Starting phenix.real_space_refine on Thu Aug 6 03:11:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/24vd_69836/08_2026/24vd_69836.cif Found real_map, /net/cci-nas-00/data/ceres_data/24vd_69836/08_2026/24vd_69836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/24vd_69836/08_2026/24vd_69836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/24vd_69836/08_2026/24vd_69836.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/24vd_69836/08_2026/24vd_69836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/24vd_69836/08_2026/24vd_69836.map" } resolution = 2.83 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= 0.002 sd= 0.031 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: 7 Type Number sf(0) Gaussians Co 1 6.85 5 P 7 5.49 5 Mg 2 5.21 5 S 60 5.16 5 C 8354 2.51 5 N 2109 2.21 5 O 2273 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12806 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: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 151 Unusual residues: {' MG': 1, 'ATP': 1, 'B12': 1, 'CLR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unsupported chir.volume_sign: {'cros': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.44, per 1000 atoms: 0.27 Number of scatterers: 12806 At special positions: 0 Unit cell: (81.576, 118.656, 152.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Co 1 26.99 S 60 16.00 P 7 15.00 Mg 2 11.99 O 2273 8.00 N 2109 7.00 C 8354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 317 " distance=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 475 " distance=2.03 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: 1.36 Conformation dependent library (CDL) restraints added in 599.3 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: 60 helices and 7 sheets defined 73.2% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 38 through 62 removed outlier: 3.955A pdb=" N LEU A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 72 removed outlier: 3.667A pdb=" N GLY A 69 " --> pdb=" O SER A 65 " (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 180 removed outlier: 3.625A pdb=" N ASP A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET A 160 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 186 through 204 Processing helix chain 'A' and resid 205 through 232 removed outlier: 3.957A pdb=" N VAL A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 241 through 294 removed outlier: 3.514A pdb=" N LEU A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 302 through 330 removed outlier: 3.562A pdb=" N SER A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 321 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 327 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 354 removed outlier: 3.736A pdb=" N MET A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) 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 487 through 500 removed outlier: 3.770A pdb=" N ILE A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 4.049A pdb=" N VAL A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 541 removed outlier: 3.506A pdb=" N GLN A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.830A 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: 3.638A pdb=" N LEU B 62 " --> pdb=" O TYR B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 73 removed outlier: 3.511A pdb=" N GLY B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 71 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 73 " --> pdb=" O GLY B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.676A pdb=" N LYS B 80 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 141 through 158 removed outlier: 3.504A pdb=" N ASP B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 181 removed outlier: 3.786A pdb=" N ILE B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.939A pdb=" N VAL B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 232 removed outlier: 3.767A pdb=" N VAL B 209 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 4.025A 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 280 removed outlier: 4.285A pdb=" N TRP B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 Processing helix chain 'B' and resid 302 through 330 removed outlier: 3.892A pdb=" N SER B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE B 321 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 327 " --> pdb=" O CYS B 323 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 354 removed outlier: 4.811A pdb=" N ASP B 336 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 343 " --> pdb=" O GLY B 339 " (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 486 through 500 removed outlier: 4.234A pdb=" N ASP B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.929A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 555 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 3.917A pdb=" N LYS B 584 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 37 Processing helix chain 'C' and resid 43 through 72 removed outlier: 4.002A pdb=" N ILE C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 88 through 114 removed outlier: 3.603A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 134 through 160 removed outlier: 3.739A pdb=" N TYR C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY C 146 " --> pdb=" O LYS C 142 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE C 147 " --> pdb=" O TYR C 143 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 211 removed outlier: 3.752A pdb=" N LEU C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 removed outlier: 4.371A pdb=" N SER C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Proline residue: C 220 - end of helix removed outlier: 3.585A pdb=" N LEU C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.609A 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 262 through 291 removed outlier: 3.581A pdb=" N ALA C 268 " --> pdb=" O ARG C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 333 removed outlier: 3.638A pdb=" N ALA C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 332 " --> pdb=" O LEU C 328 " (cutoff:3.500A) 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 364 through 389 removed outlier: 3.599A pdb=" N LEU C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 432 removed outlier: 4.123A pdb=" N SER C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 478 through 485 removed outlier: 3.868A pdb=" N LEU C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 515 removed outlier: 3.688A pdb=" N ASN C 498 " --> pdb=" O TYR C 494 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TRP C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.105A 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: 3.879A pdb=" N ASP A 406 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 392 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.879A pdb=" N ASP A 406 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL A 392 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU A 389 " --> pdb=" O GLN A 446 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N GLN A 446 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG A 391 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N SER A 444 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.773A 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: 6.437A pdb=" N ALA A 545 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 576 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU A 547 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.667A pdb=" N LYS B 405 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B 394 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.667A pdb=" N LYS B 405 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE B 394 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU B 389 " --> pdb=" O GLN B 446 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN B 446 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ARG B 391 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER B 444 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 442 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 419 removed outlier: 6.433A pdb=" N ALA B 545 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 576 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B 547 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 390 through 391 removed outlier: 6.986A pdb=" N ILE C 390 " --> pdb=" O LEU C 397 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2475 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: 2.18 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 4911 1.38 - 1.54: 7993 1.54 - 1.70: 108 1.70 - 1.86: 96 1.86 - 2.02: 3 Bond restraints: 13111 Sorted by residual: bond pdb=" C16 B12 A 702 " pdb=" N24 B12 A 702 " ideal model delta sigma weight residual 1.416 1.291 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C4 B12 A 702 " pdb=" N21 B12 A 702 " ideal model delta sigma weight residual 1.416 1.294 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C4 B12 A 702 " pdb=" C5 B12 A 702 " ideal model delta sigma weight residual 1.460 1.343 0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" N23 B12 A 702 " pdb="CO B12 A 702 " ideal model delta sigma weight residual 1.900 1.784 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" N22 B12 A 702 " pdb="CO B12 A 702 " ideal model delta sigma weight residual 1.900 2.016 -0.116 2.00e-02 2.50e+03 3.36e+01 ... (remaining 13106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 17721 4.35 - 8.69: 67 8.69 - 13.04: 18 13.04 - 17.39: 3 17.39 - 21.74: 4 Bond angle restraints: 17813 Sorted by residual: angle pdb=" C16 B12 A 702 " pdb=" N24 B12 A 702 " pdb="CO B12 A 702 " ideal model delta sigma weight residual 109.50 131.24 -21.74 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C18 B12 A 702 " pdb=" C19 B12 A 702 " pdb=" N24 B12 A 702 " ideal model delta sigma weight residual 120.00 100.70 19.30 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C4 B12 A 702 " pdb=" N21 B12 A 702 " pdb="CO B12 A 702 " ideal model delta sigma weight residual 109.50 128.03 -18.53 3.00e+00 1.11e-01 3.82e+01 angle pdb=" C11 B12 A 702 " pdb=" N23 B12 A 702 " pdb="CO B12 A 702 " ideal model delta sigma weight residual 109.50 127.80 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" N GLN B 461 " pdb=" CA GLN B 461 " pdb=" C GLN B 461 " ideal model delta sigma weight residual 111.82 106.29 5.53 1.16e+00 7.43e-01 2.27e+01 ... (remaining 17808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.72: 7020 23.72 - 47.43: 644 47.43 - 71.15: 125 71.15 - 94.86: 20 94.86 - 118.58: 2 Dihedral angle restraints: 7811 sinusoidal: 3260 harmonic: 4551 Sorted by residual: dihedral pdb=" C2P B12 A 702 " pdb=" O3 B12 A 702 " pdb=" P B12 A 702 " pdb=" O4 B12 A 702 " ideal model delta sinusoidal sigma weight residual -64.57 54.01 -118.58 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" C16 B12 A 702 " pdb=" C17 B12 A 702 " pdb=" C55 B12 A 702 " pdb=" C56 B12 A 702 " ideal model delta sinusoidal sigma weight residual -171.32 -64.28 -107.04 1 2.00e+01 2.50e-03 3.10e+01 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 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 7808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.055: 2032 1.055 - 2.111: 2 2.111 - 3.166: 1 3.166 - 4.222: 1 4.222 - 5.277: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" C12 B12 A 702 " pdb=" C11 B12 A 702 " pdb=" C46 B12 A 702 " pdb=" C47 B12 A 702 " both_signs ideal model delta sigma weight residual False -2.64 2.64 -5.28 2.00e-01 2.50e+01 6.96e+02 chirality pdb=" N22 B12 A 702 " pdb=" C6 B12 A 702 " pdb=" C9 B12 A 702 " pdb="CO B12 A 702 " both_signs ideal model delta sigma weight residual False -2.93 1.08 -4.01 2.00e-01 2.50e+01 4.02e+02 chirality pdb=" N23 B12 A 702 " pdb=" C11 B12 A 702 " pdb=" C14 B12 A 702 " pdb="CO B12 A 702 " both_signs ideal model delta sigma weight residual False 2.93 0.15 2.78 2.00e-01 2.50e+01 1.93e+02 ... (remaining 2034 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C35 B12 A 702 " 0.394 2.00e-02 2.50e+03 3.41e-01 1.75e+03 pdb=" C4 B12 A 702 " -0.425 2.00e-02 2.50e+03 pdb=" C5 B12 A 702 " -0.035 2.00e-02 2.50e+03 pdb=" C6 B12 A 702 " 0.023 2.00e-02 2.50e+03 pdb=" C7 B12 A 702 " -0.402 2.00e-02 2.50e+03 pdb=" N22 B12 A 702 " 0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 B12 A 702 " -0.142 2.00e-02 2.50e+03 2.25e-01 5.05e+02 pdb=" C18 B12 A 702 " -0.133 2.00e-02 2.50e+03 pdb=" C19 B12 A 702 " 0.389 2.00e-02 2.50e+03 pdb=" N24 B12 A 702 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 118 " 0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C PHE C 118 " -0.077 2.00e-02 2.50e+03 pdb=" O PHE C 118 " 0.029 2.00e-02 2.50e+03 pdb=" N VAL C 119 " 0.026 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.21: 4 2.21 - 2.88: 4722 2.88 - 3.55: 18807 3.55 - 4.23: 30004 4.23 - 4.90: 53267 Nonbonded interactions: 106804 Sorted by model distance: nonbonded pdb=" OG1 THR B 428 " pdb="MG MG B 702 " model vdw 1.534 2.170 nonbonded pdb=" OG1 THR A 428 " pdb="MG MG A 703 " model vdw 1.691 2.170 nonbonded pdb=" OE1 GLN B 461 " pdb="MG MG B 702 " model vdw 1.837 2.170 nonbonded pdb=" OE1 GLN A 461 " pdb="MG MG A 703 " model vdw 2.026 2.170 nonbonded pdb=" O SER A 282 " pdb=" OG SER A 285 " model vdw 2.223 3.040 ... (remaining 106799 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: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:8.