Starting phenix.real_space_refine on Wed Mar 4 00:20:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwp_10634/03_2026/6xwp_10634.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwp_10634/03_2026/6xwp_10634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2026/6xwp_10634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2026/6xwp_10634.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2026/6xwp_10634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2026/6xwp_10634.map" } resolution = 3.38 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= 1.000 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 48 5.16 5 C 6299 2.51 5 N 1544 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9552 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "C" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.25 Number of scatterers: 9552 At special positions: 0 Unit cell: (79.948, 102.212, 107.272, 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 48 16.00 O 1661 8.00 N 1544 7.00 C 6299 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: 0.78 Conformation dependent library (CDL) restraints added in 663.9 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 13 through 35 removed outlier: 3.723A pdb=" N TRP A 20 " --> pdb=" O TRP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 46 through 74 removed outlier: 3.746A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix removed outlier: 3.802A pdb=" N SER A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 110 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 171 removed outlier: 4.009A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 226 through 256 removed outlier: 3.765A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.928A pdb=" N LYS A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.535A pdb=" N PHE A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 3.980A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.691A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.152A pdb=" N VAL A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.672A pdb=" N ILE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 419 removed outlier: 3.703A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N MET A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 13 through 35 removed outlier: 3.758A pdb=" N VAL B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.761A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.736A pdb=" N SER B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 3.569A pdb=" N TYR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.658A pdb=" N GLY B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 171 removed outlier: 3.839A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 211 removed outlier: 3.946A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 228 through 255 removed outlier: 4.297A pdb=" N TYR B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 3.892A pdb=" N ARG B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 301 through 313 Proline residue: B 307 - end of helix removed outlier: 4.665A pdb=" N THR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.742A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 353 removed outlier: 4.087A pdb=" N VAL B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 removed outlier: 4.327A pdb=" N ILE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.815A pdb=" N MET B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 420 removed outlier: 4.764A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.912A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.530A pdb=" N ILE C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 110 Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 152 through 171 removed outlier: 3.838A pdb=" N VAL C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 222 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 229 through 248 removed outlier: 3.785A pdb=" N VAL C 233 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 removed outlier: 4.302A pdb=" N LYS C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 removed outlier: 5.455A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 282 removed outlier: 3.503A pdb=" N GLY C 282 " --> pdb=" O SER C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 298 through 309 removed outlier: 5.331A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 314 through 333 Processing helix chain 'C' and resid 337 through 354 removed outlier: 3.723A pdb=" N LEU C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 373 removed outlier: 