Starting phenix.real_space_refine on Fri Jul 3 05:24:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vbp_64930/07_2026/9vbp_64930_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vbp_64930/07_2026/9vbp_64930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vbp_64930/07_2026/9vbp_64930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vbp_64930/07_2026/9vbp_64930.map" model { file = "/net/cci-nas-00/data/ceres_data/9vbp_64930/07_2026/9vbp_64930_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vbp_64930/07_2026/9vbp_64930_neut_trim.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7860 2.51 5 N 1869 2.21 5 O 2037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11823 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3934 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 17, 'TRANS': 486} Chain: "B" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3934 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 17, 'TRANS': 486} Chain: "C" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3934 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 17, 'TRANS': 486} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.73, per 1000 atoms: 0.23 Number of scatterers: 11823 At special positions: 0 Unit cell: (109.431, 115.668, 82.782, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2037 8.00 N 1869 7.00 C 7860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 465.3 milliseconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 1 sheets defined 87.8% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 14 through 35 Processing helix chain 'A' and resid 35 through 54 removed outlier: 3.522A pdb=" N TRP A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.620A pdb=" N TYR A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 108 through 121 removed outlier: 4.836A pdb=" N VAL A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Proline residue: A 117 - end of helix Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.624A pdb=" N MET A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 166 removed outlier: 4.150A pdb=" N MET A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 178 through 183 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 188 through 225 removed outlier: 4.205A pdb=" N ALA A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 251 Processing helix chain 'A' and resid 253 through 277 Processing helix chain 'A' and resid 280 through 303 removed outlier: 3.548A pdb=" N VAL A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N MET A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLY A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 Processing helix chain 'A' and resid 319 through 342 removed outlier: 3.598A pdb=" N PHE A 323 " --> pdb=" O TRP A 319 " (cutoff:3.500A) Proline residue: A 332 - end of helix removed outlier: 3.560A pdb=" N LEU A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 356 through 379 removed outlier: 3.998A pdb=" N PHE A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.691A pdb=" N TYR A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 437 removed outlier: 3.607A pdb=" N TYR A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 427 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 470 removed outlier: 3.602A pdb=" N ARG A 451 " --> pdb=" O PRO A 447 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 removed outlier: 3.527A pdb=" N LEU A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 480 " --> pdb=" O ASN A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 512 removed outlier: 3.710A pdb=" N PHE A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE A 490 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 35 Processing helix chain 'B' and resid 35 through 54 removed outlier: 3.528A pdb=" N TRP B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 75 removed outlier: 3.519A pdb=" N TYR B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 107 through 123 removed outlier: 4.425A pdb=" N VAL B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.590A pdb=" N MET B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 167 removed outlier: 3.931A pdb=" N MET B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 188 through 225 Processing helix chain 'B' and resid 230 through 252 Processing helix chain 'B' and resid 255 through 278 removed outlier: 3.986A pdb=" N VAL B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 303 removed outlier: 3.548A pdb=" N VAL B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N MET B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLY B 301 " --> pdb=" O ASN