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.005 0.125 13113 Z= 0.240 Angle : 0.818 21.736 17817 Z= 0.384 Chirality : 0.170 5.277 2037 Planarity : 0.010 0.341 2180 Dihedral : 18.242 118.578 4877 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.15 % Allowed : 27.01 % Favored : 71.84 % 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: 0.73 (0.21), residues: 1541 helix: 1.49 (0.16), residues: 1099 sheet: None (None), residues: 0 loop : -2.16 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 442 TYR 0.030 0.001 TYR C 426 PHE 0.025 0.001 PHE B 179 TRP 0.006 0.001 TRP B 184 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (13111) covalent geometry : angle 0.81781 / 0.38 (17813) SS BOND : bond 0.00554 / 0.29 ( 2) SS BOND : angle 1.21725 / 0.68 ( 4) hydrogen bonds : bond 0.15679 / 9.91 ( 836) hydrogen bonds : angle 5.65721 / 4.07 ( 2475) *********************** 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 196 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7657 (t0) cc_final: 0.6979 (m-30) REVERT: A 140 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7229 (p0) REVERT: A 152 ARG cc_start: 0.7800 (mtt-85) cc_final: 0.7450 (mtt90) REVERT: A 202 LYS cc_start: 0.6958 (tppt) cc_final: 0.6454 (tmtt) REVERT: A 227 MET cc_start: 0.7714 (ttp) cc_final: 0.6922 (tpt) REVERT: A 251 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7523 (ttp-110) REVERT: A 334 LEU cc_start: 0.6228 (mt) cc_final: 0.6018 (mt) REVERT: A 342 HIS cc_start: 0.7375 (m-70) cc_final: 0.6074 (t70) REVERT: A 401 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7511 (ptmm) REVERT: A 406 ASP cc_start: 0.8031 (t0) cc_final: 0.7780 (t0) REVERT: A 557 GLU cc_start: 0.7573 (mp0) cc_final: 0.7134 (mp0) REVERT: A 564 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7040 (mtt90) REVERT: A 591 LYS cc_start: 0.7854 (mttm) cc_final: 0.6978 (tttm) REVERT: A 597 ARG cc_start: 0.7547 (mtm110) cc_final: 0.6713 (mtm-85) REVERT: A 602 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7455 (ttt-90) REVERT: A 604 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.4401 (mttt) REVERT: B 75 ASP cc_start: 0.7571 (t70) cc_final: 0.7339 (t70) REVERT: B 176 TYR cc_start: 0.7749 (t80) cc_final: 0.6249 (t80) REVERT: B 277 PHE cc_start: 0.7045 (m-80) cc_final: 0.6492 (m-10) REVERT: B 278 ASP cc_start: 0.7648 (m-30) cc_final: 0.7153 (t0) REVERT: B 462 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7443 (mppt) REVERT: B 510 GLU cc_start: 0.7461 (mt-10) cc_final: 0.6523 (mm-30) REVERT: B 557 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7573 (mp0) REVERT: B 564 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7350 (mtp180) REVERT: B 580 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 599 GLU cc_start: 0.7486 (tp30) cc_final: 0.6982 (mt-10) REVERT: C 31 ILE cc_start: 0.7553 (tp) cc_final: 0.7182 (mp) REVERT: C 34 ARG cc_start: 0.6932 (mtp85) cc_final: 0.5838 (tpm-80) REVERT: C 256 LYS cc_start: 0.6718 (tppt) cc_final: 0.5870 (pttm) REVERT: C 296 LYS cc_start: 0.5398 (mppt) cc_final: 0.4145 (ttmm) REVERT: C 354 MET cc_start: 0.6074 (tmm) cc_final: 0.5820 (mtm) REVERT: C 374 ILE cc_start: 0.6870 (mt) cc_final: 0.6646 (mt) REVERT: C 408 GLN cc_start: 0.6248 (pm20) cc_final: 0.5575 (mt0) outliers start: 16 outliers final: 6 residues processed: 188 average time/residue: 0.6524 time to fit residues: 132.8241 Evaluate side-chains 176 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123376 restraints weight = 13793.061| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.65 r_work: 0.3243 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13113 Z= 0.170 Angle : 0.773 27.956 17817 Z= 0.337 Chirality : 0.070 2.452 2037 Planarity : 0.004 0.044 2180 Dihedral : 10.170 118.057 1921 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.32 % Allowed : 23.35 % Favored : 71.34 % 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: 1.09 (0.21), residues: 1541 helix: 1.76 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -2.19 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 442 TYR 0.020 0.001 TYR B 340 PHE 0.019 0.001 PHE A 277 TRP 0.006 0.001 TRP A 520 HIS 0.004 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (13111) covalent geometry : angle 0.77287 / 0.34 (17813) SS BOND : bond 0.00664 / 0.35 ( 2) SS BOND : angle 1.58494 / 0.89 ( 4) hydrogen bonds : bond 0.05378 / 3.46 ( 836) hydrogen bonds : angle 4.23848 / 3.08 ( 2475) *********************** 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 248 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 174 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7607 (t0) cc_final: 0.6922 (m-30) REVERT: A 140 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7271 (p0) REVERT: A 152 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7423 (mtt90) REVERT: A 166 ILE cc_start: 0.6773 (tp) cc_final: 0.6541 (tp) REVERT: A 202 LYS cc_start: 0.6783 (tppt) cc_final: 0.6213 (tptm) REVERT: A 227 MET cc_start: 0.7746 (ttp) cc_final: 0.6951 (tpt) REVERT: A 342 HIS cc_start: 0.7354 (m-70) cc_final: 0.6040 (t70) REVERT: A 401 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7477 (ptmm) REVERT: A 406 ASP cc_start: 0.8045 (t0) cc_final: 0.7761 (t0) REVERT: A 420 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.9004 (p) REVERT: A 479 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7478 (ttmm) REVERT: A 498 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: A 557 GLU cc_start: 0.7175 (mp0) cc_final: 0.6868 (mt-10) REVERT: A 564 ARG cc_start: 0.7835 (mmt180) cc_final: 0.6919 (mtt90) REVERT: A 591 LYS cc_start: 0.7803 (mttm) cc_final: 0.6962 (tmtm) REVERT: A 597 ARG cc_start: 0.7523 (mtm110) cc_final: 0.6681 (mtm-85) REVERT: A 602 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7660 (ttt-90) REVERT: A 604 LYS cc_start: 0.5463 (OUTLIER) cc_final: 0.3658 (mppt) REVERT: B 36 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8424 (t) REVERT: B 75 ASP cc_start: 0.7330 (t70) cc_final: 0.7103 (t70) REVERT: B 80 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6907 (mttt) REVERT: B 127 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7515 (mtt-85) REVERT: B 145 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7483 (mtt90) REVERT: B 204 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6109 (mt) REVERT: B 277 PHE cc_start: 0.7071 (m-80) cc_final: 0.6634 (m-10) REVERT: B 278 ASP cc_start: 0.7490 (m-30) cc_final: 0.6897 (t0) REVERT: B 323 CYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7113 (t) REVERT: B 442 ARG cc_start: 0.6914 (ttm-80) cc_final: 0.6237 (ttp-110) REVERT: B 510 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6557 (mm-30) REVERT: B 557 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7479 (mp0) REVERT: B 561 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: B 564 ARG cc_start: 0.7969 (mmt180) cc_final: 0.7276 (mtp180) REVERT: B 599 GLU cc_start: 0.7494 (tp30) cc_final: 0.6928 (mt-10) REVERT: C 31 ILE cc_start: 0.7543 (tp) cc_final: 0.7192 (mp) REVERT: C 34 ARG cc_start: 0.6919 (mtp85) cc_final: 0.5892 (tpm-80) REVERT: C 245 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6782 (mm-30) REVERT: C 256 LYS cc_start: 0.6732 (tppt) cc_final: 0.5882 (pttm) REVERT: C 354 MET cc_start: 0.6073 (tmm) cc_final: 0.5765 (mtm) REVERT: C 408 GLN cc_start: 0.6355 (pm20) cc_final: 0.5669 (mt0) REVERT: C 496 PHE cc_start: 0.5903 (OUTLIER) cc_final: 0.5581 (t80) outliers start: 74 outliers final: 18 residues processed: 225 average time/residue: 