3.887A pdb=" N VAL C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 420 removed outlier: 4.045A pdb=" N MET C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2088 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: 1.52 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2967 1.34 - 1.46: 1676 1.46 - 1.57: 4988 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9727 Sorted by residual: bond pdb=" C SER A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.337 1.316 0.021 1.11e-02 8.12e+03 3.45e+00 bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.11e+00 bond pdb=" CB ILE A 162 " pdb=" CG2 ILE A 162 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB MET A 368 " pdb=" CG MET A 368 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CB ILE B 162 " pdb=" CG2 ILE B 162 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.82e+00 ... (remaining 9722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 12665 1.51 - 3.02: 457 3.02 - 4.53: 83 4.53 - 6.03: 29 6.03 - 7.54: 4 Bond angle restraints: 13238 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 112.96 107.98 4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" N VAL C 373 " pdb=" CA VAL C 373 " pdb=" C VAL C 373 " ideal model delta sigma weight residual 111.91 107.51 4.40 8.90e-01 1.26e+00 2.44e+01 angle pdb=" C ILE A 301 " pdb=" N PHE A 302 " pdb=" CA PHE A 302 " ideal model delta sigma weight residual 122.38 114.84 7.54 1.81e+00 3.05e-01 1.74e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 113.39 108.10 5.29 1.47e+00 4.63e-01 1.29e+01 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 109.81 116.51 -6.70 2.21e+00 2.05e-01 9.19e+00 ... (remaining 13233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5184 17.15 - 34.29: 457 34.29 - 51.44: 85 51.44 - 68.59: 6 68.59 - 85.73: 2 Dihedral angle restraints: 5734 sinusoidal: 2127 harmonic: 3607 Sorted by residual: dihedral pdb=" CA PRO B 129 " pdb=" C PRO B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER C 76 " pdb=" C SER C 76 " pdb=" N PRO C 77 " pdb=" CA PRO C 77 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP C 16 " pdb=" C TRP C 16 " pdb=" N LYS C 17 " pdb=" CA LYS C 17 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 906 0.032 - 0.065: 531 0.065 - 0.097: 154 0.097 - 0.130: 52 0.130 - 0.162: 6 Chirality restraints: 1649 Sorted by residual: chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA PRO C 47 " pdb=" N PRO C 47 " pdb=" C PRO C 47 " pdb=" CB PRO C 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1646 not shown) Planarity restraints: 1627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 129 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO B 130 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 228 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 229 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 208 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.029 5.00e-02 4.00e+02 ... (remaining 1624 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 120 2.67 - 3.22: 10212 3.22 - 3.78: 15450 3.78 - 4.34: 20598 4.34 - 4.90: 34303 Nonbonded interactions: 80683 Sorted by model distance: nonbonded pdb=" OH TYR B 9 " pdb=" O GLN B 205 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASP C 424 " pdb=" OG SER C 426 " model vdw 2.163 3.040 nonbonded pdb=" NZ LYS B 17 " pdb=" OE1 GLN B 205 " model vdw 2.174 3.120 nonbonded pdb=" O ALA C 363 " pdb=" OH TYR C 387 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR B 249 " pdb=" OD2 ASP B 315 " model vdw 2.204 3.040 ... (remaining 80678 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' selection = (chain 'B' and resid 5 through 430) selection = (chain 'C' and resid 5 through 430) } 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: 1.740 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.180 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 : 0.007 0.058 9727 Z= 0.307 Angle : 0.716 7.542 13238 Z= 0.386 Chirality : 0.044 0.162 1649 Planarity : 0.006 0.079 1627 Dihedral : 12.987 85.734 3444 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % 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: -3.13 (0.20), residues: 1272 helix: -1.65 (0.14), residues: 1003 sheet: None (None), residues: 0 loop : -3.00 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.014 0.002 TYR B 238 PHE 0.021 0.002 PHE B 302 TRP 0.007 0.001 TRP C 16 HIS 0.003 0.001 HIS B 334 Details of bonding type rmsd covalent geometry : bond 0.00748 ( 9727) covalent geometry : angle 0.71566 (13238) hydrogen bonds : bond 0.10996 ( 702) hydrogen bonds : angle 5.97784 ( 2088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8566 (tp) cc_final: 0.8325 (tt) REVERT: A 134 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8214 (tp40) REVERT: A 150 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8499 (mttm) REVERT: A 244 GLN cc_start: 0.8944 (tp40) cc_final: 0.8356 (tp40) REVERT: A 341 GLN cc_start: 0.8969 (mt0) cc_final: 0.8765 (mt0) REVERT: A 368 MET cc_start: 0.8243 (ttp) cc_final: 0.7909 (ttm) REVERT: B 205 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8153 (mm-40) REVERT: C 100 PHE cc_start: 0.8042 (t80) cc_final: 0.7110 (m-10) REVERT: C 219 MET cc_start: 0.8292 (mmm) cc_final: 0.7828 (mmm) REVERT: C 371 GLN cc_start: 0.7905 (mm110) cc_final: 0.7683 (mm-40) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.0888 time to fit residues: 23.6357 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 ASN B 128 GLN B 321 GLN C 172 ASN C 371 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108488 restraints weight = 13370.191| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.70 r_work: 0.3110 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9727 Z= 0.137 Angle : 0.588 6.394 13238 Z= 0.302 Chirality : 0.039 0.151 1649 Planarity : 0.006 0.070 1627 Dihedral : 4.621 51.792 1364 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.09 % Allowed : 11.95 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.23), residues: 1272 helix: -0.22 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.03 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 179 TYR 0.013 0.001 TYR B 320 PHE 0.025 0.001 PHE A 302 TRP 0.005 0.001 TRP A 20 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9727) covalent geometry : angle 0.58804 (13238) hydrogen bonds : bond 0.03841 ( 702) hydrogen bonds : angle 4.49757 ( 2088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8650 (tp) cc_final: 0.8407 (tt) REVERT: A 150 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8720 (mttm) REVERT: A 219 MET cc_start: 0.8345 (mmm) cc_final: 0.8092 (mmm) REVERT: A 244 GLN cc_start: 0.8819 (tp40) cc_final: 0.8428 (tp40) REVERT: A 295 MET cc_start: 0.8200 (mpp) cc_final: 0.7723 (mpp) REVERT: A 368 MET cc_start: 0.8546 (ttp) cc_final: 0.8233 (ttm) REVERT: B 100 PHE cc_start: 0.8398 (t80) cc_final: 0.8011 (t80) REVERT: C 59 LEU cc_start: 0.8643 (mt) cc_final: 0.8379 (mt) REVERT: C 100 PHE cc_start: 0.8163 (t80) cc_final: 0.7201 (m-10) REVERT: C 196 MET cc_start: 0.8783 (mmt) cc_final: 0.8565 (mmt) REVERT: C 204 MET cc_start: 0.8486 (mmt) cc_final: 0.8264 (mmt) REVERT: C 219 MET cc_start: 0.8271 (mmm) cc_final: 0.7932 (mmp) REVERT: C 221 GLU cc_start: 0.7879 (tp30) cc_final: 0.7582 (tp30) REVERT: C 244 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8069 (tm-30) outliers start: 21 outliers final: 12 residues processed: 189 average time/residue: 0.0833 time to fit residues: 22.7922 Evaluate side-chains 166 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 4 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107082 restraints weight = 13325.872| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.69 r_work: 0.3093 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9727 Z= 0.144 Angle : 0.584 7.807 13238 Z= 0.298 Chirality : 0.039 0.137 1649 Planarity : 0.006 0.070 1627 Dihedral : 4.489 47.998 1364 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.89 % Allowed : 15.64 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.24), residues: 1272 helix: 0.41 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -1.74 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.010 0.001 TYR B 238 PHE 0.022 0.001 PHE A 302 TRP 0.004 0.001 TRP A 20 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9727) covalent geometry : angle 0.58443 (13238) hydrogen bonds : bond 0.03809 ( 702) hydrogen bonds : angle 4.28923 ( 2088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8100 (m-10) cc_final: 0.7844 (m-10) REVERT: A 110 ASN cc_start: 0.8800 (t0) cc_final: 0.8135 (t0) REVERT: A 132 LEU cc_start: 0.8693 (tp) cc_final: 0.8442 (tt) REVERT: A 150 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8733 (mttm) REVERT: A 244 GLN cc_start: 0.8816 (tp40) cc_final: 0.8398 (tp40) REVERT: A 295 MET cc_start: 0.8147 (mpp) cc_final: 0.7843 (mpp) REVERT: A 368 MET cc_start: 0.8610 (ttp) cc_final: 0.8304 (ttm) REVERT: B 100 PHE cc_start: 0.8400 (t80) cc_final: 0.8022 (t80) REVERT: B 399 MET cc_start: 0.8196 (mtm) cc_final: 0.7978 (mtm) REVERT: C 11 ASP cc_start: 0.8521 (m-30) cc_final: 0.8250 (m-30) REVERT: C 100 PHE cc_start: 0.8215 (t80) cc_final: 0.7182 (m-10) REVERT: C 219 MET cc_start: 0.8403 (mmm) cc_final: 0.8069 (mmp) REVERT: C 221 GLU cc_start: 0.7901 (tp30) cc_final: 0.7639 (tp30) outliers start: 19 outliers final: 11 residues processed: 179 average time/residue: 0.0825 time to fit residues: 21.4784 Evaluate side-chains 165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 116 ASN C 321 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110674 restraints weight = 13407.567| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.65 r_work: 0.3143 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9727 Z= 0.132 Angle : 0.572 8.743 13238 Z= 0.290 Chirality : 0.039 0.220 1649 Planarity : 0.005 0.070 1627 Dihedral : 4.318 37.686 1364 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 16.73 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1272 helix: 0.77 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.59 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 187 TYR 0.011 0.001 TYR C 387 PHE 0.019 0.001 PHE A 302 TRP 0.004 0.001 TRP A 20 HIS 0.002 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9727) covalent geometry : angle 0.57227 (13238) hydrogen bonds : bond 0.03646 ( 702) hydrogen bonds : angle 4.17182 ( 2088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8054 (m-10) cc_final: 0.7744 (m-10) REVERT: A 51 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9002 (tp) REVERT: A 110 ASN cc_start: 0.8770 (t0) cc_final: 0.8120 (t0) REVERT: A 132 LEU cc_start: 0.8667 (tp) cc_final: 0.8439 (tt) REVERT: A 150 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8739 (mttm) REVERT: A 244 GLN cc_start: 0.8663 (tp40) cc_final: 0.8359 (tp40) REVERT: A 295 MET cc_start: 0.8189 (mpp) cc_final: 0.7844 (mpp) REVERT: A 368 MET cc_start: 0.8470 (ttp) cc_final: 0.8194 (ttm) REVERT: B 100 PHE cc_start: 0.8339 (t80) cc_final: 0.8108 (t80) REVERT: B 128 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.4583 (tm130) REVERT: B 295 MET cc_start: 0.8961 (mtp) cc_final: 0.8642 (mtt) REVERT: C 11 ASP cc_start: 0.8451 (m-30) cc_final: 0.8064 (m-30) REVERT: C 100 PHE cc_start: 0.8171 (t80) cc_final: 0.7265 (m-10) outliers start: 23 outliers final: 15 residues processed: 174 average time/residue: 0.0848 time to fit residues: 21.4637 Evaluate side-chains 170 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 80 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109507 restraints weight = 13314.366| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.72 r_work: 0.3131 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9727 Z= 0.142 Angle : 0.580 7.389 13238 Z= 0.293 Chirality : 0.039 0.169 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.271 35.194 1364 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.59 % Allowed : 18.03 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1272 helix: 0.94 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 187 TYR 0.011 0.001 TYR C 387 PHE 0.018 0.001 PHE A 302 TRP 0.003 0.001 TRP A 20 HIS 0.001 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9727) covalent geometry : angle 0.58019 (13238) hydrogen bonds : bond 0.03680 ( 702) hydrogen bonds : angle 4.15018 ( 2088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8093 (m-10) cc_final: 0.7817 (m-10) REVERT: A 51 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9023 (tp) REVERT: A 110 ASN cc_start: 0.8766 (t0) cc_final: 0.8200 (t0) REVERT: A 132 LEU cc_start: 0.8700 (tp) cc_final: 0.8460 (tt) REVERT: A 150 LYS cc_start: 0.8958 (mtmt) cc_final: 0.8734 (mttm) REVERT: A 244 GLN cc_start: 0.8594 (tp40) cc_final: 0.8322 (tp40) REVERT: B 295 MET cc_start: 0.8955 (mtp) cc_final: 0.8584 (mtt) REVERT: B 399 MET cc_start: 0.8120 (mtm) cc_final: 0.7883 (mtm) REVERT: C 100 PHE cc_start: 0.8167 (t80) cc_final: 0.7237 (m-10) outliers start: 26 outliers final: 21 residues processed: 172 average time/residue: 0.0779 time to fit residues: 19.7271 Evaluate side-chains 173 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 125 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110625 restraints weight = 13286.461| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.74 r_work: 0.3129 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9727 Z= 0.132 Angle : 0.574 8.064 13238 Z= 0.290 Chirality : 0.039 0.157 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.206 32.124 1364 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.29 % Allowed : 19.02 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.24), residues: 1272 helix: 1.11 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.41 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.010 