Starting phenix.real_space_refine on Fri Mar 14 02:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwp_10634/03_2025/6xwp_10634.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwp_10634/03_2025/6xwp_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2025/6xwp_10634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2025/6xwp_10634.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2025/6xwp_10634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwp_10634/03_2025/6xwp_10634.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.34, per 1000 atoms: 0.66 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: 3.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.80 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: 2.69 Time building geometry restraints manager: 3.06 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: 5.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.930 Find NCS groups from input model: 0.500 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.550 ------------------------------------------------------------------------------- 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= 0.488 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP C 16 HIS 0.003 0.001 HIS B 334 PHE 0.021 0.002 PHE B 302 TYR 0.014 0.002 TYR B 238 ARG 0.003 0.000 ARG B 79 *********************** 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 : 1.163 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: 0.2522 time to fit residues: 68.7300 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 : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.4980 chunk 95 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.0970 overall best weight: 0.3296 ------------------------------------------------------------------------------- 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 = 0.3638 r_free = 0.3638 target = 0.137673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109468 restraints weight = 13111.143| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.64 r_work: 0.3145 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9727 Z= 0.172 Angle : 0.578 6.338 13238 Z= 0.297 Chirality : 0.039 0.139 1649 Planarity : 0.006 0.069 1627 Dihedral : 4.509 46.222 1364 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.99 % Allowed : 11.95 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1272 helix: -0.16 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : -1.98 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 20 HIS 0.002 0.001 HIS A 334 PHE 0.024 0.001 PHE A 302 TYR 0.013 0.001 TYR B 320 ARG 0.003 0.000 ARG C 179 *********************** 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 203 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.949 Fit side-chains REVERT: A 132 LEU cc_start: 0.8579 (tp) cc_final: 0.8346 (tt) REVERT: A 150 LYS cc_start: 0.8951 (mtmt) cc_final: 0.8712 (mttm) REVERT: A 219 MET cc_start: 0.8366 (mmm) cc_final: 0.8083 (mmm) REVERT: A 244 GLN cc_start: 0.8827 (tp40) cc_final: 0.8405 (tp-100) REVERT: A 295 MET cc_start: 0.8154 (mpp) cc_final: 0.7687 (mpp) REVERT: A 368 MET cc_start: 0.8552 (ttp) cc_final: 0.8252 (ttm) REVERT: A 422 GLU cc_start: 0.7975 (mp0) cc_final: 0.7046 (mt-10) REVERT: B 100 PHE cc_start: 0.8333 (t80) cc_final: 0.7961 (t80) REVERT: B 128 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.4406 (tm130) REVERT: C 11 ASP cc_start: 0.8475 (m-30) cc_final: 0.8206 (m-30) REVERT: C 59 LEU cc_start: 0.8605 (mt) cc_final: 0.8391 (mt) REVERT: C 100 PHE cc_start: 0.8206 (t80) cc_final: 0.7221 (m-10) REVERT: C 204 MET cc_start: 0.8409 (mmt) cc_final: 0.8183 (mmt) REVERT: C 219 MET cc_start: 0.8303 (mmm) cc_final: 0.7937 (mmp) REVERT: C 221 GLU cc_start: 0.7935 (tp30) cc_final: 0.7627 (tp30) REVERT: C 244 GLN cc_start: 0.8276 (tm-30) cc_final: 0.8050 (tm-30) outliers start: 20 outliers final: 10 residues processed: 193 average time/residue: 0.1909 time to fit residues: 53.0420 Evaluate side-chains 175 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU 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 128 GLN 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 9 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 98 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN C 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107318 restraints weight = 13429.435| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.69 r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9727 Z= 0.219 Angle : 0.582 6.844 13238 Z= 0.296 Chirality : 0.040 0.207 1649 Planarity : 0.005 0.070 1627 Dihedral : 4.361 38.763 1364 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.29 % Allowed : 14.