0.5974 time to fit residues: 146.5124 Evaluate side-chains 199 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 127 ARG Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 22 optimal weight: 0.0060 chunk 39 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.183890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.133106 restraints weight = 13855.388| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.88 r_work: 0.3287 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13113 Z= 0.132 Angle : 0.739 29.020 17817 Z= 0.317 Chirality : 0.067 2.385 2037 Planarity : 0.004 0.039 2180 Dihedral : 9.202 104.906 1905 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.09 % Allowed : 24.93 % Favored : 70.98 % 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: 1.53 (0.22), residues: 1541 helix: 2.03 (0.16), residues: 1096 sheet: -1.64 (0.87), residues: 36 loop : -1.64 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 479 TYR 0.021 0.001 TYR B 340 PHE 0.017 0.001 PHE A 277 TRP 0.006 0.001 TRP C 30 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (13111) covalent geometry : angle 0.73848 / 0.32 (17813) SS BOND : bond 0.00464 / 0.24 ( 2) SS BOND : angle 1.13607 / 0.63 ( 4) hydrogen bonds : bond 0.04687 / 3.01 ( 836) hydrogen bonds : angle 3.93000 / 2.86 ( 2475) *********************** 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 240 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7684 (t0) cc_final: 0.7035 (m-30) REVERT: A 152 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7433 (mtt90) REVERT: A 202 LYS cc_start: 0.6827 (tppt) cc_final: 0.6362 (tmtt) REVERT: A 227 MET cc_start: 0.7799 (ttp) cc_final: 0.7041 (tpt) REVERT: A 251 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7538 (ttp-110) REVERT: A 293 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 342 HIS cc_start: 0.7295 (m-70) cc_final: 0.6070 (t70) REVERT: A 401 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7462 (ptmm) REVERT: A 406 ASP cc_start: 0.8114 (t0) cc_final: 0.7817 (t0) REVERT: A 420 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9035 (p) REVERT: A 564 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7010 (mtm110) REVERT: A 580 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7022 (mp-120) REVERT: A 591 LYS cc_start: 0.7888 (mttm) cc_final: 0.7078 (tmtm) REVERT: A 597 ARG cc_start: 0.7565 (mtm110) cc_final: 0.6722 (mtm-85) REVERT: A 602 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7728 (ttt-90) REVERT: A 604 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.3560 (mppt) REVERT: B 36 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8483 (t) REVERT: B 234 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8303 (tt0) REVERT: B 277 PHE cc_start: 0.7051 (m-80) cc_final: 0.6546 (m-10) REVERT: B 278 ASP cc_start: 0.7563 (m-30) cc_final: 0.6911 (t0) REVERT: B 309 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7316 (tm) REVERT: B 442 ARG cc_start: 0.7018 (ttm-80) cc_final: 0.6339 (ttt-90) REVERT: B 510 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6562 (mm-30) REVERT: B 557 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7471 (mp0) REVERT: B 561 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: B 564 ARG cc_start: 0.8013 (mmt180) cc_final: 0.7359 (mtp180) REVERT: B 599 GLU cc_start: 0.7542 (tp30) cc_final: 0.6961 (mt-10) REVERT: C 31 ILE cc_start: 0.7419 (tp) cc_final: 0.7065 (mp) REVERT: C 34 ARG cc_start: 0.6881 (mtp85) cc_final: 0.5751 (tpm-80) REVERT: C 245 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6925 (mm-30) REVERT: C 256 LYS cc_start: 0.6717 (tppt) cc_final: 0.5926 (pttm) REVERT: C 354 MET cc_start: 0.6021 (tmm) cc_final: 0.5786 (mtm) REVERT: C 408 GLN cc_start: 0.6442 (pm20) cc_final: 0.5804 (mt0) outliers start: 57 outliers final: 15 residues processed: 221 average time/residue: 0.5919 time to fit residues: 142.1081 Evaluate side-chains 195 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 561 GLU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN B 66 GLN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.185139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.136595 restraints weight = 13863.454| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.87 r_work: 0.3294 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13113 Z= 0.124 Angle : 0.729 29.483 17817 Z= 0.311 Chirality : 0.066 2.370 2037 Planarity : 0.004 0.040 2180 Dihedral : 8.677 93.317 1901 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.60 % Allowed : 25.22 % Favored : 70.19 % 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: 1.63 (0.22), residues: 1541 helix: 2.11 (0.16), residues: 1104 sheet: -1.77 (0.84), residues: 36 loop : -1.66 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 479 TYR 0.023 0.001 TYR C 426 PHE 0.020 0.001 PHE B 179 TRP 0.004 0.000 TRP B 184 HIS 0.003 0.001 HIS A 586 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (13111) covalent geometry : angle 0.72911 / 0.31 (17813) SS BOND : bond 0.00388 / 0.20 ( 2) SS BOND : angle 1.03509 / 0.57 ( 4) hydrogen bonds : bond 0.04417 / 2.82 ( 836) hydrogen bonds : angle 3.79706 / 2.77 ( 2475) *********************** 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 243 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7676 (t0) cc_final: 0.7011 (m-30) REVERT: A 152 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7391 (mtt90) REVERT: A 202 LYS cc_start: 0.6860 (tppt) cc_final: 0.6323 (tmtt) REVERT: A 227 MET cc_start: 0.7771 (ttp) cc_final: 0.6990 (tpt) REVERT: A 251 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7461 (ttp-110) REVERT: A 293 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7056 (mt) REVERT: A 342 HIS cc_start: 0.7168 (m-70) cc_final: 0.5968 (t70) REVERT: A 401 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7412 (ptmm) REVERT: A 406 ASP cc_start: 0.8071 (t0) cc_final: 0.7773 (t0) REVERT: A 420 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9026 (p) REVERT: A 479 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7025 (tttm) REVERT: A 564 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7041 (mtm110) REVERT: A 580 GLN cc_start: 0.7361 (tm-30) cc_final: 0.6985 (mp-120) REVERT: A 591 LYS cc_start: 0.7881 (mttm) cc_final: 0.7027 (tttm) REVERT: A 597 ARG cc_start: 0.7584 (mtm110) cc_final: 0.6738 (mtm-85) REVERT: A 602 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7763 (ttt-90) REVERT: A 604 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.3786 (mptt) REVERT: B 36 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8550 (t) REVERT: B 140 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6731 (p0) REVERT: B 145 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7682 (mtt180) REVERT: B 245 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8544 (mm-30) REVERT: B 277 PHE cc_start: 0.7052 (m-80) cc_final: 0.6620 (m-10) REVERT: B 278 ASP cc_start: 0.7523 (m-30) cc_final: 0.6558 (t0) REVERT: B 309 