Starting phenix.real_space_refine on Thu Aug 6 02:45:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vc_69835/08_2026/24vc_69835.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vc_69835/08_2026/24vc_69835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24vc_69835/08_2026/24vc_69835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vc_69835/08_2026/24vc_69835.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24vc_69835/08_2026/24vc_69835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vc_69835/08_2026/24vc_69835.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 8292 2.51 5 N 2096 2.21 5 O 2259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12715 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4552 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 545} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3519 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 417} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ATP': 1, 'CLR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.33, per 1000 atoms: 0.18 Number of scatterers: 12715 At special positions: 0 Unit cell: (80.752, 117.008, 149.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 6 15.00 Mg 2 11.99 O 2259 8.00 N 2096 7.00 C 8292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 475 " distance=2.04 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: 1.00 Conformation dependent library (CDL) restraints added in 606.8 milliseconds 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 73.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 37 through 62 removed outlier: 3.527A pdb=" N PHE A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 62 " --> pdb=" O TYR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 72 removed outlier: 3.505A pdb=" N TYR A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 124 Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 141 through 160 removed outlier: 3.543A pdb=" N ASP A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 182 removed outlier: 4.084A pdb=" N ILE A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 184 through 205 removed outlier: 3.678A pdb=" N VAL A 188 " --> pdb=" O TRP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 232 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 241 through 289 removed outlier: 3.629A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP A 269 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 283 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 309 through 330 removed outlier: 3.827A pdb=" N TYR A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 355 Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 486 through 500 removed outlier: 4.165A pdb=" N ASP A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 4.069A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.876A pdb=" N LYS A 584 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 Processing helix chain 'B' and resid 37 through 62 removed outlier: 3.853A pdb=" N LEU B 62 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 72 removed outlier: 3.637A pdb=" N TYR B 68 " --> pdb=" O PRO B 64 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 141 through 160 removed outlier: 3.849A pdb=" N ASP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 160 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 183 Processing helix chain 'B' and resid 184 through 205 Processing helix chain 'B' and resid 205 through 232 removed outlier: 3.508A pdb=" N VAL B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 241 through 289 removed outlier: 4.094A pdb=" N TRP B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 283 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TYR B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 329 removed outlier: 3.793A pdb=" N CYS B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 327 " --> pdb=" O CYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 354 removed outlier: 3.723A pdb=" N ASP B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'B' and resid 503 through 510 removed outlier: 4.377A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 555 through 569 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.736A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 37 removed outlier: 3.626A pdb=" N LEU C 22 " --> pdb=" O PHE C 18 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 75 removed outlier: 4.044A pdb=" N LEU C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Proline residue: C 65 - end of helix removed outlier: 3.618A pdb=" N MET C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 114 removed outlier: 3.886A pdb=" N VAL C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 3.609A pdb=" N GLU C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 160 removed outlier: 4.270A pdb=" N GLY C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE C 147 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 211 removed outlier: 4.259A pdb=" N LEU C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 224 removed outlier: 4.537A pdb=" N SER C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Proline residue: C 220 - end of helix removed outlier: 3.652A pdb=" N ILE C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 253 Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 262 through 291 Processing helix chain 'C' and resid 292 through 297 removed outlier: 3.650A pdb=" N THR C 295 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 296 " --> pdb=" O TRP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 333 Processing helix chain 'C' and resid 350 through 359 Proline residue: C 357 - end of helix Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 365 through 389 Processing helix chain 'C' and resid 406 through 432 removed outlier: 3.942A pdb=" N SER C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 438 removed outlier: 3.553A pdb=" N VAL C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 486 removed outlier: 3.765A pdb=" N LEU C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 514 removed outlier: 3.533A pdb=" N ASN C 498 " --> pdb=" O TYR C 494 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TRP C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 500 " --> pdb=" O PHE C 496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 404 through 407 removed outlier: 5.472A pdb=" N LYS A 405 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 394 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 387 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 404 through 407 removed outlier: 5.472A pdb=" N LYS A 405 " --> pdb=" O ILE A 394 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 394 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU A 389 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN A 446 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG A 391 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER A 444 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 442 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 419 removed outlier: 6.494A pdb=" N ALA A 545 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 576 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU A 547 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA5, first strand: chain 'B' and resid 404 through 411 removed outlier: 6.997A pdb=" N LYS B 405 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 393 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU B 407 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE B 387 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU B 389 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLN B 446 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG B 391 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N SER B 444 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 442 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 456 through 459 removed outlier: 6.435A pdb=" N ALA B 545 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL B 576 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU B 547 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU B 592 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR B 420 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 390 through 392 removed outlier: 6.879A pdb=" N ILE C 390 " --> pdb=" O LEU C 397 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2511 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: 1.63 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3930 1.34 - 1.46: 2473 1.46 - 1.58: 6503 1.58 - 1.69: 9 1.69 - 1.81: 95 Bond restraints: 13010 Sorted by residual: bond pdb=" CA GLY B 486 " pdb=" C GLY B 486 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.77e+00 bond pdb=" C LEU B 478 " pdb=" N LYS B 479 " ideal model delta sigma weight residual 1.332 1.312 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" N GLY B 486 " pdb=" CA GLY B 486 " ideal model delta sigma weight residual 1.464 1.449 0.016 1.12e-02 7.97e+03 1.97e+00 bond pdb=" C ARG B 13 " pdb=" N PRO B 14 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 bond pdb=" C17 CLR B 702 " pdb=" C20 CLR B 702 " ideal model delta sigma weight residual 1.535 1.559 -0.024 2.00e-02 2.50e+03 1.41e+00 ... (remaining 13005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 17390 2.16 - 4.32: 204 4.32 - 6.48: 43 6.48 - 8.65: 6 8.65 - 10.81: 4 Bond angle restraints: 17647 Sorted by residual: angle pdb=" N ILE B 289 " pdb=" CA ILE B 289 " pdb=" C ILE B 289 " ideal model delta sigma weight residual 111.91 108.16 3.75 8.90e-01 1.26e+00 1.78e+01 angle pdb=" CA SER B 581 " pdb=" C SER B 581 " pdb=" N LEU B 582 " ideal model delta sigma weight residual 118.14 113.39 4.75 1.31e+00 5.83e-01 1.31e+01 angle pdb=" CB MET C 437 " pdb=" CG MET C 437 " pdb=" SD MET C 437 " ideal model delta sigma weight residual 112.70 123.51 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" O SER B 581 " pdb=" C SER B 581 " pdb=" N LEU B 582 " ideal model delta sigma weight residual 122.43 127.23 -4.80 1.34e+00 5.57e-01 1.28e+01 angle pdb=" C PHE C 297 " pdb=" N CYS C 298 " pdb=" CA CYS C 298 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.49e+00 ... (remaining 17642 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 6597 17.67 - 35.35: 830 35.35 - 53.02: 264 53.02 - 70.69: 48 70.69 - 88.37: 21 Dihedral angle restraints: 7760 sinusoidal: 3209 harmonic: 4551 Sorted by residual: dihedral pdb=" CA ILE A 475 " pdb=" C ILE A 475 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ILE B 475 " pdb=" C ILE B 475 " pdb=" N TYR B 476 " pdb=" CA TYR B 476 " ideal model delta harmonic sigma weight residual -180.00 -152.72 -27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CB CYS C 466 " pdb=" SG CYS C 466 " pdb=" SG CYS C 475 " pdb=" CB CYS C 475 " ideal model delta sinusoidal sigma weight residual 93.00 127.45 -34.45 1 1.00e+01 1.00e-02 1.68e+01 ... (remaining 7757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1827 0.067 - 0.133: 180 0.133 - 0.200: 11 0.200 - 0.267: 0 0.267 - 0.333: 1 Chirality restraints: 2019 Sorted by residual: chirality pdb=" C17 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C16 CLR B 702 " pdb=" C20 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C20 CLR B 702 " pdb=" C17 CLR B 702 " pdb=" C21 CLR B 702 " pdb=" C22 CLR B 702 " both_signs ideal model delta sigma weight residual False 2.59 2.40 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CG LEU C 317 " pdb=" CB LEU C 317 " pdb=" CD1 LEU C 317 " pdb=" CD2 LEU C 317 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2016 not shown) Planarity restraints: 2165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 64 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.68e+00 pdb=" N PRO C 65 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 65 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 65 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 452 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 453 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 453 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 453 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 470 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 471 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 471 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 471 " -0.021 5.00e-02 4.00e+02 ... (remaining 2162 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 10 2.51 - 3.11: 9369 3.11 - 3.71: 20092 3.71 - 4.30: 28667 4.30 - 4.90: 48253 Nonbonded interactions: 106391 Sorted by model distance: nonbonded pdb=" OG1 THR A 428 " pdb="MG MG A 702 " model vdw 1.918 2.170 nonbonded pdb=" OG1 THR B 428 " pdb="MG MG B 703 " model vdw 1.970 2.170 nonbonded pdb=" OE1 GLN A 461 " pdb="MG MG A 702 " model vdw 2.082 2.170 nonbonded pdb=" OE1 GLN B 461 " pdb="MG MG B 703 " model vdw 2.187 2.170 nonbonded pdb=" O3G ATP B 701 " pdb="MG MG B 703 " model vdw 2.226 2.170 ... (remaining 106386 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 13 through 701) selection = (chain 'B' and resid 13 through 701) } 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: 4.140 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 10.340 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.004 0.041 13011 Z= 0.166 Angle : 0.636 10.806 17649 Z= 0.327 Chirality : 0.042 0.333 2019 Planarity : 0.004 0.048 2165 Dihedral : 17.547 88.366 4829 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.79 % Allowed : 28.09 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 0.49 (0.21), residues: 1541 helix: 1.16 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -1.89 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.022 0.001 TYR C 123 PHE 0.013 0.001 PHE B 465 