 (pt0) cc_final: 0.7766 (tp30) outliers start: 112 outliers final: 85 residues processed: 465 average time/residue: 0.2115 time to fit residues: 159.4827 Evaluate side-chains 459 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 364 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 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 546 TYR Chi-restraints excluded: chain B residue 1 MET 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 184 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 267 LEU 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 105 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 TYR 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 483 SER Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 533 VAL Chi-restraints excluded: chain C residue 543 VAL 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 127 THR 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 484 GLU 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 210 VAL Chi-restraints excluded: chain E residue 229 ARG 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 385 THR 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 115 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 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 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 387 ILE 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: 0.5980 chunk 42 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 286 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 271 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 491 ASN D 174 ASN E 278 GLN F 275 HIS G 263 HIS H 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.150827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.123663 restraints weight = 82355.647| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.50 r_work: 0.3633 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34928 Z= 0.108 Angle : 0.574 11.462 47318 Z= 0.293 Chirality : 0.042 0.272 5268 Planarity : 0.003 0.051 6004 Dihedral : 9.854 137.855 5149 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.37 % Allowed : 20.14 % Favored : 77.49 % 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: -0.08 (0.13), residues: 4238 helix: 1.57 (0.13), residues: 1749 sheet: -0.71 (0.20), residues: 670 loop : -1.43 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.023 0.001 TYR A 150 PHE 0.032 0.002 PHE A 181 TRP 0.018 0.001 TRP A 305 HIS 0.010 0.001 HIS G 351 Details of bonding type rmsd covalent geometry : bond 0.00237 (34928) covalent geometry : angle 0.57398 (47318) hydrogen bonds : bond 0.03240 ( 1604) hydrogen bonds : angle 4.77989 ( 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 478 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 393 time to evaluate : 1.223 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: 0.7029 (OUTLIER) cc_final: 0.6425 (pp) REVERT: A 230 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 327 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8835 (tmm) REVERT: B 17 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6586 (pp20) REVERT: B 103 GLU cc_start: 0.8473 (tp30) cc_final: 0.8245 (tp30) REVERT: B 178 SER cc_start: 0.8580 (m) cc_final: 0.8334 (p) REVERT: B 327 MET cc_start: 0.9118 (mmm) cc_final: 0.8788 (mmm) REVERT: B 383 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6298 (t80) REVERT: C 64 VAL cc_start: 0.6752 (t) cc_final: 0.6441 (m) REVERT: C 110 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7818 (t-170) REVERT: C 139 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6638 (tt) REVERT: C 150 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7425 (p90) REVERT: C 311 GLN cc_start: 0.8747 (mm110) cc_final: 0.8393 (mp10) REVERT: C 451 LYS cc_start: 0.7716 (mttt) cc_final: 0.7247 (mttm) REVERT: C 478 ARG cc_start: 0.6527 (tpm170) cc_final: 0.6185 (tpp-160) REVERT: C 513 GLN cc_start: 0.7505 (mp10) cc_final: 0.7088 (mp-120) REVERT: C 527 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6359 (tptp) REVERT: D 179 ARG cc_start: 0.8272 (mmt90) cc_final: 0.7906 (mmt-90) REVERT: D 262 GLN cc_start: 0.8157 (tp-100) cc_final: 0.7412 (tp-100) REVERT: D 315 LEU cc_start: 0.7641 (tp) cc_final: 0.7120 (tt) REVERT: D 335 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7043 (tmm160) REVERT: D 380 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8648 (tt0) REVERT: D 420 PHE cc_start: 0.8718 (t80) cc_final: 0.8346 (t80) REVERT: D 422 ARG cc_start: 0.8587 (mmt-90) cc_final: 0.8205 (mmp80) REVERT: D 426 LYS cc_start: 0.7951 (mmpt) cc_final: 0.7704 (mmmt) REVERT: D 571 ARG cc_start: 0.7266 (ptt90) cc_final: 0.6954 (ttp80) REVERT: E 461 ILE cc_start: 0.8762 (mt) cc_final: 0.8552 (mt) REVERT: F 1 MET cc_start: 0.7840 (ttt) cc_final: 0.7436 (ttt) REVERT: F 74 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8732 (pp) REVERT: F 219 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6632 (t80) REVERT: F 349 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7424 (mt) REVERT: F 422 ARG cc_start: 0.8371 (mtt90) cc_final: 0.8105 (mpt90) REVERT: G 16 LEU cc_start: 0.7278 (tp) cc_final: 0.6878 (mp) REVERT: G 140 LYS cc_start: 0.8823 (mttt) cc_final: 0.8564 (mptt) REVERT: G 146 GLU cc_start: 0.8980 (pt0) cc_final: 0.8724 (pp20) REVERT: G 153 LYS cc_start: 0.7669 (mttt) cc_final: 0.7275 (ptpp) REVERT: G 166 ASP cc_start: 0.8186 (m-30) cc_final: 0.7895 (m-30) REVERT: G 168 HIS cc_start: 0.6737 (t-170) cc_final: 0.6462 (t-170) REVERT: G 190 ASP cc_start: 0.7909 (m-30) cc_final: 0.7052 (p0) REVERT: H 19 ARG cc_start: 0.8275 (ttt180) cc_final: 0.6926 (mpt180) REVERT: H 168 HIS cc_start: 0.7701 (t-90) cc_final: 0.7427 (t-170) REVERT: H 199 PHE cc_start: 0.8435 (m-80) cc_final: 0.8224 (m-80) REVERT: H 314 ARG cc_start: 0.7944 (ttt180) cc_final: 0.7319 (tpt90) REVERT: H 430 GLU cc_start: 0.8593 (pt0) cc_final: 0.7789 (tp30) outliers start: 85 outliers final: 63 residues processed: 462 average time/residue: 0.2084 time to fit residues: 156.1132 Evaluate side-chains 449 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 125 VAL Chi-restraints excluded: chain A residue 175 GLU 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 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 203 VAL Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 522 ILE Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 150 TYR 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 527 LYS Chi-restraints excluded: chain C residue 533 VAL 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 387 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 484 GLU Chi-restraints excluded: chain D residue 522 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 229 ARG Chi-restraints excluded: chain E residue 247 GLU Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 359 ASN 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 115 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 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 65 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 98 GLN Chi-restraints excluded: chain H residue 387 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 216 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 289 optimal weight: 0.0970 chunk 116 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN C 73 ASN D 174 ASN D 448 HIS F 275 HIS H 98 GLN H 168 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.149673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.122656 restraints weight = 82273.962| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.42 r_work: 0.3614 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34928 Z= 0.149 Angle : 0.590 9.679 47318 Z= 0.302 Chirality : 0.043 0.221 5268 Planarity : 0.004 0.068 6004 Dihedral : 9.890 138.511 5144 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.74 % Allowed : 20.06 % Favored : 77.21 % 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: -0.11 (0.13), residues: 4238 helix: 1.54 (0.13), residues: 1748 sheet: -0.77 (0.20), residues: 659 loop : -1.42 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 509 TYR 0.026 0.001 TYR H 200 PHE 0.029 0.002 PHE A 181 TRP 0.014 0.001 TRP A 305 HIS 0.013 0.001 HIS E 290 Details of bonding type rmsd covalent geometry : bond 0.00343 (34928) covalent geometry : angle 0.59033 (47318) hydrogen bonds : bond 0.03512 ( 1604) hydrogen bonds : angle 4.81328 ( 4665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9133.30 seconds wall clock time: 156 minutes 36.09 seconds (9396.09 seconds total)