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7273 (tm) REVERT: B 329 ASP cc_start: 0.7374 (m-30) cc_final: 0.6999 (t0) REVERT: B 442 ARG cc_start: 0.7033 (ttm-80) cc_final: 0.6368 (ttp-110) REVERT: B 510 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6536 (mm-30) REVERT: B 557 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7407 (mp0) REVERT: B 564 ARG cc_start: 0.7986 (mmt180) cc_final: 0.7329 (mtp180) REVERT: B 599 GLU cc_start: 0.7565 (tp30) cc_final: 0.6991 (mt-10) REVERT: C 34 ARG cc_start: 0.6795 (mtp85) cc_final: 0.5660 (tpm-80) REVERT: C 40 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6090 (ptt90) REVERT: C 48 ILE cc_start: 0.7732 (pt) cc_final: 0.7372 (mm) REVERT: C 245 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: C 256 LYS cc_start: 0.6684 (tppt) cc_final: 0.5953 (pttm) REVERT: C 264 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5724 (mtm110) REVERT: C 354 MET cc_start: 0.5916 (tmm) cc_final: 0.5676 (mtm) REVERT: C 408 GLN cc_start: 0.6351 (pm20) cc_final: 0.5639 (mt0) outliers start: 64 outliers final: 19 residues processed: 220 average time/residue: 0.5745 time to fit residues: 137.5590 Evaluate side-chains 196 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 133 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 122 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 GLN A 243 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.185445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136703 restraints weight = 13872.704| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.85 r_work: 0.3294 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13113 Z= 0.130 Angle : 0.731 29.529 17817 Z= 0.314 Chirality : 0.066 2.374 2037 Planarity : 0.004 0.041 2180 Dihedral : 8.482 88.928 1897 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.81 % Allowed : 26.08 % Favored : 70.11 % 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: 1.69 (0.21), residues: 1541 helix: 2.17 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -1.76 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.021 0.001 TYR C 32 PHE 0.016 0.001 PHE A 277 TRP 0.004 0.000 TRP C 394 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (13111) covalent geometry : angle 0.73048 / 0.31 (17813) SS BOND : bond 0.00472 / 0.25 ( 2) SS BOND : angle 1.17648 / 0.65 ( 4) hydrogen bonds : bond 0.04400 / 2.82 ( 836) hydrogen bonds : angle 3.76665 / 2.74 ( 2475) *********************** 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 228 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 36 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 66 GLN cc_start: 0.7527 (mt0) cc_final: 0.7305 (mt0) REVERT: A 100 ASP cc_start: 0.7637 (t0) cc_final: 0.6947 (m-30) REVERT: A 152 ARG cc_start: 0.7568 (mtt-85) cc_final: 0.7297 (mtt90) REVERT: A 202 LYS cc_start: 0.6763 (tppt) cc_final: 0.6274 (tmtt) REVERT: A 227 MET cc_start: 0.7715 (ttp) cc_final: 0.6909 (tpt) REVERT: A 251 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7437 (ttp-110) REVERT: A 293 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7016 (mt) REVERT: A 342 HIS cc_start: 0.7196 (m-70) cc_final: 0.5961 (t70) REVERT: A 401 LYS cc_start: 0.8037 (mtpp) cc_final: 0.7306 (ptmm) REVERT: A 406 ASP cc_start: 0.8046 (t0) cc_final: 0.7762 (t0) REVERT: A 420 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8985 (p) REVERT: A 479 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7029 (tttm) REVERT: A 498 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7863 (tt0) REVERT: A 564 ARG cc_start: 0.7810 (mmt180) cc_final: 0.6930 (mtm110) REVERT: A 580 GLN cc_start: 0.7306 (tm-30) cc_final: 0.6936 (mp-120) REVERT: A 591 LYS cc_start: 0.7775 (mttm) cc_final: 0.6931 (tttm) REVERT: A 597 ARG cc_start: 0.7515 (mtm110) cc_final: 0.6651 (mtm-85) REVERT: A 602 ARG cc_start: 0.8245 (ttp-170) cc_final: 0.7707 (ttt-90) REVERT: A 604 LYS cc_start: 0.5304 (OUTLIER) cc_final: 0.3795 (mptt) REVERT: B 36 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8525 (t) REVERT: B 80 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6917 (mttt) REVERT: B 140 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6732 (p0) REVERT: B 145 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7628 (mtt180) REVERT: B 234 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: B 277 PHE cc_start: 0.7029 (m-80) cc_final: 0.6597 (m-10) REVERT: B 278 ASP cc_start: 0.7550 (m-30) cc_final: 0.6886 (t0) REVERT: B 442 ARG cc_start: 0.6951 (ttm-80) cc_final: 0.6258 (ttp-110) REVERT: B 510 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6469 (mm-30) REVERT: B 557 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7289 (mp0) REVERT: B 564 ARG cc_start: 0.7973 (mmt180) cc_final: 0.7267 (mtp180) REVERT: B 599 GLU cc_start: 0.7494 (tp30) cc_final: 0.6916 (mt-10) REVERT: C 34 ARG cc_start: 0.6795 (mtp85) cc_final: 0.5623 (tpm-80) REVERT: C 48 ILE cc_start: 0.7768 (pt) cc_final: 0.7363 (mm) REVERT: C 245 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: C 264 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5718 (mtm110) REVERT: C 274 GLU cc_start: 0.7266 (tm-30) cc_final: 0.7061 (tm-30) REVERT: C 408 GLN cc_start: 0.6354 (pm20) cc_final: 0.5717 (mt0) outliers start: 53 outliers final: 21 residues processed: 211 average time/residue: 0.6108 time to fit residues: 139.4200 Evaluate side-chains 203 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS B 215 GLN B 415 GLN ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.183994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135969 restraints weight = 13642.818| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.60 r_work: 0.3251 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13113 Z= 0.142 Angle : 0.737 29.567 17817 Z= 0.318 Chirality : 0.067 2.378 2037 Planarity : 0.004 0.041 2180 Dihedral : 8.560 87.144 1897 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.67 % Allowed : 25.29 % Favored : 70.04 % 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: 1.70 (0.21), residues: 1541 helix: 2.18 (0.15), residues: 1103 sheet: None (None), residues: 0 loop : -1.76 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 391 TYR 0.027 0.001 TYR C 426 PHE 0.023 0.001 PHE B 179 TRP 0.005 0.001 TRP C 30 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13111) covalent geometry : angle 0.73711 / 0.32 (17813) SS BOND : bond 0.00542 / 0.29 ( 2) SS BOND : angle 1.34164 / 0.74 ( 4) hydrogen bonds : bond 0.04516 / 2.88 ( 836) hydrogen bonds : angle 3.79539 / 2.76 ( 2475) *********************** 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 237 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 36 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8725 (m) REVERT: A 100 ASP cc_start: 0.7960 (t0) cc_final: 0.7357 (m-30) REVERT: A 152 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7721 (mtt90) REVERT: A 202 LYS cc_start: 0.7106 (tppt) cc_final: 0.6640 (tmtt) REVERT: A 227 MET cc_start: 0.7909 (ttp) cc_final: 