TRP 0.021 0.001 TRP B 518 HIS 0.003 0.001 HIS C 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (13010) covalent geometry : angle 0.63638 / 0.33 (17647) SS BOND : bond 0.00591 / 0.31 ( 1) SS BOND : angle 0.30219 / 0.16 ( 2) hydrogen bonds : bond 0.14731 / 9.08 ( 847) hydrogen bonds : angle 5.65723 / 4.11 ( 2511) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.462 Fit side-chains REVERT: A 17 ASP cc_start: 0.6966 (p0) cc_final: 0.6429 (p0) REVERT: A 251 ARG cc_start: 0.8001 (ttm170) cc_final: 0.7416 (mtm110) REVERT: A 318 ILE cc_start: 0.7865 (mm) cc_final: 0.7495 (mp) REVERT: A 322 SER cc_start: 0.8470 (t) cc_final: 0.7928 (p) REVERT: A 348 ARG cc_start: 0.7990 (ptm-80) cc_final: 0.7447 (ttp80) REVERT: A 401 LYS cc_start: 0.7986 (pttp) cc_final: 0.7029 (ttpt) REVERT: A 413 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 442 ARG cc_start: 0.7317 (mtm110) cc_final: 0.6673 (mtp180) REVERT: A 462 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6762 (mptt) REVERT: A 479 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7503 (ptpt) REVERT: A 480 GLU cc_start: 0.7529 (pt0) cc_final: 0.6888 (tt0) REVERT: A 495 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7263 (ttp-170) REVERT: A 543 LYS cc_start: 0.7611 (tttt) cc_final: 0.7186 (tptt) REVERT: A 556 GLU cc_start: 0.8043 (tt0) cc_final: 0.6846 (mp0) REVERT: A 557 GLU cc_start: 0.8154 (tt0) cc_final: 0.7501 (mp0) REVERT: A 580 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7593 (tm-30) REVERT: B 100 ASP cc_start: 0.7658 (t70) cc_final: 0.7074 (m-30) REVERT: B 137 ASP cc_start: 0.8000 (p0) cc_final: 0.7729 (p0) REVERT: B 189 SER cc_start: 0.8400 (t) cc_final: 0.8152 (m) REVERT: B 251 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.6662 (ttp80) REVERT: B 319 TYR cc_start: 0.8066 (m-10) cc_final: 0.7638 (m-80) REVERT: B 491 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7015 (mp0) REVERT: B 599 GLU cc_start: 0.7394 (mp0) cc_final: 0.6923 (mt-10) REVERT: C 22 LEU cc_start: 0.6967 (tm) cc_final: 0.6185 (mt) REVERT: C 40 ARG cc_start: 0.7144 (mpt180) cc_final: 0.6375 (mtp-110) REVERT: C 115 TRP cc_start: 0.7329 (t-100) cc_final: 0.6293 (t60) REVERT: C 221 LEU cc_start: 0.7045 (tt) cc_final: 0.6230 (mm) REVERT: C 266 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6680 (ttmm) REVERT: C 273 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6647 (mt-10) REVERT: C 284 ARG cc_start: 0.6852 (mmm160) cc_final: 0.6377 (ptm-80) REVERT: C 291 ASN cc_start: 0.5675 (m110) cc_final: 0.4718 (p0) REVERT: C 315 VAL cc_start: 0.8353 (m) cc_final: 0.8096 (p) REVERT: C 330 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6435 (tmtt) REVERT: C 363 PHE cc_start: 0.6671 (t80) cc_final: 0.6432 (t80) REVERT: C 375 MET cc_start: 0.6419 (mtp) cc_final: 0.6061 (mpp) REVERT: C 402 ARG cc_start: 0.6827 (ptp-170) cc_final: 0.6186 (ptt90) outliers start: 11 outliers final: 6 residues processed: 209 average time/residue: 0.5217 time to fit residues: 118.5160 Evaluate side-chains 192 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 183 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain C residue 266 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 243 HIS B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.179623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117242 restraints weight = 13412.684| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.70 r_work: 0.3152 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13011 Z= 0.133 Angle : 0.562 10.149 17649 Z= 0.278 Chirality : 0.040 0.330 2019 Planarity : 0.004 0.037 2165 Dihedral : 8.731 84.925 1874 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.53 % Allowed : 24.57 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.10 (0.21), residues: 1541 helix: 1.65 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.84 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.012 0.001 TYR C 214 PHE 0.019 0.001 PHE C 28 TRP 0.020 0.001 TRP B 518 HIS 0.002 0.001 HIS C 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13010) covalent geometry : angle 0.56233 / 0.28 (17647) SS BOND : bond 0.00601 / 0.32 ( 1) SS BOND : angle 0.23819 / 0.13 ( 2) hydrogen bonds : bond 0.04703 / 3.09 ( 847) hydrogen bonds : angle 4.18143 / 3.03 ( 2511) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 0.352 Fit side-chains REVERT: A 25 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7840 (mm) REVERT: A 251 ARG cc_start: 0.8225 (ttm170) cc_final: 0.7731 (mtm110) REVERT: A 318 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7744 (mp) REVERT: A 322 SER cc_start: 0.8447 (t) cc_final: 0.7986 (p) REVERT: A 348 ARG cc_start: 0.8030 (ptm-80) cc_final: 0.7736 (ttp80) REVERT: A 401 LYS cc_start: 0.7987 (pttp) cc_final: 0.7140 (ttpt) REVERT: A 413 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 442 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7054 (mtp180) REVERT: A 462 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7043 (mppt) REVERT: A 480 GLU cc_start: 0.7673 (pt0) cc_final: 0.7129 (tt0) REVERT: A 495 ARG cc_start: 0.8017 (ttp-110) cc_final: 0.7646 (ttp-170) REVERT: A 543 LYS cc_start: 0.7914 (tttt) cc_final: 0.7615 (tptt) REVERT: A 556 GLU cc_start: 0.7848 (tt0) cc_final: 0.7059 (mp0) REVERT: A 557 GLU cc_start: 0.7900 (tt0) cc_final: 0.7514 (mm-30) REVERT: A 580 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 17 ASP cc_start: 0.6810 (t70) cc_final: 0.6509 (t0) REVERT: B 90 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7320 (mp) REVERT: B 100 ASP cc_start: 0.7906 (t70) cc_final: 0.7449 (m-30) REVERT: B 137 ASP cc_start: 0.8199 (p0) cc_final: 0.7901 (p0) REVERT: B 251 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7043 (ttp80) REVERT: B 318 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7226 (mp) REVERT: B 319 TYR cc_start: 0.8383 (m-10) cc_final: 0.7994 (m-80) REVERT: B 326 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: B 491 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7336 (mp0) REVERT: B 515 GLN cc_start: 0.7799 (tt0) cc_final: 0.7345 (tp-100) REVERT: B 599 GLU cc_start: 0.7631 (mp0) cc_final: 0.7248 (mt-10) REVERT: C 22 LEU cc_start: 0.7118 (tm) cc_final: 0.6425 (mt) REVERT: C 40 ARG cc_start: 0.7087 (mpt180) cc_final: 0.6423 (mtp-110) REVERT: C 43 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5677 (tm-30) REVERT: C 77 GLN cc_start: 0.5821 (OUTLIER) cc_final: 0.5053 (tp40) REVERT: C 115 TRP cc_start: 0.7362 (t-100) cc_final: 0.6508 (t60) REVERT: C 206 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7562 (tt) REVERT: C 221 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6482 (mm) REVERT: C 273 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6851 (mt-10) REVERT: C 284 ARG cc_start: 0.6848 (mmm160) cc_final: 0.6436 (ptm-80) REVERT: C 291 ASN cc_start: 0.5694 (m110) cc_final: 0.4718 (p0) REVERT: C 326 SER cc_start: 0.7697 (t) cc_final: 0.7381 (m) REVERT: C 330 LYS cc_start: 0.7403 (mtmt) cc_final: 0.6742 (tmtt) REVERT: C 375 MET cc_start: 0.6561 (mtp) cc_final: 0.6241 (mpp) REVERT: C 402 ARG cc_start: 0.6909 (ptp-170) cc_final: 0.6204 (ptt90) REVERT: C 431 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8335 (mm) outliers start: 63 outliers final: 21 residues processed: 236 average time/residue: 0.4819 time to fit residues: 124.5769 Evaluate side-chains 209 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 180 GLN B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.177713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115026 restraints weight = 13570.028| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.70 r_work: 0.3119 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13011 Z= 0.166 Angle : 0.584 10.389 17649 Z= 0.290 Chirality : 0.042 0.334 2019 Planarity : 0.004 0.038 2165 Dihedral : 8.550 82.263 1860 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.17 % Allowed : 25.07 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.18 (0.21), residues: 1541 helix: 1.72 (0.15), residues: 1121 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.014 0.001 TYR A 123 PHE 0.012 0.001 PHE B 99 TRP 0.021 0.001 TRP B 518 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13010) covalent geometry : angle 0.58442 / 0.29 (17647) SS BOND : bond 0.00482 / 0.25 ( 1) SS BOND : angle 0.20438 / 0.11 ( 2) hydrogen bonds : bond 0.04914 / 3.24 ( 847) hydrogen bonds : angle 4.10903 / 2.97 ( 2511) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 0.499 Fit side-chains REVERT: A 25 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 322 SER cc_start: 0.8488 (t) cc_final: 0.8006 (p) REVERT: A 348 ARG cc_start: 0.8141 (ptm-80) cc_final: 0.7633 (ttp80) REVERT: A 401 LYS cc_start: 0.7970 (pttp) cc_final: 0.7103 (ttpt) REVERT: A 413 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 442 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7091 (mtp85) REVERT: A 462 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7040 (mppt) REVERT: A 480 GLU cc_start: 0.7695 (pt0) cc_final: 0.7105 (tt0) REVERT: A 495 ARG cc_start: 0.8039 (ttp-110) cc_final: 0.7593 (ttp-170) REVERT: A 543 LYS cc_start: 0.7975 (tttt) cc_final: 0.7610 (tptt) REVERT: A 556 GLU cc_start: 0.7868 (tt0) cc_final: 0.7085 (mp0) REVERT: A 557 GLU cc_start: 0.7901 (tt0) cc_final: 0.7541 (mm-30) REVERT: A 580 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 17 ASP cc_start: 0.6877 (t70) cc_final: 0.6587 (t0) REVERT: B 25 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7739 (mp) REVERT: B 90 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7334 (mp) REVERT: B 100 ASP cc_start: 0.7983 (t70) cc_final: 0.7486 (m-30) REVERT: B 137 ASP cc_start: 0.8190 (p0) cc_final: 0.7883 (p0) REVERT: B 155 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7782 (ttp-110) REVERT: B 251 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7119 (ttp80) REVERT: B 318 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7178 (mp) REVERT: B 319 TYR cc_start: 0.8390 (m-10) cc_final: 0.7964 (m-80) REVERT: B 326 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: B 491 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7349 (mp0) REVERT: B 515 GLN cc_start: 0.7838 (tt0) cc_final: 0.7343 (tp-100) REVERT: B 571 MET cc_start: 0.8207 (mmt) cc_final: 0.7961 (mmt) REVERT: B 599 GLU cc_start: 0.7664 (mp0) cc_final: 0.7218 (tt0) REVERT: C 22 LEU cc_start: 0.7122 (tm) cc_final: 0.6434 (mt) REVERT: C 40 ARG cc_start: 0.7142 (mpt180) cc_final: 0.6443 (mtp-110) REVERT: C 43 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5576 (tm-30) REVERT: C 77 GLN cc_start: 0.5865 (OUTLIER) cc_final: 0.5038 (tp40) REVERT: C 115 TRP cc_start: 0.7411 (t-100) cc_final: 0.6551 (t60) REVERT: C 206 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7465 (tt) REVERT: C 221 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6514 (mm) REVERT: C 273 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6862 (mt-10) REVERT: C 284 ARG cc_start: 0.6857 (mmm160) cc_final: 0.6413 (ttt-90) REVERT: C 291 ASN cc_start: 0.5687 (m110) cc_final: 0.4708 (p0) REVERT: C 313 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7733 (mt) REVERT: C 330 LYS cc_start: 0.7484 (mtmt) cc_final: 0.6812 (tmtt) REVERT: C 375 MET cc_start: 0.6554 (mtp) cc_final: 0.6229 (mpp) REVERT: C 402 ARG cc_start: 0.6917 (ptp-170) cc_final: 0.6219 (ptt90) REVERT: C 434 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6564 (tp40) outliers start: 58 outliers final: 26 residues processed: 221 average time/residue: 0.5336 time to fit residues: 128.7879 Evaluate side-chains 212 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 GLN Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 180 GLN B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.175480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.119884 restraints weight = 13427.164| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.96 r_work: 0.3125 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13011 Z= 0.186 Angle : 0.596 10.208 17649 Z= 0.296 Chirality : 0.043 0.337 2019 Planarity : 0.004 0.040 2165 Dihedral : 8.733 85.954 1860 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.32 % Allowed : 23.92 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.21 (0.21), residues: 1541 helix: 1.74 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.015 0.002 TYR C 123 PHE 0.013 0.001 PHE B 99 TRP 0.022 0.001 TRP B 518 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (13010) covalent geometry : angle 0.59595 / 0.30 (17647) SS BOND : bond 0.00411 / 0.22 ( 1) SS BOND : angle 0.18340 / 0.10 ( 2) hydrogen bonds : bond 0.05018 / 3.31 ( 847) hydrogen bonds : angle 4.11108 / 2.97 ( 2511) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 176 time to evaluate : 0.465 Fit side-chains REVERT: A 25 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7625 (mm) REVERT: A 251 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7761 (mtm110) REVERT: A 322 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7678 (p) REVERT: A 348 ARG cc_start: 0.8029 (ptm-80) cc_final: 0.7458 (ttp80) REVERT: A 401 LYS cc_start: 0.7861 (pttp) cc_final: 0.6995 (ttpt) REVERT: A 442 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6805 (mtp85) REVERT: A 462 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.6872 (mptt) REVERT: A 480 GLU cc_start: 0.7623 (pt0) cc_final: 0.6977 (tt0) REVERT: A 495 ARG cc_start: 0.7841 (ttp-110) cc_final: 0.7358 (ttp-170) REVERT: A 543 LYS cc_start: 0.7820 (tttt) cc_final: 0.7504 (tttt) REVERT: A 556 GLU cc_start: 0.7682 (tt0) cc_final: 0.6770 (mp0) REVERT: A 557 GLU cc_start: 0.7756 (tt0) cc_final: 0.7363 (mp0) REVERT: A 580 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7354 (tm-30) REVERT: B 25 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7456 (mp) REVERT: B 90 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7134 (mp) REVERT: B 100 ASP cc_start: 0.7934 (t70) cc_final: 0.7334 (m-30) REVERT: B 137 ASP cc_start: 0.8074 (p0) cc_final: 0.7789 (p0) REVERT: B 251 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.6941 (ttp80) REVERT: B 318 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.6947 (mp) REVERT: B 319 TYR cc_start: 0.8233 (m-10) cc_final: 0.7800 (m-80) REVERT: B 326 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: B 491 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7143 (mp0) REVERT: B 515 GLN cc_start: 0.7809 (tt0) cc_final: 0.7292 (tp-100) REVERT: C 22 LEU cc_start: 0.7060 (tm) cc_final: 0.6426 (mt) REVERT: C 37 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7381 (tp40) REVERT: C 40 ARG cc_start: 0.7161 (mpt180) cc_final: 0.6394 (mtp-110) REVERT: C 43 GLU cc_start: 0.5693 (OUTLIER) cc_final: 0.5435 (tm-30) REVERT: C 64 LEU cc_start: 0.7326 (tt) cc_final: 0.7090 (tt) REVERT: C 115 TRP cc_start: 0.7379 (t-100) cc_final: 0.6454 (t60) REVERT: C 206 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7264 (tt) REVERT: C 221 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6523 (mm) REVERT: C 273 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6758 (mt-10) REVERT: C 284 ARG cc_start: 0.6910 (mmm160) cc_final: 0.6409 (ttt-90) REVERT: C 291 ASN cc_start: 0.5820 (m110) cc_final: 0.4817 (p0) REVERT: C 313 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7697 (mt) REVERT: C 330 LYS cc_start: 0.7465 (mtmt) cc_final: 0.6770 (tmtt) REVERT: C 375 MET cc_start: 0.6556 (mtp) cc_final: 0.6190 (mpp) REVERT: C 434 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6576 (tp40) outliers start: 74 outliers final: 29 residues processed: 234 average time/residue: 0.5027 time to fit residues: 128.9427 Evaluate side-chains 215 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 137 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 180 GLN B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.179222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.123289 restraints weight = 13473.681| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.17 r_work: 0.3134 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13011 Z= 0.133 Angle : 0.550 10.202 17649 Z= 0.273 Chirality : 0.040 0.331 2019 Planarity : 0.004 0.042 2165 Dihedral : 8.386 82.606 1860 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.45 % Allowed : 24.93 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.45 (0.21), residues: 1541 helix: 1.92 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 564 TYR 0.014 0.001 TYR C 143 PHE 0.012 0.001 PHE A 464 TRP 0.019 0.001 TRP B 518 HIS 0.003 0.001 HIS C 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (13010) covalent geometry : angle 0.55021 / 0.27 (17647) SS BOND : bond 0.00697 / 0.37 ( 1) SS BOND : angle 0.13240 / 0.07 ( 2) hydrogen bonds : bond 0.04434 / 2.93 ( 847) hydrogen bonds : angle 3.95216 / 2.86 ( 2511) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.456 Fit side-chains REVERT: A 251 ARG cc_start: 0.8387 (ttm170) cc_final: 0.7903 (mtm110) REVERT: A 318 ILE cc_start: 0.8145 (mm) cc_final: 0.7769 (mp) REVERT: A 322 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 348 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7654 (ttp80) REVERT: A 401 LYS cc_start: 0.7858 (pttp) cc_final: 0.7062 (ttpt) REVERT: A 413 GLU cc_start: 0.8264 (tt0) cc_final: 0.8032 (tt0) REVERT: A 442 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7111 (mtp180) REVERT: A 462 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7096 (mppt) REVERT: A 480 GLU cc_start: 0.7614 (pt0) cc_final: 0.7005 (tt0) REVERT: A 495 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7611 (ttp-170) REVERT: A 543 LYS cc_start: 0.8043 (tttt) cc_final: 0.7783 (tttt) REVERT: A 556 GLU cc_start: 0.7829 (tt0) cc_final: 0.7017 (mp0) REVERT: A 557 GLU cc_start: 0.7966 (tt0) cc_final: 0.7633 (mp0) REVERT: A 580 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 17 ASP cc_start: 0.6843 (t70) cc_final: 0.6559 (t0) REVERT: B 25 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7780 (mp) REVERT: B 90 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7320 (mp) REVERT: B 100 ASP cc_start: 0.8001 (t70) cc_final: 0.7547 (m-30) REVERT: B 137 ASP cc_start: 0.8191 (p0) cc_final: 0.7896 (p0) REVERT: B 155 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7799 (ttp-110) REVERT: B 251 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7193 (ttp80) REVERT: B 318 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7237 (mp) REVERT: B 319 TYR cc_start: 0.8411 (m-10) cc_final: 0.7960 (m-80) REVERT: B 326 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: B 349 GLU cc_start: 0.8615 (pt0) cc_final: 0.8364 (pt0) REVERT: B 491 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7399 (mp0) REVERT: B 515 GLN cc_start: 0.7735 (tt0) cc_final: 0.7299 (tp-100) REVERT: B 599 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: C 37 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7314 (tp40) REVERT: C 40 ARG cc_start: 0.7133 (mpt180) cc_final: 0.6376 (mtp-110) REVERT: C 43 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5521 (tm-30) REVERT: C 77 GLN cc_start: 0.5818 (OUTLIER) cc_final: 0.5020 (tp40) REVERT: C 115 TRP cc_start: 0.7387 (t-100) cc_final: 0.6502 (t60) REVERT: C 206 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7462 (tt) REVERT: C 221 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6664 (mm) REVERT: C 273 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6927 (mt-10) REVERT: C 284 ARG cc_start: 0.6782 (mmm160) cc_final: 0.6330 (tmt-80) REVERT: C 291 ASN cc_start: 0.5811 (m110) cc_final: 0.4803 (p0) REVERT: C 313 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7738 (mt) REVERT: C 330 LYS cc_start: 0.7474 (mtmt) cc_final: 0.6829 (tmtt) REVERT: C 375 MET cc_start: 0.6547 (mtp) cc_final: 0.6171 (mpp) outliers start: 62 outliers final: 31 residues processed: 236 average time/residue: 0.5437 time to fit residues: 140.0128 Evaluate side-chains 222 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 180 GLN B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.176553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121921 restraints weight = 13409.234| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.17 r_work: 0.3124 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13011 Z= 0.159 Angle : 0.588 10.293 17649 Z= 0.288 Chirality : 0.041 0.336 2019 Planarity : 0.004 0.040 2165 Dihedral : 8.482 81.623 1860 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.03 % Allowed : 25.07 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.40 (0.21), residues: 1541 helix: 1.88 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -1.81 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.020 0.001 TYR C 123 PHE 0.011 0.001 PHE B 