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1272 helix: 0.43 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 20 HIS 0.002 0.000 HIS A 334 PHE 0.022 0.001 PHE A 302 TYR 0.010 0.001 TYR B 238 ARG 0.008 0.000 ARG C 401 *********************** 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 200 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.050 Fit side-chains REVERT: A 51 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9024 (tp) REVERT: A 110 ASN cc_start: 0.8761 (t0) cc_final: 0.8120 (t0) REVERT: A 132 LEU cc_start: 0.8675 (tp) cc_final: 0.8423 (tt) REVERT: A 150 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8727 (mttm) REVERT: A 244 GLN cc_start: 0.8815 (tp40) cc_final: 0.8419 (tp-100) REVERT: A 295 MET cc_start: 0.8175 (mpp) cc_final: 0.7720 (mpp) REVERT: A 368 MET cc_start: 0.8604 (ttp) cc_final: 0.8313 (ttm) REVERT: B 100 PHE cc_start: 0.8384 (t80) cc_final: 0.8012 (t80) REVERT: C 11 ASP cc_start: 0.8516 (m-30) cc_final: 0.8236 (m-30) REVERT: C 100 PHE cc_start: 0.8208 (t80) cc_final: 0.7152 (m-10) REVERT: C 219 MET cc_start: 0.8392 (mmm) cc_final: 0.8084 (mmp) REVERT: C 221 GLU cc_start: 0.7905 (tp30) cc_final: 0.7635 (tp30) outliers start: 23 outliers final: 13 residues processed: 188 average time/residue: 0.1997 time to fit residues: 54.1851 Evaluate side-chains 174 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 346 LEU Chi-restraints excluded: chain C residue 116 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.134950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106324 restraints weight = 13347.938| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.62 r_work: 0.3100 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9727 Z= 0.283 Angle : 0.594 6.925 13238 Z= 0.302 Chirality : 0.040 0.144 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.389 41.374 1364 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.29 % Allowed : 16.53 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.24), residues: 1272 helix: 0.65 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 20 HIS 0.001 0.001 HIS B 34 PHE 0.022 0.001 PHE C 101 TYR 0.012 0.001 TYR B 238 ARG 0.006 0.000 ARG A 187 *********************** 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 179 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.038 Fit side-chains REVERT: A 35 PHE cc_start: 0.8151 (m-10) cc_final: 0.7843 (m-10) REVERT: A 51 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9031 (tp) REVERT: A 110 ASN cc_start: 0.8762 (t0) cc_final: 0.8168 (t0) REVERT: A 132 LEU cc_start: 0.8725 (tp) cc_final: 0.8472 (tt) REVERT: A 150 LYS cc_start: 0.8978 (mtmt) cc_final: 0.8746 (mttm) REVERT: A 244 GLN cc_start: 0.8835 (tp40) cc_final: 0.8458 (tp40) REVERT: A 295 MET cc_start: 0.8210 (mpp) cc_final: 0.7821 (mpp) REVERT: A 368 MET cc_start: 0.8535 (ttp) cc_final: 0.8243 (ttm) REVERT: B 100 PHE cc_start: 0.8386 (t80) cc_final: 0.8135 (t80) REVERT: C 11 ASP cc_start: 0.8511 (m-30) cc_final: 0.8228 (m-30) REVERT: C 92 LEU cc_start: 0.8519 (mm) cc_final: 0.8315 (mm) REVERT: C 100 PHE cc_start: 0.8246 (t80) cc_final: 0.7247 (m-10) outliers start: 23 outliers final: 18 residues processed: 168 average time/residue: 0.1982 time to fit residues: 49.0966 Evaluate side-chains 167 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 221 GLU 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 326 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 233 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 110 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 64 optimal weight: 0.0050 chunk 67 optimal weight: 0.6980 overall best weight: 0.2204 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114511 restraints weight = 13082.135| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.58 r_work: 0.3167 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9727 Z= 0.153 Angle : 0.548 8.500 13238 Z= 0.277 Chirality : 0.038 0.129 1649 Planarity : 0.005 0.070 1627 Dihedral : 4.089 25.642 1364 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.79 % Allowed : 18.03 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1272 helix: 1.07 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -1.56 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.020 0.001 PHE B 242 TYR 0.010 0.001 TYR C 387 ARG 0.008 0.000 ARG A 187 *********************** 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 183 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.022 Fit side-chains REVERT: A 35 PHE cc_start: 0.7967 (m-10) cc_final: 0.7705 (m-10) REVERT: A 110 ASN cc_start: 0.8736 (t0) cc_final: 0.8078 (t0) REVERT: A 150 LYS cc_start: 0.8898 (mtmt) cc_final: 0.8696 (mttm) REVERT: A 295 MET cc_start: 0.8153 (mpp) cc_final: 0.7632 (mpp) REVERT: C 100 PHE cc_start: 0.8177 (t80) cc_final: 0.7291 (m-10) REVERT: C 204 MET cc_start: 0.8338 (mmt) cc_final: 0.8043 (mmt) outliers start: 18 outliers final: 14 residues processed: 177 average time/residue: 0.1831 time to fit residues: 47.5380 Evaluate side-chains 164 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 221 GLU 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 B residue 157 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 116 ASN 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 95 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.140385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112386 restraints weight = 13148.481| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.77 r_work: 0.3152 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2475 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= 0.184 Angle : 0.568 9.326 13238 Z= 0.285 Chirality : 0.039 0.273 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.069 27.054 1364 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.19 % Allowed : 18.