Starting phenix.real_space_refine on Thu Feb 13 23:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xwp_10634/02_2025/6xwp_10634.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xwp_10634/02_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_10634/02_2025/6xwp_10634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xwp_10634/02_2025/6xwp_10634.map" model { file = "/net/cci-nas-00/data/ceres_data/6xwp_10634/02_2025/6xwp_10634.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xwp_10634/02_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-5592/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: 5.88, per 1000 atoms: 0.62 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 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: 0.81 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: 2.90 Time building geometry restraints manager: 2.97 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: 0.800 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.010 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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 : 1.024 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: 0.2030 time to fit residues: 53.8684 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 : 1.003 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.137639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109440 restraints weight = 13110.871| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.64 r_work: 0.3146 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1610 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 6.336 13238 Z= 0.297 Chirality : 0.039 0.139 1649 Planarity : 0.006 0.069 1627 Dihedral : 4.508 46.111 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 : 11.75 % Favored : 86.25 % 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: -0.15 (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 0.014 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 : 0.817 Fit side-chains REVERT: A 132 LEU cc_start: 0.8579 (tp) cc_final: 0.8346 (tt) REVERT: A 150 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8711 (mttm) REVERT: A 219 MET cc_start: 0.8364 (mmm) cc_final: 0.8081 (mmm) REVERT: A 244 GLN cc_start: 0.8825 (tp40) cc_final: 0.8401 (tp-100) REVERT: A 295 MET cc_start: 0.8152 (mpp) cc_final: 0.7689 (mpp) REVERT: A 368 MET cc_start: 0.8549 (ttp) cc_final: 0.8250 (ttm) REVERT: A 422 GLU cc_start: 0.7973 (mp0) cc_final: 0.7044 (mt-10) REVERT: B 100 PHE cc_start: 0.8331 (t80) cc_final: 0.7959 (t80) REVERT: B 128 GLN cc_start: 0.5961 (OUTLIER) cc_final: 0.4407 (tm130) REVERT: C 11 ASP cc_start: 0.8470 (m-30) cc_final: 0.8200 (m-30) REVERT: C 59 LEU cc_start: 0.8602 (mt) cc_final: 0.8390 (mt) REVERT: C 100 PHE cc_start: 0.8203 (t80) cc_final: 0.7220 (m-10) REVERT: C 204 MET cc_start: 0.8407 (mmt) cc_final: 0.8181 (mmt) REVERT: C 219 MET cc_start: 0.8302 (mmm) cc_final: 0.7936 (mmp) REVERT: C 221 GLU cc_start: 0.7932 (tp30) cc_final: 0.7624 (tp30) outliers start: 20 outliers final: 10 residues processed: 193 average time/residue: 0.2001 time to fit residues: 55.5253 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 : 1.098 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 6.9990 chunk 98 optimal weight: 0.0470 chunk 11 optimal weight: 0.0370 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 109 optimal weight: 0.0870 overall best weight: 0.5936 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.137811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108904 restraints weight = 13381.121| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.69 r_work: 0.3137 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9727 Z= 0.185 Angle : 0.570 7.350 13238 Z= 0.290 Chirality : 0.039 0.150 1649 Planarity : 0.005 0.068 1627 Dihedral : 4.281 34.052 1364 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.19 % Allowed : 14.84 % Favored : 82.97 % 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: 0.01 (0.24), residues: 1272 helix: 0.51 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -1.79 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 20 HIS 0.002 0.000 HIS A 334 PHE 0.021 0.001 PHE A 302 TYR 0.009 0.001 TYR C 387 ARG 0.005 0.000 ARG A 187 *********************** 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 199 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.046 Fit side-chains REVERT: A 110 ASN cc_start: 0.8751 (t0) cc_final: 0.8062 (t0) REVERT: A 132 LEU cc_start: 0.8636 (tp) cc_final: 0.8394 (tt) REVERT: A 150 LYS cc_start: 0.8937 (mtmt) cc_final: 0.8719 (mttm) REVERT: A 244 GLN cc_start: 0.8756 (tp40) cc_final: 0.8406 (tp40) REVERT: A 295 MET cc_start: 0.8168 (mpp) cc_final: 0.7739 (mpp) REVERT: A 368 MET cc_start: 0.8551 (ttp) cc_final: 0.8263 (ttm) REVERT: B 100 PHE cc_start: 0.8335 (t80) cc_final: 0.7986 (t80) REVERT: C 11 ASP cc_start: 0.8432 (m-30) cc_final: 0.7993 (m-30) REVERT: C 100 PHE cc_start: 0.8188 (t80) cc_final: 0.7136 (m-10) REVERT: C 204 MET cc_start: 0.8408 (mmt) cc_final: 0.8159 (mmt) REVERT: C 219 MET cc_start: 0.8391 (mmm) cc_final: 0.8102 (mmp) outliers start: 22 outliers final: 13 residues processed: 188 average time/residue: 0.2006 time to fit residues: 54.2532 Evaluate side-chains 172 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.354 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 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 = 0.3604 r_free = 0.3604 target = 0.134990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106929 restraints weight = 13347.313| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.64 r_work: 0.3083 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1888 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= 0.285 Angle : 0.600 6.884 13238 Z= 0.304 Chirality : 0.041 0.248 1649 Planarity : 0.005 0.070 1627 Dihedral : 4.360 41.180 1364 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.29 % Allowed : 16.24 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.29 (0.24), residues: 1272 helix: 0.69 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -1.62 (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 0.023 0.001 PHE C 101 TYR 0.012 0.001 TYR B 238 ARG 0.005 0.000 ARG C 401 *********************** 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 182 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.026 Fit side-chains REVERT: A 35 PHE cc_start: 0.8118 (m-10) cc_final: 0.7790 (m-10) REVERT: A 51 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9028 (tp) REVERT: A 110 ASN cc_start: 0.8772 (t0) cc_final: 0.8184 (t0) REVERT: A 132 LEU cc_start: 0.8718 (tp) cc_final: 0.8461 (tt) REVERT: A 150 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8752 (mttm) REVERT: A 219 MET cc_start: 0.8399 (mmm) cc_final: 0.8198 (mmm) REVERT: A 244 GLN cc_start: 0.8797 (tp40) cc_final: 0.8423 (tp40) REVERT: A 295 MET cc_start: 0.8222 (mpp) cc_final: 0.7827 (mpp) REVERT: A 368 MET cc_start: 0.8555 (ttp) cc_final: 0.8271 (ttm) REVERT: B 100 PHE cc_start: 0.8398 (t80) cc_final: 0.8160 (t80) REVERT: B 295 MET cc_start: 0.8997 (mtp) cc_final: 0.8672 (mtt) REVERT: C 11 ASP cc_start: 0.8493 (m-30) cc_final: 0.8216 (m-30) REVERT: C 100 PHE cc_start: 0.8252 (t80) cc_final: 0.7265 (m-10) outliers start: 23 outliers final: 19 residues processed: 172 average time/residue: 0.2024 time to fit residues: 51.2541 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 : 1.161 ------------------------------------------------------------------------------- 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 221 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 120 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 64 optimal weight: 0.0470 chunk 67 optimal weight: 0.8980 overall best weight: 0.5080 ------------------------------------------------------------------------------- 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 = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111966 restraints weight = 13158.143| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.72 r_work: 0.3134 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2323 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= 0.171 Angle : 0.560 8.283 13238 Z= 0.284 Chirality : 0.038 0.164 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.171 28.729 1364 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.99 % Allowed : 18.03 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.24), residues: 1272 helix: 1.04 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 250 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 0.010 0.001 TYR C 387 ARG 0.003 0.000 ARG C 401 *********************** 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 181 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.973 Fit side-chains REVERT: A 35 PHE cc_start: 0.8011 (m-10) cc_final: 0.7741 (m-10) REVERT: A 51 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9009 (tp) REVERT: A 110 ASN cc_start: 0.8789 (t0) cc_final: 0.8140 (t0) REVERT: A 150 