B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 319 through 342 removed outlier: 3.584A pdb=" N PHE B 323 " --> pdb=" O TRP B 319 " (cutoff:3.500A) Proline residue: B 332 - end of helix Processing helix chain 'B' and resid 346 through 379 Proline residue: B 358 - end of helix removed outlier: 3.863A pdb=" N PHE B 361 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.599A pdb=" N LEU B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 436 removed outlier: 3.737A pdb=" N SER B 427 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 469 removed outlier: 3.781A pdb=" N ASN B 469 " --> pdb=" O MET B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.532A pdb=" N VAL B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 512 removed outlier: 3.597A pdb=" N PHE B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 488 " --> pdb=" O PRO B 484 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 35 Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.508A pdb=" N TRP C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 75 removed outlier: 3.669A pdb=" N TYR C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 92 through 105 removed outlier: 3.773A pdb=" N ALA C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.637A pdb=" N PHE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 115 " --> pdb=" O PHE C 111 " (cutoff:3.500A) Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.637A pdb=" N MET C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 167 removed outlier: 4.074A pdb=" N MET C 153 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 188 through 226 Processing helix chain 'C' and resid 230 through 250 removed outlier: 3.513A pdb=" N ALA C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 277 removed outlier: 3.584A pdb=" N LEU C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.533A pdb=" N MET C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 319 through 342 Proline residue: C 332 - end of helix removed outlier: 3.640A pdb=" N PHE C 337 " --> pdb=" O PHE C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 356 through 379 removed outlier: 3.699A pdb=" N PHE C 361 " --> pdb=" O ILE C 357 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 391 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.656A pdb=" N TYR C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 437 removed outlier: 3.634A pdb=" N SER C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER C 427 " --> pdb=" O THR C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 470 removed outlier: 3.698A pdb=" N ARG C 451 " --> pdb=" O PRO C 447 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN C 469 " --> pdb=" O MET C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.559A pdb=" N LEU C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 479 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 480 " --> pdb=" O ASN C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 512 removed outlier: 3.557A pdb=" N PHE C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 490 " --> pdb=" O SER C 486 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN C 511 " --> pdb=" O ARG C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 12 through 13 removed outlier: 3.775A pdb=" N LYS B 12 " --> pdb=" O GLN B 438 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2721 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3552 1.34 - 1.46: 3270 1.46 - 1.58: 5220 1.58 - 1.70: 0 1.70 - 1.81: 108 Bond restraints: 12150 Sorted by residual: bond pdb=" N ILE C 107 " pdb=" CA ILE C 107 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.33e+00 bond pdb=" N ASP C 108 " pdb=" CA ASP C 108 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.33e-02 5.65e+03 8.03e+00 bond pdb=" N ILE B 107 " pdb=" CA ILE B 107 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.31e-02 5.83e+03 6.27e+00 bond pdb=" N ASP B 108 " pdb=" CA ASP B 108 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N LEU B 109 " pdb=" CA LEU B 109 " ideal model delta sigma weight residual 1.458 1.486 -0.027 1.27e-02 6.20e+03 4.64e+00 ... (remaining 12145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 16214 1.41 - 2.83: 245 2.83 - 4.24: 59 4.24 - 5.66: 29 5.66 - 7.07: 10 Bond angle restraints: 16557 Sorted by residual: angle pdb=" N ILE B 107 " pdb=" CA ILE B 107 " pdb=" C ILE B 107 " ideal model delta sigma weight residual 113.07 108.38 4.69 1.37e+00 5.33e-01 1.17e+01 angle pdb=" CA ASP C 108 " pdb=" CB ASP C 108 " pdb=" CG ASP C 108 " ideal model delta sigma weight residual 112.60 115.98 -3.38 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA GLN A 86 " pdb=" CB GLN A 86 " pdb=" CG GLN A 86 " ideal model delta sigma weight residual 114.10 120.30 -6.20 2.00e+00 2.50e-01 9.60e+00 angle pdb=" CA GLN C 86 " pdb=" CB GLN C 86 " pdb=" CG GLN C 86 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.07e+00 angle pdb=" CA LYS C 88 " pdb=" CB LYS C 88 " pdb=" CG LYS C 88 " ideal model delta sigma weight residual 114.10 120.08 -5.98 2.00e+00 2.50e-01 8.95e+00 ... (remaining 16552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 6121 14.39 - 28.79: 489 28.79 - 43.18: 192 43.18 - 57.57: 64 57.57 - 71.96: 22 Dihedral angle restraints: 6888 sinusoidal: 2556 harmonic: 4332 Sorted by residual: dihedral pdb=" C ASP C 108 " pdb=" N ASP C 108 " pdb=" CA ASP C 108 " pdb=" CB ASP C 108 " ideal model delta harmonic sigma weight residual -122.60 -131.01 8.41 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA TRP C 324 " pdb=" CB TRP C 324 " pdb=" CG TRP C 324 " pdb=" CD1 TRP C 324 " ideal model delta sinusoidal sigma weight residual 90.00 161.96 -71.96 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TRP B 324 " pdb=" CB TRP B 324 " pdb=" CG TRP B 324 " pdb=" CD1 TRP B 324 " ideal model delta sinusoidal sigma weight residual 90.00 161.71 -71.71 2 2.00e+01 2.50e-03 1.08e+01 ... (remaining 6885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1569 0.046 - 0.091: 298 0.091 - 0.137: 32 0.137 - 0.182: 1 0.182 - 0.228: 2 Chirality restraints: 1902 Sorted by residual: chirality pdb=" CA ASP C 108 " pdb=" N ASP C 108 " pdb=" C ASP C 108 " pdb=" CB ASP C 108 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE C 107 " pdb=" N ILE C 107 " pdb=" C ILE C 107 " pdb=" CB ILE C 107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 1899 not shown) Planarity restraints: 2022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 319 " 0.009 2.00e-02 2.50e+03 7.30e-03 1.33e+00 pdb=" CG TRP C 319 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP C 319 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP C 319 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 319 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 319 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 319 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 319 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 319 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 319 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 227 " -0.018 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO B 228 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 179 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 180 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " 0.015 5.00e-02 4.00e+02 ... (remaining 2019 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 6304 3.00 - 3.47: 13087 3.47 - 3.95: 18836 3.95 - 4.42: 21560 4.42 - 4.90: 34566 Nonbonded interactions: 94353 Sorted by model distance: nonbonded pdb=" OD1 ASP A 108 " pdb=" O6 CHT A 601 " model vdw 2.520 3.040 nonbonded pdb=" N ILE A 105 " pdb=" N GLY A 106 " model vdw 2.622 2.560 nonbonded pdb=" N SER B 444 " pdb=" O SER B 444 " model vdw 2.630 2.496 nonbonded pdb=" N ILE B 107 " pdb=" N ASP B 108 " model vdw 2.637 2.560 nonbonded pdb=" C SER A 261 " pdb=" OG SER A 261 " model vdw 2.646 2.616 ... (remaining 94348 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 9.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12150 Z= 0.120 Angle : 0.517 7.070 16557 Z= 0.283 Chirality : 0.034 0.228 1902 Planarity : 0.003 0.029 2022 Dihedral : 13.878 71.964 4122 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.29 % Allowed : 15.37 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1506 helix: 1.54 (0.14), residues: 1173 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 507 TYR 0.010 0.001 TYR C 505 PHE 0.012 0.001 PHE C 28 TRP 0.019 0.001 TRP C 319 HIS 0.001 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.12 (12150) covalent geometry : angle 0.51651 / 0.28 (16557) hydrogen bonds : bond 0.27541 / 18.38 ( 923) hydrogen bonds : angle 7.05126 / 5.03 ( 2721) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.439 Fit side-chains REVERT: A 99 MET cc_start: 0.8898 (mmm) cc_final: 0.8674 (mmm) REVERT: A 190 ILE cc_start: 0.8892 (mm) cc_final: 0.8645 (mt) REVERT: A 231 MET cc_start: 0.7580 (tmm) cc_final: 0.6711 (tpp) REVERT: A 345 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7040 (ptp90) REVERT: B 74 CYS cc_start: 0.8066 (t) cc_final: 0.7510 (p) REVERT: B 86 GLN cc_start: 0.9373 (tm-30) cc_final: 0.9107 (tm-30) REVERT: B 99 MET cc_start: 0.8031 (mtp) cc_final: 0.7420 (mpp) REVERT: B 126 GLU cc_start: 0.8685 (pp20) cc_final: 0.8162 (pm20) REVERT: B 231 MET cc_start: 0.7802 (tmm) cc_final: 0.7111 (tpp) REVERT: C 57 TYR cc_start: 0.8032 (t80) cc_final: 0.7810 (t80) REVERT: C 74 CYS cc_start: 0.7974 (t) cc_final: 0.7502 (p) REVERT: C 96 TRP cc_start: 0.8219 (t60) cc_final: 0.7849 (t60) REVERT: C 190 ILE cc_start: 0.9007 (mm) cc_final: 0.8803 (mt) outliers start: 16 outliers final: 10 residues processed: 189 average time/residue: 0.0748 time to fit residues: 22.1348 Evaluate side-chains 177 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 402 GLN Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.073663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.055727 restraints weight = 31286.321| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.11 r_work: 0.2518 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12150 Z= 0.202 Angle : 0.607 7.135 16557 Z= 0.328 Chirality : 0.041 0.169 1902 Planarity : 0.004 0.031 2022 Dihedral : 5.265 85.408 1650 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.64 % Allowed : 14.32 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.21), residues: 1506 helix: 2.20 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.80 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 507 TYR 0.026 0.001 TYR B 421 PHE 0.018 0.002 PHE B 420 TRP 0.018 0.002 TRP B 96 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (12150) covalent geometry : angle 0.60725 / 0.33 (16557) hydrogen bonds : bond 0.07765 / 5.15 ( 923) hydrogen bonds : angle 4.56629 / 3.30 ( 2721) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.339 Fit side-chains REVERT: A 99 MET cc_start: 0.9024 (mmm) cc_final: 0.8702 (mmm) REVERT: A 190 ILE cc_start: 0.8476 (mm) cc_final: 0.8200 (mt) REVERT: A 345 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6804 (ptp90) REVERT: B 86 GLN cc_start: 0.9387 (tm-30) cc_final: 0.9101 (tm-30) REVERT: B 99 MET cc_start: 0.8008 (mtp) cc_final: 0.7394 (mpp) REVERT: B 300 MET cc_start: 0.9285 (tpp) cc_final: 0.8985 (tpp) REVERT: C 13 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6493 (pt) REVERT: C 96 TRP cc_start: 0.8362 (t60) cc_final: 0.7842 (t60) outliers start: 45 outliers final: 24 residues processed: 194 average time/residue: 0.0798 time to fit residues: 23.9746 Evaluate side-chains 178 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 13 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 135 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 HIS C 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.076357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.057863 restraints weight = 31109.620| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.17 r_work: 0.2631 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12150 Z= 0.128 Angle : 0.503 8.998 16557 Z= 0.262 Chirality : 0.037 0.141 1902 Planarity : 0.003 0.032 2022 Dihedral : 4.564 82.776 1640 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.51 % Allowed : 15.78 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.22), residues: 1506 helix: 2.49 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 507 TYR 0.021 0.001 TYR C 421 PHE 0.015 0.001 PHE B 420 TRP 0.012 0.001 TRP A 449 HIS 0.001 0.000 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (12150) covalent geometry : angle 0.50343 / 0.26 (16557) hydrogen bonds : bond 0.05828 / 3.90 ( 923) hydrogen bonds : angle 4.09839 / 2.94 ( 2721) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.459 Fit side-chains REVERT: A 99 MET cc_start: 0.8962 (mmm) cc_final: 0.8682 (mmm) REVERT: A 345 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.6976 (ptp90) REVERT: B 86 GLN cc_start: 0.9398 (tm-30) cc_final: 0.9102 (tm-30) REVERT: B 99 MET cc_start: 0.7791 (mtp) cc_final: 0.6584 (mtp) REVERT: B 300 MET cc_start: 0.9227 (tpp) cc_final: 0.8982 (tpp) REVERT: B 384 PHE cc_start: 0.8455 (t80) cc_final: 0.8193 (t80) REVERT: B 444 SER cc_start: 0.8481 (t) cc_final: 0.8153 (t) REVERT: C 74 CYS cc_start: 0.7326 (t) cc_final: 0.6575 (p) REVERT: C 96 TRP cc_start: 0.8245 (t60) cc_final: 0.7789 (t60) outliers start: 31 outliers final: 13 residues processed: 197 average time/residue: 0.0827 time to fit residues: 25.0332 Evaluate side-chains 170 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 247 ILE Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 324 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN B 137 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.071973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.053709 restraints weight = 31413.630| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.15 r_work: 0.2559 