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.24), residues: 1272 helix: 1.23 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -1.45 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.036 0.001 PHE B 100 TYR 0.011 0.001 TYR C 387 ARG 0.003 0.000 ARG A 187 *********************** 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: 22 poor density : 156 time to evaluate : 1.023 Fit side-chains REVERT: A 35 PHE cc_start: 0.8022 (m-10) cc_final: 0.7735 (m-10) REVERT: A 51 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9017 (tp) REVERT: A 110 ASN cc_start: 0.8780 (t0) cc_final: 0.8162 (t0) REVERT: A 134 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8582 (tp40) REVERT: A 150 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8754 (mttm) REVERT: A 172 ASN cc_start: 0.9148 (m-40) cc_final: 0.8907 (m110) REVERT: A 295 MET cc_start: 0.8165 (mpp) cc_final: 0.7742 (mpp) REVERT: A 355 THR cc_start: 0.8365 (m) cc_final: 0.8155 (m) REVERT: C 100 PHE cc_start: 0.8162 (t80) cc_final: 0.7239 (m-10) REVERT: C 196 MET cc_start: 0.8848 (mmt) cc_final: 0.8427 (mmt) outliers start: 22 outliers final: 15 residues processed: 169 average time/residue: 0.1821 time to fit residues: 45.3997 Evaluate side-chains 166 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 157 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 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 2 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3618 r_free = 0.3618 target = 0.135961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108498 restraints weight = 13365.257| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.62 r_work: 0.3059 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9727 Z= 0.290 Angle : 0.627 10.188 13238 Z= 0.313 Chirality : 0.042 0.293 1649 Planarity : 0.005 0.073 1627 Dihedral : 4.280 39.700 1364 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.69 % Allowed : 19.22 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.24), residues: 1272 helix: 1.12 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.34 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.002 0.001 HIS C 34 PHE 0.029 0.001 PHE A 242 TYR 0.012 0.001 TYR B 238 ARG 0.002 0.000 ARG C 401 *********************** 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 180 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.088 Fit side-chains REVERT: A 5 LEU cc_start: 0.7795 (pt) cc_final: 0.7496 (pp) REVERT: A 35 PHE cc_start: 0.8068 (m-10) cc_final: 0.7788 (m-10) REVERT: A 51 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9007 (tp) REVERT: A 110 ASN cc_start: 0.8754 (t0) cc_final: 0.8253 (t0) REVERT: A 150 LYS cc_start: 0.8982 (mtmt) cc_final: 0.8774 (mttm) REVERT: B 35 PHE cc_start: 0.7443 (m-10) cc_final: 0.7202 (m-10) REVERT: B 100 PHE cc_start: 0.8382 (t80) cc_final: 0.8178 (t80) REVERT: B 399 MET cc_start: 0.8159 (mtm) cc_final: 0.7903 (mtm) REVERT: C 100 PHE cc_start: 0.8111 (t80) cc_final: 0.7266 (m-10) REVERT: C 403 MET cc_start: 0.8494 (tmm) cc_final: 0.7929 (tmm) outliers start: 27 outliers final: 22 residues processed: 168 average time/residue: 0.1839 time to fit residues: 45.4938 Evaluate side-chains 170 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 269 ASP Chi-restraints excluded: chain A residue 277 THR 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 68 LEU Chi-restraints excluded: chain B residue 157 ILE 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 132 LEU 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 314 MET 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 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112360 restraints weight = 13298.073| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.76 r_work: 0.3159 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2621 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= 0.185 Angle : 0.601 11.299 13238 Z= 0.298 Chirality : 0.040 0.263 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.114 26.348 1364 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.19 % Allowed : 19.62 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.24), residues: 1272 helix: 1.28 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.016 0.001 PHE A 302 TYR 0.009 0.001 TYR C 387 ARG 0.003 0.000 ARG C 401 *********************** 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 184 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 1.106 Fit side-chains REVERT: A 35 PHE cc_start: 0.7975 (m-10) cc_final: 0.7726 (m-10) REVERT: A 51 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8989 (tp) REVERT: A 110 ASN cc_start: 0.8755 (t0) cc_final: 0.8197 (t0) REVERT: A 150 LYS cc_start: 0.8938 (mtmt) cc_final: 0.8732 (mttm) REVERT: B 8 ARG cc_start: 0.6790 (ppt170) cc_final: 0.6122 (tmm160) REVERT: B 35 PHE cc_start: 0.7302 (m-10) cc_final: 0.7078 (m-10) REVERT: B 100 PHE cc_start: 0.8217 (t80) cc_final: 0.8011 (t80) REVERT: C 100 