99 TRP 0.021 0.001 TRP B 518 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (13010) covalent geometry : angle 0.58786 / 0.29 (17647) SS BOND : bond 0.00548 / 0.29 ( 1) SS BOND : angle 0.18419 / 0.11 ( 2) hydrogen bonds : bond 0.04681 / 3.09 ( 847) hydrogen bonds : angle 3.98940 / 2.88 ( 2511) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 0.450 Fit side-chains REVERT: A 322 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.7955 (p) REVERT: A 348 ARG cc_start: 0.8144 (ptm-80) cc_final: 0.7629 (ttp80) REVERT: A 401 LYS cc_start: 0.7850 (pttp) cc_final: 0.7050 (ttpt) REVERT: A 413 GLU cc_start: 0.8284 (tt0) cc_final: 0.8073 (tt0) REVERT: A 442 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7100 (mtp180) REVERT: A 462 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7050 (mptt) REVERT: A 480 GLU cc_start: 0.7639 (pt0) cc_final: 0.7048 (tt0) REVERT: A 495 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7670 (ttp-170) REVERT: A 543 LYS cc_start: 0.8089 (tttt) cc_final: 0.7810 (tttt) REVERT: A 556 GLU cc_start: 0.7854 (tt0) cc_final: 0.7018 (mp0) REVERT: A 557 GLU cc_start: 0.7968 (tt0) cc_final: 0.7628 (mp0) REVERT: A 580 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 25 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 90 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7334 (mp) REVERT: B 100 ASP cc_start: 0.8035 (t70) cc_final: 0.7537 (m-30) REVERT: B 137 ASP cc_start: 0.8193 (p0) cc_final: 0.7893 (p0) REVERT: B 251 ARG cc_start: 0.7825 (mtp-110) cc_final: 0.7153 (ttp80) REVERT: B 318 ILE cc_start: 0.7774 (OUTLIER) cc_final: 0.7185 (mp) REVERT: B 319 TYR cc_start: 0.8417 (m-10) cc_final: 0.7985 (m-80) REVERT: B 326 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: B 491 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7376 (mp0) REVERT: B 515 GLN cc_start: 0.7718 (tt0) cc_final: 0.7292 (tp-100) REVERT: B 599 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: C 22 LEU cc_start: 0.7138 (tm) cc_final: 0.6409 (mt) REVERT: C 37 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: C 40 ARG cc_start: 0.7097 (mpt180) cc_final: 0.6366 (mtp-110) REVERT: C 43 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5517 (tm-30) REVERT: C 115 TRP cc_start: 0.7384 (t-100) cc_final: 0.6490 (t60) REVERT: C 206 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7480 (tt) REVERT: C 221 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6651 (mm) REVERT: C 273 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6945 (mt-10) REVERT: C 284 ARG cc_start: 0.6768 (mmm160) cc_final: 0.6349 (tmt-80) REVERT: C 291 ASN cc_start: 0.5816 (m110) cc_final: 0.4794 (p0) REVERT: C 313 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7756 (mt) REVERT: C 330 LYS cc_start: 0.7533 (mtmt) cc_final: 0.6831 (tmtt) REVERT: C 434 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.6611 (tp40) outliers start: 70 outliers final: 34 residues processed: 231 average time/residue: 0.5236 time to fit residues: 132.1908 Evaluate side-chains 225 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 84 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 180 GLN B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.175877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.121453 restraints weight = 13455.165| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.39 r_work: 0.3111 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13011 Z= 0.171 Angle : 0.598 10.209 17649 Z= 0.294 Chirality : 0.042 0.338 2019 Planarity : 0.004 0.043 2165 Dihedral : 8.607 83.350 1860 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.96 % Allowed : 25.50 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.34 (0.21), residues: 1541 helix: 1.82 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.77 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.019 0.001 TYR C 123 PHE 0.012 0.001 PHE B 465 TRP 0.021 0.001 TRP B 518 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (13010) covalent geometry : angle 0.59758 / 0.29 (17647) SS BOND : bond 0.00498 / 0.26 ( 1) SS BOND : angle 0.19617 / 0.11 ( 2) hydrogen bonds : bond 0.04801 / 3.17 ( 847) hydrogen bonds : angle 4.02607 / 2.91 ( 2511) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 178 time to evaluate : 0.417 Fit side-chains REVERT: A 251 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7820 (mtm110) REVERT: A 322 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.7967 (p) REVERT: A 348 ARG cc_start: 0.8169 (ptm-80) cc_final: 0.7653 (ttp80) REVERT: A 401 LYS cc_start: 0.7869 (pttp) cc_final: 0.7073 (ttpt) REVERT: A 442 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7094 (mtp180) REVERT: A 462 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7107 (mptt) REVERT: A 480 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7089 (tt0) REVERT: A 495 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7666 (ttp-170) REVERT: A 543 LYS cc_start: 0.8065 (tttt) cc_final: 0.7844 (tttt) REVERT: A 556 GLU cc_start: 0.7859 (tt0) cc_final: 0.7031 (mp0) REVERT: A 557 GLU cc_start: 0.7987 (tt0) cc_final: 0.7627 (mp0) REVERT: A 580 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 17 ASP cc_start: 0.6953 (t70) cc_final: 0.6662 (t0) REVERT: B 25 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7744 (mp) REVERT: B 90 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7317 (mp) REVERT: B 100 ASP cc_start: 0.8030 (t70) cc_final: 0.7536 (m-30) REVERT: B 137 ASP cc_start: 0.8244 (p0) cc_final: 0.7953 (p0) REVERT: B 251 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7197 (ttp80) REVERT: B 318 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7199 (mp) REVERT: B 319 TYR cc_start: 0.8434 (m-10) cc_final: 0.8016 (m-80) REVERT: B 326 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: B 442 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7347 (mtm110) REVERT: B 491 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7371 (mp0) REVERT: B 515 GLN cc_start: 0.7753 (tt0) cc_final: 0.7315 (tp-100) REVERT: B 571 MET cc_start: 0.8229 (mmt) cc_final: 0.7938 (mmt) REVERT: C 22 LEU cc_start: 0.7119 (tm) cc_final: 0.6413 (mt) REVERT: C 37 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: C 40 ARG cc_start: 0.7168 (mpt180) cc_final: 0.6414 (mtp-110) REVERT: C 43 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.5498 (tm-30) REVERT: C 77 GLN cc_start: 0.5860 (OUTLIER) cc_final: 0.4966 (tp40) REVERT: C 115 TRP cc_start: 0.7376 (t-100) cc_final: 0.6457 (t60) REVERT: C 206 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7478 (tt) REVERT: C 221 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6601 (mm) REVERT: C 273 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6942 (mt-10) REVERT: C 284 ARG cc_start: 0.6781 (mmm160) cc_final: 0.6139 (tmm160) REVERT: C 291 ASN cc_start: 0.5846 (m110) cc_final: 0.4826 (p0) REVERT: C 313 