0.7240 (tpt) REVERT: A 251 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7762 (ttp-110) REVERT: A 293 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7253 (mt) REVERT: A 342 HIS cc_start: 0.7506 (m-70) cc_final: 0.6373 (t70) REVERT: A 391 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7755 (mtp85) REVERT: A 401 LYS cc_start: 0.8131 (mtpp) cc_final: 0.7524 (ptmm) REVERT: A 406 ASP cc_start: 0.8086 (t0) cc_final: 0.7673 (t0) REVERT: A 479 LYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7007 (ttmm) REVERT: A 498 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 564 ARG cc_start: 0.8075 (mmt180) cc_final: 0.7382 (mtm110) REVERT: A 580 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7171 (mp-120) REVERT: A 591 LYS cc_start: 0.8015 (mttm) cc_final: 0.7336 (tmtm) REVERT: A 597 ARG cc_start: 0.7706 (mtm110) cc_final: 0.6947 (mtm-85) REVERT: A 602 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7899 (ttt-90) REVERT: A 604 LYS cc_start: 0.5420 (OUTLIER) cc_final: 0.3899 (mptt) REVERT: B 36 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8610 (t) REVERT: B 80 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7339 (mttt) REVERT: B 140 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6811 (p0) REVERT: B 145 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7756 (mtt90) REVERT: B 205 MET cc_start: 0.6199 (mtp) cc_final: 0.5938 (mtt) REVERT: B 234 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: B 277 PHE cc_start: 0.7146 (m-80) cc_final: 0.6722 (m-10) REVERT: B 278 ASP cc_start: 0.7657 (m-30) cc_final: 0.6967 (t0) REVERT: B 309 LEU cc_start: 0.7566 (tt) cc_final: 0.7364 (tm) REVERT: B 442 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.6680 (ttt-90) REVERT: B 462 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.7688 (mppt) REVERT: B 510 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6774 (mm-30) REVERT: B 557 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7781 (mp0) REVERT: B 564 ARG cc_start: 0.8250 (mmt180) cc_final: 0.7757 (mtp180) REVERT: B 599 GLU cc_start: 0.7711 (tp30) cc_final: 0.7302 (mt-10) REVERT: C 34 ARG cc_start: 0.6835 (mtp85) cc_final: 0.5671 (tpm-80) REVERT: C 40 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6108 (ptt90) REVERT: C 48 ILE cc_start: 0.7835 (pt) cc_final: 0.7393 (mm) REVERT: C 245 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: C 264 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5937 (mtm110) REVERT: C 408 GLN cc_start: 0.6605 (pm20) cc_final: 0.5943 (mt0) outliers start: 65 outliers final: 24 residues processed: 216 average time/residue: 0.5778 time to fit residues: 135.7351 Evaluate side-chains 204 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 413 GLU 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 514 GLN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 604 LYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 89 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.182820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134472 restraints weight = 13718.427| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.59 r_work: 0.3284 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13113 Z= 0.157 Angle : 0.755 29.597 17817 Z= 0.328 Chirality : 0.068 2.382 2037 Planarity : 0.004 0.041 2180 Dihedral : 8.742 87.580 1897 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.02 % Allowed : 26.01 % Favored : 69.97 % 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: 1.68 (0.21), residues: 1541 helix: 2.13 (0.15), residues: 1105 sheet: -1.70 (0.81), residues: 36 loop : -1.63 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 442 TYR 0.018 0.001 TYR A 68 PHE 0.018 0.001 PHE A 277 TRP 0.006 0.001 TRP A 520 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (13111) covalent geometry : angle 0.75435 / 0.33 (17813) SS BOND : bond 0.00617 / 0.32 ( 2) SS BOND : angle 1.49910 / 0.82 ( 4) hydrogen bonds : bond 0.04696 / 3.00 ( 836) hydrogen bonds : angle 3.84782 / 2.79 ( 2475) *********************** 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 227 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 171 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8024 (t0) cc_final: 0.7408 (m-30) REVERT: A 152 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7733 (mtt90) REVERT: A 202 LYS cc_start: 0.7138 (tppt) cc_final: 0.6698 (tmtt) REVERT: A 227 MET cc_start: 0.7940 (ttp) cc_final: 0.7270 (tpt) REVERT: A 342 HIS cc_start: 0.7550 (m-70) cc_final: 0.6413 (t70) REVERT: A 401 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7537 (ptmm) REVERT: A 406 ASP cc_start: 0.8079 (t0) cc_final: 0.7841 (t0) REVERT: A 479 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7097 (ttmm) REVERT: A 498 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: A 564 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7388 (mtt90) REVERT: A 580 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7212 (mp-120) REVERT: A 591 LYS cc_start: 0.7980 (mttm) cc_final: 0.7296 (tttm) REVERT: A 597 ARG cc_start: 0.7702 (mtm110) cc_final: 0.6959 (mtm-85) REVERT: A 602 ARG cc_start: 0.8286 (ttp-170) cc_final: 0.7920 (ttt-90) REVERT: A 604 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.3878 (mptt) REVERT: B 36 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8637 (t) REVERT: B 80 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7404 (mttt) REVERT: B 140 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6876 (p0) REVERT: B 145 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7786 (mtt90) REVERT: B 234 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: B 277 PHE cc_start: 0.7181 (m-80) cc_final: 0.6772 (m-10) REVERT: B 278 ASP cc_start: 0.7645 (m-30) cc_final: 0.6988 (t0) REVERT: B 309 LEU cc_start: 0.7677 (tt) cc_final: 0.7422 (tm) REVERT: B 442 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6706 (ttt-90) REVERT: B 462 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7709 (mppt) REVERT: B 510 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6800 (mm-30) REVERT: B 557 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7790 (mp0) REVERT: B 564 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7767 (mtp180) REVERT: B 599 GLU cc_start: 0.7651 (tp30) cc_final: 0.7298 (mt-10) REVERT: C 34 ARG cc_start: 0.6867 (mtp85) cc_final: 0.5825 (tpm-80) REVERT: C 40 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6069 (ptt90) REVERT: C 48 ILE cc_start: 0.7827 (pt) cc_final: 0.7401 (mm) REVERT: C 245 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: C 264 ARG cc_start: 0.6479 (OUTLIER) cc_final: 0.5850 (mtm110) REVERT: C 408 GLN cc_start: 0.6679 (pm20) cc_final: 0.6031 (mt0) REVERT: C 496 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5778 (t80) outliers start: 56 outliers final: 26 residues processed: 211 average time/residue: 0.5263 time to fit residues: 120.6491 Evaluate side-chains 201 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 390 GLU 