PHE cc_start: 0.8097 (t80) cc_final: 0.7241 (m-10) REVERT: C 196 MET cc_start: 0.8831 (mmt) cc_final: 0.8346 (mmp) REVERT: C 401 ARG cc_start: 0.7841 (mtm180) cc_final: 0.7531 (mtm180) outliers start: 22 outliers final: 16 residues processed: 174 average time/residue: 0.2359 time to fit residues: 58.6981 Evaluate side-chains 165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 221 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 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 314 MET 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 61 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN C 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110347 restraints weight = 13303.463| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.66 r_work: 0.3110 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9727 Z= 0.272 Angle : 0.642 10.132 13238 Z= 0.318 Chirality : 0.041 0.261 1649 Planarity : 0.005 0.072 1627 Dihedral : 4.214 34.158 1364 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.29 % Allowed : 20.52 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1272 helix: 1.22 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.23 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 16 HIS 0.001 0.001 HIS C 34 PHE 0.023 0.001 PHE B 242 TYR 0.012 0.001 TYR C 387 ARG 0.003 0.000 ARG C 401 *********************** 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 176 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9023 (tp) REVERT: A 110 ASN cc_start: 0.8773 (t0) cc_final: 0.8296 (t0) REVERT: A 150 LYS cc_start: 0.8964 (mtmt) cc_final: 0.8745 (mttm) REVERT: B 35 PHE cc_start: 0.7378 (m-10) cc_final: 0.7119 (m-10) REVERT: C 100 PHE cc_start: 0.8097 (t80) cc_final: 0.7219 (m-10) REVERT: C 219 MET cc_start: 0.8426 (mmm) cc_final: 0.8128 (mmp) outliers start: 23 outliers final: 20 residues processed: 167 average time/residue: 0.2621 time to fit residues: 63.7733 Evaluate side-chains 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 221 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 111 VAL 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 243 LEU Chi-restraints excluded: chain C residue 314 MET 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 125 optimal weight: 0.9980 chunk 111 optimal weight: 0.0020 chunk 8 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.139985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113177 restraints weight = 13283.049| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.56 r_work: 0.3190 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2740 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= 0.193 Angle : 0.628 10.270 13238 Z= 0.310 Chirality : 0.040 0.246 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.125 27.428 1364 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.99 % Allowed : 21.12 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1272 helix: 1.30 (0.17), residues: 1020 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 16 HIS 0.001 0.000 HIS A 334 PHE 0.023 0.001 PHE C 101 TYR 0.010 0.001 TYR C 387 ARG 0.004 0.000 ARG A 401 ********************** 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 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.018 Fit side-chains REVERT: A 51 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8984 (tp) REVERT: A 110 ASN cc_start: 0.8755 (t0) cc_final: 0.8081 (t0) REVERT: A 150 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8685 (mttm) REVERT: B 8 ARG cc_start: 0.6785 (ppt170) cc_final: 0.6120 (tmm160) REVERT: B 35 PHE cc_start: 0.7324 (m-10) cc_final: 0.7109 (m-10) REVERT: C 28 PHE cc_start: 0.8577 (t80) cc_final: 0.8351 (t80) REVERT: C 100 PHE cc_start: 0.7983 (t80) cc_final: 0.7090 (m-10) REVERT: C 219 MET cc_start: 0.8428 (mmm) cc_final: 0.8082 (mmp) outliers start: 20 outliers final: 16 residues processed: 159 average time/residue: 0.1929 time to fit residues: 44.4653 Evaluate side-chains 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 221 GLU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 342 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 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 76 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.140100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112630 restraints weight = 13283.951| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.63 r_work: 0.3141 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2715 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= 0.221 Angle : 0.644 10.508 13238 Z= 0.314 Chirality : 0.040 0.248 1649 Planarity : 0.005 0.072 1627 Dihedral : 4.132 28.777 1364 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.09 % Allowed : 21.02 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1272 helix: 1.31 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.15 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 20 HIS 0.001 0.000 HIS C 34 PHE 0.026 0.001 PHE C 101 TYR 0.010 0.001 TYR C 387 ARG 0.003 0.000 ARG A 401 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4745.21 seconds wall clock time: 84 minutes 9.31 seconds (5049.31 seconds total)