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7741 (mt) REVERT: C 330 LYS cc_start: 0.7538 (mtmt) cc_final: 0.6840 (tmtt) REVERT: C 434 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6609 (tp40) outliers start: 69 outliers final: 37 residues processed: 229 average time/residue: 0.5184 time to fit residues: 129.8466 Evaluate side-chains 226 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain C residue 37 GLN Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 0.0040 chunk 76 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 180 GLN B 258 GLN C 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.178407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124342 restraints weight = 13280.330| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.16 r_work: 0.3163 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13011 Z= 0.130 Angle : 0.564 10.622 17649 Z= 0.276 Chirality : 0.040 0.336 2019 Planarity : 0.004 0.042 2165 Dihedral : 8.219 85.098 1860 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.09 % Allowed : 26.58 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.52 (0.21), residues: 1541 helix: 1.94 (0.15), residues: 1126 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 442 TYR 0.018 0.001 TYR C 123 PHE 0.011 0.001 PHE A 464 TRP 0.018 0.001 TRP B 518 HIS 0.002 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13010) covalent geometry : angle 0.56357 / 0.28 (17647) SS BOND : bond 0.00527 / 0.28 ( 1) SS BOND : angle 0.28165 / 0.15 ( 2) hydrogen bonds : bond 0.04306 / 2.84 ( 847) hydrogen bonds : angle 3.89732 / 2.82 ( 2511) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 185 time to evaluate : 0.456 Fit side-chains REVERT: A 251 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7763 (mtm110) REVERT: A 318 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7739 (mp) REVERT: A 322 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7965 (p) REVERT: A 348 ARG cc_start: 0.8086 (ptm-80) cc_final: 0.7604 (ttp80) REVERT: A 401 LYS cc_start: 0.7822 (pttp) cc_final: 0.7028 (ttpt) REVERT: A 442 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7102 (mtp180) REVERT: A 462 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7011 (mppt) REVERT: A 480 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: A 495 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7564 (ttp-170) REVERT: A 543 LYS cc_start: 0.8085 (tttt) cc_final: 0.7859 (tttt) REVERT: A 556 GLU cc_start: 0.7744 (tt0) cc_final: 0.6974 (mp0) REVERT: A 557 GLU cc_start: 0.7897 (tt0) cc_final: 0.7592 (mp0) REVERT: B 17 ASP cc_start: 0.6812 (t70) cc_final: 0.6544 (t0) REVERT: B 25 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7751 (mp) REVERT: B 90 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7271 (mp) REVERT: B 100 ASP cc_start: 0.8007 (t70) cc_final: 0.7519 (m-30) REVERT: B 137 ASP cc_start: 0.8207 (p0) cc_final: 0.7943 (p0) REVERT: B 251 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7124 (ttp80) REVERT: B 319 TYR cc_start: 0.8414 (m-10) cc_final: 0.7984 (m-80) REVERT: B 326 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6990 (mp10) REVERT: B 442 ARG cc_start: 0.8068 (ttp-110) cc_final: 0.7365 (mtm110) REVERT: B 491 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7353 (mp0) REVERT: B 515 GLN cc_start: 0.7625 (tt0) cc_final: 0.7223 (tp-100) REVERT: B 599 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7353 (mt-10) REVERT: C 22 LEU cc_start: 0.7126 (tm) cc_final: 0.6425 (mt) REVERT: C 40 ARG cc_start: 0.7158 (mpt180) cc_final: 0.6406 (mtp-110) REVERT: C 43 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5524 (tm-30) REVERT: C 77 GLN cc_start: 0.5907 (OUTLIER) cc_final: 0.4992 (tp40) REVERT: C 115 TRP cc_start: 0.7371 (t-100) cc_final: 0.6448 (t60) REVERT: C 206 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7478 (tt) REVERT: C 221 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6666 (mm) REVERT: C 273 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7040 (mt-10) REVERT: C 284 ARG cc_start: 0.6646 (mmm160) cc_final: 0.6060 (tmm160) REVERT: C 291 ASN cc_start: 0.5796 (m110) cc_final: 0.4786 (p0) REVERT: C 330 LYS cc_start: 0.7532 (mtmt) cc_final: 0.6850 (tmtt) outliers start: 57 outliers final: 33 residues processed: 228 average time/residue: 0.5105 time to fit residues: 127.3727 Evaluate side-chains 222 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain B residue 601 MET Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 258 GLN B 415 GLN C 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.176692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115713 restraints weight = 13347.448| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.59 r_work: 0.3101 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13011 Z= 0.139 Angle : 0.577 10.288 17649 Z= 0.284 Chirality : 0.041 0.337 2019 Planarity : 0.004 0.041 2165 Dihedral : 8.235 83.836 1860 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.45 % Allowed : 27.30 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.51 (0.21), residues: 1541 helix: 1.94 (0.15), residues: 1126 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.020 0.001 TYR C 123 PHE 0.010 0.001 PHE A 464 TRP 0.019 0.001 TRP B 518 HIS 0.002 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (13010) covalent geometry : angle 0.57669 / 0.28 (17647) SS BOND : bond 0.00497 / 0.26 ( 1) SS BOND : angle 0.31173 / 0.17 ( 2) hydrogen bonds : bond 0.04427 / 2.92 ( 847) hydrogen bonds : angle 3.91368 / 2.84 ( 2511) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.413 Fit side-chains REVERT: A 251 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7471 (mtm110) REVERT: A 318 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 322 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7555 (p) REVERT: A 348 ARG cc_start: 0.7896 (ptm-80) cc_final: 0.7333 (ttp80) REVERT: A 401 LYS cc_start: 0.7743 (pttp) cc_final: 0.6894 (ttpt) REVERT: A 442 ARG cc_start: 0.7393 (mtm110) cc_final: 0.6754 (mtp180) REVERT: A 480 GLU cc_start: 0.7390 (pt0) cc_final: 0.6800 (tt0) REVERT: A 495 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7265 (ttp-170) REVERT: A 543 LYS cc_start: 0.7865 (tttt) cc_final: 0.7598 (tttt) REVERT: A 556 GLU cc_start: 0.7506 (tt0) cc_final: 0.6596 (mp0) REVERT: A 557 GLU cc_start: 0.7656 (tt0) cc_final: 0.7260 (mp0) REVERT: B 17 ASP cc_start: 0.6672 (t70) cc_final: 0.6339 (t0) REVERT: B 25 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7434 (mp) REVERT: B 90 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.6968 (mp) REVERT: B 100 ASP cc_start: 0.7831 (t70) cc_final: 0.7218 (m-30) REVERT: B 137 ASP cc_start: 0.8037 (p0) cc_final: 0.7790 (p0) REVERT: B 251 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.6845 (ttp80) REVERT: B 318 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6875 (pp) REVERT: B 319 TYR cc_start: 0.8119 (m-10) cc_final: 0.7691 (m-80) REVERT: B 326 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6713 (mp10) REVERT: B 442 ARG cc_start: 0.7800 (ttp-110) cc_final: 0.7026 (mtm110) REVERT: B 491 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7025 (mp0) REVERT: B 515 GLN cc_start: 0.7590 (tt0) cc_final: 0.7130 (tp-100) REVERT: B 599 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7180 (mt-10) REVERT: C 22 LEU cc_start: 0.7080 (tm) cc_final: 0.6429 (mt) REVERT: C 40 ARG cc_start: 0.7268 (mpt180) cc_final: 0.6376 (mtp-110) REVERT: C 43 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.5162 (tm-30) REVERT: C 77 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.4954 (tp40) REVERT: C 115 TRP cc_start: 0.7332 (t-100) cc_final: 0.6358 (t60) REVERT: C 221 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6517 (mm) REVERT: C 273 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6644 (mt-10) REVERT: C 284 ARG cc_start: 0.6730 (mmm160) cc_final: 0.6020 (tmm160) REVERT: C 291 ASN cc_start: 0.5820 (m110) cc_final: 0.4824 (p0) REVERT: C 330 LYS cc_start: 0.7472 (mtmt) cc_final: 0.6798 (tmtt) outliers start: 48 outliers final: 34 residues processed: 218 average time/residue: 0.5153 time to fit residues: 122.9773 Evaluate side-chains 223 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 150 optimal weight: 0.0040 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 258 GLN C 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.177111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122269 restraints weight = 13439.609| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.10 r_work: 0.3159 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13011 Z= 0.152 Angle : 0.588 12.098 17649 Z= 0.289 Chirality : 0.041 0.338 2019 Planarity : 0.004 0.041 2165 Dihedral : 8.232 82.292 1856 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.45 % Allowed : 27.66 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.49 (0.21), residues: 1541 helix: 1.91 (0.15), residues: 1126 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.021 0.001 TYR C 123 PHE 0.011 0.001 PHE B 465 TRP 0.020 0.001 TRP B 518 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (13010) covalent geometry : angle 0.58796 / 0.29 (17647) SS BOND : bond 0.00498 / 0.26 ( 1) SS BOND : angle 0.30569 / 0.17 ( 2) hydrogen bonds : bond 0.04551 / 3.01 ( 847) hydrogen bonds : angle 3.95647 / 2.87 ( 2511) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3082 Ramachandran restraints generated. 1541 Oldfield, 0 Emsley, 1541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.469 Fit side-chains REVERT: A 251 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7354 (mtm110) REVERT: A 318 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7384 (mp) REVERT: A 322 SER cc_start: 0.8105 (OUTLIER) cc_final: 0.7573 (p) REVERT: A 348 ARG cc_start: 0.7901 (ptm-80) cc_final: 0.7310 (ttp80) REVERT: A 401 LYS cc_start: 0.7760 (pttp) cc_final: 0.6899 (ttpt) REVERT: A 442 ARG cc_start: 0.7344 (mtm110) cc_final: 0.6726 (mtp180) REVERT: A 462 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.6763 (mppt) REVERT: A 480 GLU cc_start: 0.7427 (pt0) cc_final: 0.6842 (tt0) REVERT: A 495 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7284 (ttp-170) REVERT: A 543 LYS cc_start: 0.7858 (tttt) cc_final: 0.7593 (tttt) REVERT: A 556 GLU cc_start: 0.7526 (tt0) cc_final: 0.6606 (mp0) REVERT: A 557 GLU cc_start: 0.7673 (tt0) cc_final: 0.7261 (mp0) REVERT: B 17 ASP cc_start: 0.6661 (t70) cc_final: 0.6340 (t0) REVERT: B 25 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7393 (mp) REVERT: B 90 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.6968 (mp) REVERT: B 100 ASP cc_start: 0.7850 (t70) cc_final: 0.7212 (m-30) REVERT: B 137 ASP cc_start: 0.8041 (p0) cc_final: 0.7789 (p0) REVERT: B 251 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.6802 (ttp80) REVERT: B 318 ILE cc_start: 0.7320 (OUTLIER) cc_final: 0.6877 (pp) REVERT: B 319 TYR cc_start: 0.8133 (m-10) cc_final: 0.7710 (m-80) REVERT: B 326 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.6703 (mp10) REVERT: B 442 ARG cc_start: 0.7790 (ttp-110) cc_final: 0.7015 (mtm110) REVERT: B 491 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7005 (mp0) REVERT: B 515 GLN cc_start: 0.7607 (tt0) cc_final: 0.7140 (tp-100) REVERT: B 599 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7198 (mt-10) REVERT: C 40 ARG cc_start: 0.7210 (mpt180) cc_final: 0.6374 (mtp-110) REVERT: C 43 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5214 (tm-30) REVERT: C 77 GLN cc_start: 0.5864 (OUTLIER) cc_final: 0.4972 (tp40) REVERT: C 115 TRP cc_start: 0.7345 (t-100) cc_final: 0.6377 (t60) REVERT: C 221 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6564 (mm) REVERT: C 273 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6613 (mt-10) REVERT: C 284 ARG cc_start: 0.6711 (mmm160) cc_final: 0.6018 (tmm160) REVERT: C 291 ASN cc_start: 0.5831 (m110) cc_final: 0.4833 (p0) REVERT: C 313 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7678 (mt) REVERT: C 330 LYS cc_start: 0.7523 (mtmt) cc_final: 0.6849 (tmtt) outliers start: 48 outliers final: 34 residues processed: 208 average time/residue: 0.5479 time to fit residues: 124.6323 Evaluate side-chains 220 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 518 TRP Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 GLN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 489 ASP Chi-restraints excluded: chain B residue 498 GLU Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 518 TRP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 436 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN B 258 GLN B 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.180094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124414 restraints weight = 13441.181| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.10 r_work: 0.3164 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13011 Z= 0.127 Angle : 0.568 11.404 17649 Z= 0.278 Chirality : 0.040 0.334 2019 Planarity : 0.004 0.041 2165 Dihedral : 8.006 86.824 1856 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.23 % Allowed : 28.09 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: 1.58 (0.21), residues: 1541 helix: 2.01 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : -1.77 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.021 0.001 TYR C 123 PHE 0.011 0.001 PHE A 464 TRP 0.018 0.001 TRP B 518 HIS 0.002 0.000 HIS A 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (13010) covalent geometry : angle 0.56757 / 0.28 (17647) SS BOND : bond 0.00511 / 0.27 ( 1) SS BOND : angle 0.30546 / 0.17 ( 2) hydrogen bonds : bond 0.04234 / 2.80 ( 847) hydrogen bonds : angle 3.87356 / 2.82 ( 2511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4737.51 seconds wall clock time: 81 minutes 24.04 seconds (4884.04 seconds total)