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 514 GLN Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.182169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.134051 restraints weight = 13681.659| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.61 r_work: 0.3217 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13113 Z= 0.165 Angle : 0.765 29.673 17817 Z= 0.333 Chirality : 0.068 2.381 2037 Planarity : 0.004 0.045 2180 Dihedral : 8.888 88.890 1897 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.88 % Allowed : 26.29 % Favored : 69.83 % 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: 1.61 (0.21), residues: 1541 helix: 2.08 (0.15), residues: 1107 sheet: -1.62 (0.82), residues: 36 loop : -1.69 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.026 0.001 TYR C 376 PHE 0.024 0.001 PHE C 118 TRP 0.007 0.001 TRP A 520 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (13111) covalent geometry : angle 0.76474 / 0.33 (17813) SS BOND : bond 0.00650 / 0.34 ( 2) SS BOND : angle 1.53310 / 0.84 ( 4) hydrogen bonds : bond 0.04800 / 3.06 ( 836) hydrogen bonds : angle 3.85770 / 2.80 ( 2475) *********************** 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 224 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8003 (t0) cc_final: 0.7348 (m-30) REVERT: A 152 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7753 (mtt90) REVERT: A 166 ILE cc_start: 0.7159 (tp) cc_final: 0.6742 (tp) REVERT: A 202 LYS cc_start: 0.7094 (tppt) cc_final: 0.6644 (tmtt) REVERT: A 227 MET cc_start: 0.7942 (ttp) cc_final: 0.7285 (tpt) REVERT: A 251 ARG cc_start: 0.8017 (ttm170) cc_final: 0.7789 (ttp-110) REVERT: A 342 HIS cc_start: 0.7582 (m-70) cc_final: 0.6355 (t70) REVERT: A 390 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 401 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7502 (ptmm) REVERT: A 406 ASP cc_start: 0.8101 (t0) cc_final: 0.7797 (t0) REVERT: A 479 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7147 (ttmm) REVERT: A 498 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: A 564 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7350 (mtt90) REVERT: A 580 GLN cc_start: 0.7558 (tm-30) cc_final: 0.7171 (mp-120) REVERT: A 591 LYS cc_start: 0.7982 (mttm) cc_final: 0.7260 (tttm) REVERT: A 597 ARG cc_start: 0.7689 (mtm110) cc_final: 0.6923 (mtm-85) REVERT: A 602 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7954 (ttt-90) REVERT: A 604 LYS cc_start: 0.5363 (OUTLIER) cc_final: 0.3836 (mptt) REVERT: B 36 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8626 (t) REVERT: B 80 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7407 (mttt) REVERT: B 140 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 145 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7783 (mtt90) REVERT: B 234 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: B 277 PHE cc_start: 0.7236 (m-80) cc_final: 0.6829 (m-10) REVERT: B 278 ASP cc_start: 0.7651 (m-30) cc_final: 0.6949 (t0) REVERT: B 309 LEU cc_start: 0.7640 (tt) cc_final: 0.7379 (tm) REVERT: B 442 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6658 (ttt-90) REVERT: B 462 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.7693 (mppt) REVERT: B 510 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6782 (mm-30) REVERT: B 557 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7750 (mp0) REVERT: B 564 ARG cc_start: 0.8272 (mmt180) cc_final: 0.7752 (mtp180) REVERT: B 599 GLU cc_start: 0.7715 (tp30) cc_final: 0.7318 (mt-10) REVERT: C 34 ARG cc_start: 0.6862 (mtp85) cc_final: 0.5804 (tpm-80) REVERT: C 40 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6122 (ptt90) REVERT: C 48 ILE cc_start: 0.7790 (pt) cc_final: 0.7400 (mm) REVERT: C 58 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6845 (mm) REVERT: C 245 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: C 264 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.5841 (mtm110) REVERT: C 354 MET cc_start: 0.5740 (tmm) cc_final: 0.5486 (mtm) REVERT: C 408 GLN cc_start: 0.6740 (pm20) cc_final: 0.6093 (mt0) REVERT: C 496 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5745 (t80) outliers start: 54 outliers final: 25 residues processed: 211 average time/residue: 0.5499 time to fit residues: 126.2034 Evaluate side-chains 203 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.183318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135406 restraints weight = 13720.796| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.62 r_work: 0.3271 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13113 Z= 0.144 Angle : 0.749 29.785 17817 Z= 0.324 Chirality : 0.067 2.377 2037 Planarity : 0.004 0.043 2180 Dihedral : 8.715 84.918 1897 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.30 % Allowed : 26.80 % Favored : 69.90 % 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: 1.67 (0.22), residues: 1541 helix: 2.12 (0.15), residues: 1111 sheet: -1.76 (0.80), residues: 36 loop : -1.66 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 391 TYR 0.024 0.001 TYR A 68 PHE 0.018 0.001 PHE A 277 TRP 0.006 0.001 TRP C 499 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13111) covalent geometry : angle 0.74896 / 0.32 (17813) SS BOND : bond 0.00542 / 0.29 ( 2) SS BOND : angle 1.27743 / 0.71 ( 4) hydrogen bonds : bond 0.04597 / 2.93 ( 836) hydrogen bonds : angle 3.79817 / 2.76 ( 2475) *********************** 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 210 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7997 (t0) cc_final: 0.7373 (m-30) REVERT: A 152 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7691 (mtt90) REVERT: A 202 LYS cc_start: 0.7064 (tppt) cc_final: 0.6654 (tmtt) REVERT: A 227 MET cc_start: 0.7918 (ttp) cc_final: 0.7256 (tpt) REVERT: A 251 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7766 (ttp-110) REVERT: A 342 HIS cc_start: 0.7523 (m-70) cc_final: 0.6355 (t70) REVERT: A 391 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7781 (mtp85) REVERT: A 401 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7510 (ptmm) REVERT: A 406 ASP cc_start: 0.8080 (t0) cc_final: 0.7640 (t0) REVERT: A 479 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7080 (ttmm) REVERT: A 498 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: A 564 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7394 (mtm110) REVERT: A 580 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7163 (mp-120) REVERT: A 591 LYS cc_start: 0.7992 (mttm) cc_final: 0.7287 (tttm) REVERT: A 602 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7909 (ttt-90) REVERT: A 604 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.3943 (mptt) REVERT: B 80 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7419 (mttm) REVERT: B 140 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6833 (p0) REVERT: B 145 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7762 (mtt90) REVERT: B 234 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8410 (tt0) REVERT: B 277 PHE cc_start: 