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12150 Z= 0.191 Angle : 0.559 7.633 16557 Z= 0.290 Chirality : 0.039 0.183 1902 Planarity : 0.003 0.031 2022 Dihedral : 4.578 76.847 1638 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.32 % Allowed : 17.07 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.22), residues: 1506 helix: 2.36 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : -0.85 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 507 TYR 0.027 0.001 TYR B 421 PHE 0.014 0.001 PHE B 420 TRP 0.014 0.001 TRP B 96 HIS 0.003 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (12150) covalent geometry : angle 0.55884 / 0.29 (16557) hydrogen bonds : bond 0.06123 / 4.08 ( 923) hydrogen bonds : angle 4.20348 / 3.02 ( 2721) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 28 PHE cc_start: 0.8606 (t80) cc_final: 0.8357 (t80) REVERT: A 99 MET cc_start: 0.8977 (mmm) cc_final: 0.8676 (mmm) REVERT: A 345 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7085 (ptp90) REVERT: B 86 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9085 (tm-30) REVERT: B 300 MET cc_start: 0.9287 (tpp) cc_final: 0.9080 (tpp) REVERT: C 467 MET cc_start: 0.9112 (ttm) cc_final: 0.8834 (mtm) REVERT: C 506 ARG cc_start: 0.9157 (ttm-80) cc_final: 0.8891 (ttp80) outliers start: 41 outliers final: 32 residues processed: 188 average time/residue: 0.0764 time to fit residues: 22.2214 Evaluate side-chains 188 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 70 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 39 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.055897 restraints weight = 30931.858| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.16 r_work: 0.2613 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12150 Z= 0.122 Angle : 0.500 8.288 16557 Z= 0.256 Chirality : 0.037 0.148 1902 Planarity : 0.003 0.028 2022 Dihedral : 4.477 68.702 1638 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.07 % Allowed : 18.37 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.22), residues: 1506 helix: 2.50 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : -0.90 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 507 TYR 0.020 0.001 TYR C 421 PHE 0.013 0.001 PHE B 420 TRP 0.012 0.001 TRP B 327 HIS 0.001 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (12150) covalent geometry : angle 0.49950 / 0.26 (16557) hydrogen bonds : bond 0.05260 / 3.52 ( 923) hydrogen bonds : angle 3.96216 / 2.83 ( 2721) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.279 Fit side-chains REVERT: A 28 PHE cc_start: 0.8598 (t80) cc_final: 0.8337 (t80) REVERT: A 99 MET cc_start: 0.8941 (mmm) cc_final: 0.8704 (mmm) REVERT: A 345 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6993 (ptp90) REVERT: B 86 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9099 (tm-30) REVERT: B 384 PHE cc_start: 0.8512 (t80) cc_final: 0.8236 (t80) REVERT: C 96 TRP cc_start: 0.8378 (t60) cc_final: 0.7825 (t60) REVERT: C 506 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8882 (ttp80) outliers start: 38 outliers final: 25 residues processed: 192 average time/residue: 0.0787 time to fit residues: 23.1859 Evaluate side-chains 188 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 137 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.074360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.056176 restraints weight = 31035.169| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.10 r_work: 0.2620 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12150 Z= 0.125 Angle : 0.520 8.761 16557 Z= 0.260 Chirality : 0.037 0.153 1902 Planarity : 0.003 0.027 2022 Dihedral : 4.407 62.567 1638 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.24 % Allowed : 18.12 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.22), residues: 1506 helix: 2.52 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 507 TYR 0.023 0.001 TYR C 421 PHE 0.011 0.001 PHE B 420 TRP 0.011 0.001 TRP B 327 HIS 0.001 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (12150) covalent geometry : angle 0.51981 / 0.26 (16557) hydrogen bonds : bond 0.05079 / 3.39 ( 923) hydrogen bonds : angle 3.92924 / 2.81 ( 2721) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.311 Fit side-chains REVERT: A 28 PHE cc_start: 0.8674 (t80) cc_final: 0.8278 (t80) REVERT: A 345 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7188 (ptp90) REVERT: B 86 GLN cc_start: 0.9407 (tm-30) cc_final: 0.9096 (tm-30) REVERT: B 384 PHE cc_start: 0.8474 (t80) cc_final: 0.8250 (t80) REVERT: C 96 TRP cc_start: 0.8389 (t60) cc_final: 0.7815 (t60) REVERT: C 231 MET cc_start: 0.6464 (tmm) cc_final: 0.5968 (tpp) REVERT: C 506 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8866 (ttp80) outliers start: 40 outliers final: 32 residues processed: 195 average time/residue: 0.0769 time to fit residues: 23.0731 Evaluate side-chains 191 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.071987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.053979 restraints weight = 31546.858| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.10 r_work: 0.2565 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12150 Z= 0.208 Angle : 0.575 7.578 16557 Z= 0.298 Chirality : 0.039 0.174 1902 Planarity : 0.003 0.026 2022 Dihedral : 4.578 66.216 1638 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.99 % Allowed : 19.26 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.22), residues: 1506 helix: 2.41 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -0.95 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 507 TYR 0.020 0.001 TYR C 421 PHE 0.014 0.001 PHE A 333 TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.21 (12150) covalent geometry : angle 0.57528 / 0.30 (16557) hydrogen bonds : bond 0.05995 / 3.98 ( 923) hydrogen bonds : angle 4.11902 / 2.96 ( 2721) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 28 PHE cc_start: 0.8651 (t80) cc_final: 0.8373 (t80) REVERT: A 99 MET cc_start: 0.8970 (mmm) cc_final: 0.8705 (mmm) REVERT: B 86 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9086 (tm-30) REVERT: B 231 MET cc_start: 0.7011 (tmm) cc_final: 0.6485 (tpp) REVERT: C 231 MET cc_start: 0.6702 (tmm) cc_final: 0.6155 (tpp) REVERT: C 506 ARG cc_start: 0.9130 (ttm-80) cc_final: 0.8867 (ttp80) outliers start: 37 outliers final: 32 residues processed: 179 average time/residue: 0.0752 time to fit residues: 20.9210 Evaluate side-chains 183 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 GLN B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.054965 restraints weight = 31284.150| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.16 r_work: 0.2593 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12150 Z= 0.137 Angle : 0.524 8.195 16557 Z= 0.268 Chirality : 0.037 0.181 1902 Planarity : 0.003 0.025 2022 Dihedral : 4.524 62.357 1638 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.91 % Allowed : 19.42 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.22), residues: 1506 helix: 2.45 (0.15), residues: 1215 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 506 TYR 0.018 0.001 TYR C 421 PHE 0.011 0.001 PHE B 420 TRP 0.017 0.001 TRP B 327 HIS 0.002 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (12150) covalent geometry : angle 0.52368 / 0.27 (16557) hydrogen bonds : bond 0.05382 / 3.59 ( 923) hydrogen bonds : angle 3.95285 / 2.83 ( 2721) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.406 Fit side-chains REVERT: A 28 PHE cc_start: 0.8690 (t80) cc_final: 0.8344 (t80) REVERT: A 99 MET cc_start: 0.8980 (mmm) cc_final: 0.8680 (mmm) REVERT: B 86 GLN cc_start: 0.9414 (tm-30) cc_final: 0.9100 (tm-30) REVERT: B 123 GLN cc_start: 0.9368 (mm110) cc_final: 0.9129 (mm-40) REVERT: B 231 MET cc_start: 0.6906 (tmm) cc_final: 0.6370 (tpp) REVERT: C 96 TRP cc_start: 0.8497 (t60) cc_final: 0.7813 (t60) REVERT: C 216 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: C 231 MET cc_start: 0.6617 (tmm) cc_final: 0.6077 (tpp) REVERT: C 506 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8867 (ttp80) outliers start: 36 outliers final: 30 residues processed: 183 average time/residue: 0.0785 time to fit residues: 22.0967 Evaluate side-chains 188 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 333 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 481 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 chunk 141 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.075619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.057205 restraints weight = 30714.968| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.17 r_work: 0.2600 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12150 Z= 0.115 Angle : 0.519 8.928 16557 Z= 0.258 Chirality : 0.037 0.227 1902 Planarity : 0.003 0.025 2022 Dihedral : 4.408 54.967 1638 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.59 % Allowed : 19.82 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.22), residues: 1506 helix: 2.63 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -0.67 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 506 TYR 0.018 0.001 TYR C 421 PHE 0.012 0.001 PHE B 420 TRP 0.014 0.001 TRP A 96 HIS 0.001 0.000 HIS C 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (12150) covalent geometry : angle 0.51933 / 0.26 (16557) hydrogen bonds : bond 0.04597 / 3.08 ( 923) hydrogen bonds : angle 3.83583 / 2.74 ( 2721) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.277 Fit side-chains REVERT: A 28 PHE cc_start: 0.8566 (t80) cc_final: 0.8244 (t80) REVERT: A 345 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6992 (ptp90) REVERT: B 86 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9127 (tm-30) REVERT: B 99 MET cc_start: 0.7734 (mtp) cc_final: 0.6278 (mmm) REVERT: B 231 MET cc_start: 0.6703 (tmm) cc_final: 0.6199 (tpp) REVERT: B 507 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8321 (ttp80) REVERT: C 96 TRP cc_start: 0.8443 (t60) cc_final: 0.7798 (t60) REVERT: C 108 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.8086 (p0) REVERT: C 216 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6873 (tt0) REVERT: C 231 MET cc_start: 0.6390 (tmm) cc_final: 0.5903 (tpp) REVERT: C 506 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8840 (ttp80) outliers start: 32 outliers final: 24 residues processed: 197 average time/residue: 0.0773 time to fit residues: 23.4538 Evaluate side-chains 187 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Chi-restraints excluded: chain C residue 481 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 142 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057329 restraints weight = 31047.820| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.16 r_work: 0.2605 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12150 Z= 0.117 Angle : 0.547 11.812 16557 Z= 0.270 Chirality : 0.038 0.248 1902 Planarity : 0.003 0.026 2022 Dihedral : 4.381 53.328 1638 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.35 % Allowed : 19.90 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.22), residues: 1506 helix: 2.62 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -0.70 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 506 TYR 0.017 0.001 TYR C 421 PHE 0.013 0.001 PHE B 420 TRP 0.015 0.001 TRP A 96 HIS 0.001 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (12150) covalent geometry : angle 0.54678 / 0.27 (16557) hydrogen bonds : bond 0.04580 / 3.07 ( 923) hydrogen bonds : angle 3.82720 / 2.73 ( 2721) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.381 Fit side-chains REVERT: A 28 PHE cc_start: 0.8599 (t80) cc_final: 0.8213 (t80) REVERT: A 99 MET cc_start: 0.8931 (mmm) cc_final: 0.8647 (mmm) REVERT: A 100 LEU cc_start: 0.8890 (mm) cc_final: 0.8689 (mp) REVERT: A 345 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6915 (ptp90) REVERT: B 86 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9133 (tm-30) REVERT: B 99 MET cc_start: 0.7641 (mtp) cc_final: 0.6181 (mmm) REVERT: B 231 MET cc_start: 0.6713 (tmm) cc_final: 0.6218 (tpp) REVERT: C 96 TRP cc_start: 0.8435 (t60) cc_final: 0.7765 (t60) REVERT: C 108 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (p0) REVERT: C 506 ARG cc_start: 0.9073 (ttm-80) cc_final: 0.8853 (ttp80) outliers start: 29 outliers final: 25 residues processed: 186 average time/residue: 0.0858 time to fit residues: 24.5174 Evaluate side-chains 184 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 71 CYS Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 324 TRP Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 324 TRP Chi-restraints excluded: chain B residue 333 PHE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 481 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 TRP Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 435 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 4 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.057731 restraints weight = 30799.955| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.16 r_work: 0.2616 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12150 Z= 0.115 Angle : 0.549 8.842 16557 Z= 0.268 Chirality : 0.037 0.206 1902 Planarity : 0.003 0.026 2022 Dihedral : 4.342 52.046 1638 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.10 % Allowed : 20.39 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.03 (0.22), residues: 1506 helix: 2.64 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -0.67 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 506 TYR 0.017 0.001 TYR C 421 PHE 0.013 0.001 PHE B 420 TRP 0.015 0.001 TRP A 96 HIS 0.001 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (12150) covalent geometry : angle 0.54915 / 0.27 (16557) hydrogen bonds : bond 0.04459 / 2.99 ( 923) hydrogen bonds : angle 3.78886 / 2.70 ( 2721) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2408.03 seconds wall clock time: 42 minutes 1.11 seconds (2521.11 seconds total)