0.001 TYR C 387 PHE 0.035 0.001 PHE B 100 TRP 0.004 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9727) covalent geometry : angle 0.57367 (13238) hydrogen bonds : bond 0.03593 ( 702) hydrogen bonds : angle 4.09174 ( 2088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.8060 (m-10) cc_final: 0.7774 (m-10) REVERT: A 51 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9003 (tp) REVERT: A 110 ASN cc_start: 0.8770 (t0) cc_final: 0.8209 (t0) REVERT: A 132 LEU cc_start: 0.8666 (tp) cc_final: 0.8441 (tt) REVERT: A 150 LYS cc_start: 0.8963 (mtmt) cc_final: 0.8739 (mttm) REVERT: B 295 MET cc_start: 0.8912 (mtp) cc_final: 0.8507 (mtt) REVERT: C 100 PHE cc_start: 0.8136 (t80) cc_final: 0.7213 (m-10) outliers start: 23 outliers final: 16 residues processed: 167 average time/residue: 0.0794 time to fit residues: 19.6173 Evaluate side-chains 164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113882 restraints weight = 13316.603| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.65 r_work: 0.3159 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9727 Z= 0.124 Angle : 0.589 10.130 13238 Z= 0.293 Chirality : 0.039 0.152 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.134 27.488 1364 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 19.92 % Favored : 77.79 % 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: 1.09 (0.24), residues: 1272 helix: 1.24 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.29 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 187 TYR 0.010 0.001 TYR C 387 PHE 0.016 0.001 PHE A 302 TRP 0.005 0.000 TRP A 20 HIS 0.001 0.000 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9727) covalent geometry : angle 0.58888 (13238) hydrogen bonds : bond 0.03533 ( 702) hydrogen bonds : angle 4.05577 ( 2088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 35 PHE cc_start: 0.7995 (m-10) cc_final: 0.7711 (m-10) REVERT: A 51 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 110 ASN cc_start: 0.8754 (t0) cc_final: 0.8211 (t0) REVERT: A 150 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8720 (mttm) REVERT: A 265 ARG cc_start: 0.8058 (ttm170) cc_final: 0.7745 (mmm-85) REVERT: B 100 PHE cc_start: 0.8258 (t80) cc_final: 0.7932 (t80) REVERT: B 295 MET cc_start: 0.8862 (mtp) cc_final: 0.8462 (mtt) REVERT: C 100 PHE cc_start: 0.8071 (t80) cc_final: 0.7255 (m-10) outliers start: 23 outliers final: 18 residues processed: 167 average time/residue: 0.0844 time to fit residues: 20.4317 Evaluate side-chains 166 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112522 restraints weight = 13263.188| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.68 r_work: 0.3163 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9727 Z= 0.129 Angle : 0.601 10.190 13238 Z= 0.297 Chirality : 0.040 0.268 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.106 28.493 1364 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.09 % Allowed : 20.22 % Favored : 77.69 % 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: 1.19 (0.24), residues: 1272 helix: 1.31 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.24 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.011 0.001 TYR C 387 PHE 0.030 0.001 PHE A 242 TRP 0.006 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9727) covalent geometry : angle 0.60051 (13238) hydrogen bonds : bond 0.03559 ( 702) hydrogen bonds : angle 4.03571 ( 2088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.272 Fit side-chains REVERT: A 35 PHE cc_start: 0.8021 (m-10) cc_final: 0.7741 (m-10) REVERT: A 51 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8981 (tp) REVERT: A 110 ASN cc_start: 0.8736 (t0) cc_final: 0.8063 (t0) REVERT: A 172 ASN cc_start: 0.9112 (m-40) cc_final: 0.8849 (m110) REVERT: B 100 PHE cc_start: 0.8312 (t80) cc_final: 0.7969 (t80) REVERT: B 295 MET cc_start: 0.8842 (mtp) cc_final: 0.8404 (mtt) REVERT: C 100 PHE cc_start: 0.8104 (t80) cc_final: 0.7237 (m-10) outliers start: 21 outliers final: 19 residues processed: 166 average time/residue: 0.0860 time to fit residues: 20.6544 Evaluate side-chains 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 242 PHE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113591 restraints weight = 13256.682| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.66 r_work: 0.3173 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9727 Z= 0.126 Angle : 0.608 11.400 13238 Z= 0.300 Chirality : 0.040 0.220 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.050 24.548 1364 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.39 % Allowed : 21.31 % Favored : 76.29 % 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: 1.25 (0.24), residues: 1272 helix: 1.36 (0.17), residues: 1025 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 401 TYR 0.011 0.001 TYR C 387 PHE 0.031 0.001 PHE A 242 TRP 0.006 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9727) covalent geometry : angle 0.60838 (13238) hydrogen bonds : bond 0.03539 ( 702) hydrogen bonds : angle 4.02359 ( 2088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.356 Fit side-chains REVERT: A 35 PHE cc_start: 0.7893 (m-10) cc_final: 0.7643 (m-10) REVERT: A 51 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8965 (tp) REVERT: A 110 ASN cc_start: 0.8752 (t0) cc_final: 0.8086 (t0) REVERT: A 134 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8488 (tp40) REVERT: A 172 ASN cc_start: 0.9115 (m-40) cc_final: 0.8848 (m110) REVERT: A 222 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6944 (tp40) REVERT: B 8 ARG cc_start: 0.6777 (ppt170) cc_final: 0.6183 (tmm160) REVERT: B 100 PHE cc_start: 0.8193 (t80) cc_final: 0.7927 (t80) REVERT: B 295 MET cc_start: 0.8858 (mtp) cc_final: 0.8434 (mtt) REVERT: C 100 PHE cc_start: 0.8078 (t80) cc_final: 0.7219 (m-10) REVERT: C 196 MET cc_start: 0.8717 (mmp) cc_final: 0.8474 (mmt) REVERT: C 204 MET cc_start: 0.8317 (mmt) cc_final: 0.8028 (mmt) REVERT: C 219 MET cc_start: 0.8353 (mmm) cc_final: 0.8060 (mmp) REVERT: C 403 MET cc_start: 0.8412 (tmm) cc_final: 0.7834 (tmm) outliers start: 24 outliers final: 20 residues processed: 169 average time/residue: 0.0866 time to fit residues: 21.1825 Evaluate side-chains 176 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 119 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114115 restraints weight = 13255.753| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.64 r_work: 0.3165 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9727 Z= 0.133 Angle : 0.623 10.968 13238 Z= 0.308 Chirality : 0.040 0.186 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.025 24.580 1364 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.39 % Allowed : 20.92 % Favored : 76.69 % 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: 1.33 (0.24), residues: 1272 helix: 1.39 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.16 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 401 TYR 0.010 0.001 TYR C 387 PHE 0.030 0.001 PHE A 242 TRP 0.005 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9727) covalent geometry : angle 0.62345 (13238) hydrogen bonds : bond 0.03579 ( 702) hydrogen bonds : angle 4.04147 ( 2088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.240 Fit side-chains REVERT: A 35 PHE cc_start: 0.7932 (m-10) cc_final: 0.7682 (m-10) REVERT: A 51 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 110 ASN cc_start: 0.8755 (t0) cc_final: 0.8250 (t0) REVERT: A 172 ASN cc_start: 0.9124 (m-40) cc_final: 0.8852 (m110) REVERT: B 8 ARG cc_start: 0.6762 (ppt170) cc_final: 0.6163 (tmm160) REVERT: B 100 PHE cc_start: 0.8286 (t80) cc_final: 0.8018 (t80) REVERT: B 295 MET cc_start: 0.8868 (mtp) cc_final: 0.8413 (mtt) REVERT: C 100 PHE cc_start: 0.8004 (t80) cc_final: 0.7131 (m-10) REVERT: C 204 MET cc_start: 0.8320 (mmt) cc_final: 0.8008 (mmt) REVERT: C 219 MET cc_start: 0.8371 (mmm) cc_final: 0.8071 (mmp) REVERT: C 403 MET cc_start: 0.8414 (tmm) cc_final: 0.7852 (tmm) outliers start: 24 outliers final: 20 residues processed: 164 average time/residue: 0.0832 time to fit residues: 19.8432 Evaluate side-chains 164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112292 restraints weight = 13179.644| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.69 r_work: 0.3156 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9727 Z= 0.138 Angle : 0.623 10.880 13238 Z= 0.309 Chirality : 0.040 0.177 1649 Planarity : 0.005 0.069 1627 Dihedral : 4.049 24.504 1364 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.29 % Allowed : 21.51 % Favored : 76.20 % 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: 1.31 (0.24), residues: 1272 helix: 1.39 (0.17), residues: 1018 sheet: None (None), residues: 0 loop : -1.17 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 225 TYR 0.010 0.001 TYR C 387 PHE 0.032 0.001 PHE C 101 TRP 0.005 0.001 TRP A 20 HIS 0.001 0.000 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9727) covalent geometry : angle 0.62310 (13238) hydrogen bonds : bond 0.03645 ( 702) hydrogen bonds : angle 4.06060 ( 2088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.54 seconds wall clock time: 39 minutes 40.48 seconds (2380.48 seconds total)