0.7223 (m-80) cc_final: 0.6833 (m-10) REVERT: B 278 ASP cc_start: 0.7627 (m-30) cc_final: 0.6915 (t0) REVERT: B 309 LEU cc_start: 0.7589 (tt) cc_final: 0.7357 (tm) REVERT: B 442 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6693 (ttt-90) REVERT: B 510 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6797 (mm-30) REVERT: B 557 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7689 (mp0) REVERT: B 564 ARG cc_start: 0.8236 (mmt180) cc_final: 0.7737 (mtp180) REVERT: B 599 GLU cc_start: 0.7693 (tp30) cc_final: 0.7322 (mt-10) REVERT: C 34 ARG cc_start: 0.6881 (mtp85) cc_final: 0.5825 (tpm-80) REVERT: C 40 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6139 (ptt90) REVERT: C 48 ILE cc_start: 0.7817 (pt) cc_final: 0.7412 (mm) REVERT: C 58 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6864 (mm) REVERT: C 245 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7274 (mm-30) REVERT: C 264 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5842 (mtm110) REVERT: C 354 MET cc_start: 0.5734 (tmm) cc_final: 0.5436 (mtm) REVERT: C 408 GLN cc_start: 0.6750 (pm20) cc_final: 0.6047 (mt0) REVERT: C 496 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5809 (t80) outliers start: 46 outliers final: 23 residues processed: 199 average time/residue: 0.6282 time to fit residues: 135.5201 Evaluate side-chains 196 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 479 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 136 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.185085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137414 restraints weight = 13725.064| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.64 r_work: 0.3280 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13113 Z= 0.131 Angle : 0.743 29.809 17817 Z= 0.320 Chirality : 0.067 2.377 2037 Planarity : 0.004 0.043 2180 Dihedral : 8.460 84.050 1897 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.95 % Allowed : 27.23 % Favored : 69.83 % 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: 1.74 (0.21), residues: 1541 helix: 2.19 (0.15), residues: 1111 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 251 TYR 0.024 0.001 TYR A 68 PHE 0.027 0.001 PHE C 118 TRP 0.006 0.001 TRP C 499 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13111) covalent geometry : angle 0.74298 / 0.32 (17813) SS BOND : bond 0.00437 / 0.23 ( 2) SS BOND : angle 1.04726 / 0.58 ( 4) hydrogen bonds : bond 0.04402 / 2.80 ( 836) hydrogen bonds : angle 3.73268 / 2.72 ( 2475) ********************** 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 206 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7979 (t0) cc_final: 0.7339 (m-30) REVERT: A 152 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7659 (mtt90) REVERT: A 202 LYS cc_start: 0.7052 (tppt) cc_final: 0.6585 (tmtt) REVERT: A 227 MET cc_start: 0.7892 (ttp) cc_final: 0.7221 (tpt) REVERT: A 342 HIS cc_start: 0.7438 (m-70) cc_final: 0.6276 (t70) REVERT: A 391 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7826 (mtp85) REVERT: A 401 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7451 (ptmm) REVERT: A 406 ASP cc_start: 0.8060 (t0) cc_final: 0.7633 (t0) REVERT: A 498 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 564 ARG cc_start: 0.8042 (mmt180) cc_final: 0.7351 (mtm110) REVERT: A 580 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7099 (mp-120) REVERT: A 591 LYS cc_start: 0.7999 (mttm) cc_final: 0.7270 (tttm) REVERT: A 602 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7852 (ttt-90) REVERT: A 604 LYS cc_start: 0.5036 (OUTLIER) cc_final: 0.3622 (mptt) REVERT: B 80 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7344 (mtmm) REVERT: B 138 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6633 (p0) REVERT: B 140 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6851 (p0) REVERT: B 145 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7839 (mtt180) REVERT: B 234 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: B 277 PHE cc_start: 0.7163 (m-80) cc_final: 0.6764 (m-10) REVERT: B 278 ASP cc_start: 0.7605 (m-30) cc_final: 0.6885 (t0) REVERT: B 442 ARG cc_start: 0.7256 (ttm-80) cc_final: 0.6645 (ttt-90) REVERT: B 462 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7648 (mppt) REVERT: B 510 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6740 (mm-30) REVERT: B 557 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7632 (mp0) REVERT: B 564 ARG cc_start: 0.8208 (mmt180) cc_final: 0.7697 (mtp180) REVERT: B 599 GLU cc_start: 0.7641 (tp30) cc_final: 0.7281 (mt-10) REVERT: C 34 ARG cc_start: 0.6917 (mtp85) cc_final: 0.5823 (tpm-80) REVERT: C 40 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6135 (ptt90) REVERT: C 48 ILE cc_start: 0.7807 (pt) cc_final: 0.7401 (mm) REVERT: C 245 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7261 (mm-30) REVERT: C 264 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.5913 (mtm110) REVERT: C 408 GLN cc_start: 0.6704 (pm20) cc_final: 0.6148 (mt0) REVERT: C 496 PHE cc_start: 0.6198 (OUTLIER) cc_final: 0.5796 (t80) outliers start: 41 outliers final: 20 residues processed: 197 average time/residue: 0.6538 time to fit residues: 139.4058 Evaluate side-chains 193 residues out of total 1394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 603 ILE Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 145 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 390 GLU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 462 LYS Chi-restraints excluded: chain B residue 514 GLN Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 245 GLU Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 424 THR Chi-restraints excluded: chain C residue 496 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 243 HIS ** C 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.182970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.134581 restraints weight = 13616.651| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.59 r_work: 0.3284 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13113 Z= 0.154 Angle : 0.757 29.741 17817 Z= 0.329 Chirality : 0.067 2.381 2037 Planarity : 0.004 0.042 2180 Dihedral : 8.637 82.998 1897 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.95 % Allowed : 27.51 % Favored : 69.54 % 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: 1.69 (0.22), residues: 1541 helix: 2.13 (0.15), residues: 1111 sheet: -1.74 (0.80), residues: 36 loop : -1.66 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.026 0.001 TYR A 68 PHE 0.021 0.001 PHE A 277 TRP 0.006 0.001 TRP A 520 HIS 0.003 0.001 HIS A 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (13111) covalent geometry : angle 0.75662 / 0.33 (17813) SS BOND : bond 0.00603 / 0.32 ( 2) SS BOND : angle 1.39787 / 0.77 ( 4) hydrogen bonds : bond 0.04638 / 2.95 ( 836) hydrogen bonds : angle 3.82221 / 2.78 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4836.69 seconds wall clock time: 83 minutes 10.37 seconds (4990.37 seconds total)