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8720 (mttm) REVERT: A 219 MET cc_start: 0.8403 (mmm) cc_final: 0.8161 (mmm) REVERT: A 244 GLN cc_start: 0.8537 (tp40) cc_final: 0.8296 (tp40) REVERT: A 295 MET cc_start: 0.8186 (mpp) cc_final: 0.7787 (mpp) REVERT: A 368 MET cc_start: 0.8455 (ttp) cc_final: 0.8188 (ttm) REVERT: B 295 MET cc_start: 0.8898 (mtp) cc_final: 0.8493 (mtt) REVERT: C 92 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8306 (mm) REVERT: C 100 PHE cc_start: 0.8210 (t80) cc_final: 0.7263 (m-10) REVERT: C 219 MET cc_start: 0.8450 (mmm) cc_final: 0.8171 (mmp) outliers start: 20 outliers final: 15 residues processed: 174 average time/residue: 0.1830 time to fit residues: 46.8258 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 : 1.344 ------------------------------------------------------------------------------- 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 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 92 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: 9.9990 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.138490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109722 restraints weight = 13253.831| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.62 r_work: 0.3131 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9727 Z= 0.241 Angle : 0.597 8.849 13238 Z= 0.298 Chirality : 0.040 0.170 1649 Planarity : 0.005 0.072 1627 Dihedral : 4.243 35.585 1364 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 18.63 % Favored : 78.88 % 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: 0.86 (0.24), residues: 1272 helix: 1.09 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 16 HIS 0.001 0.000 HIS C 34 PHE 0.036 0.001 PHE B 100 TYR 0.011 0.001 TYR B 238 ARG 0.003 0.000 ARG C 401 *********************** 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 173 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.145 Fit side-chains REVERT: A 35 PHE cc_start: 0.8056 (m-10) cc_final: 0.7783 (m-10) REVERT: A 51 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (tp) REVERT: A 110 ASN cc_start: 0.8764 (t0) cc_final: 0.8182 (t0) REVERT: A 150 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8754 (mttm) REVERT: A 244 GLN cc_start: 0.8564 (tp40) cc_final: 0.8323 (tp40) REVERT: B 295 MET cc_start: 0.8897 (mtp) cc_final: 0.8491 (mtt) REVERT: C 100 PHE cc_start: 0.8175 (t80) cc_final: 0.7247 (m-10) REVERT: C 219 MET cc_start: 0.8467 (mmm) cc_final: 0.8182 (mmp) outliers start: 25 outliers final: 16 residues processed: 162 average time/residue: 0.1923 time to fit residues: 45.8197 Evaluate side-chains 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 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 19 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 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: 3.9990 chunk 1 optimal weight: 0.6980 chunk 111 optimal weight: 0.4980 chunk 81 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.139026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111506 restraints weight = 13293.761| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.61 r_work: 0.3173 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2427 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= 0.198 Angle : 0.594 10.294 13238 Z= 0.295 Chirality : 0.039 0.157 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.157 30.631 1364 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.09 % Allowed : 19.42 % Favored : 78.49 % 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: 1.05 (0.24), residues: 1272 helix: 1.22 (0.17), residues: 1022 sheet: None (None), residues: 0 loop : -1.35 (0.40), residues: 250 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 0.030 0.001 PHE A 242 TYR 0.010 0.001 TYR C 387 ARG 0.003 0.000 ARG A 187 *********************** 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 170 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 1.074 Fit side-chains REVERT: A 5 LEU cc_start: 0.7755 (pt) cc_final: 0.7502 (pp) REVERT: A 35 PHE cc_start: 0.7982 (m-10) cc_final: 0.7709 (m-10) REVERT: A 51 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8987 (tp) REVERT: A 110 ASN cc_start: 0.8751 (t0) cc_final: 0.8194 (t0) REVERT: A 244 GLN cc_start: 0.8415 (tp40) cc_final: 0.8208 (tp40) REVERT: B 35 PHE cc_start: 0.7380 (m-10) cc_final: 0.7172 (m-10) REVERT: B 100 PHE cc_start: 0.8292 (t80) cc_final: 0.8037 (t80) REVERT: B 295 MET cc_start: 0.8854 (mtp) cc_final: 0.8440 (mtt) REVERT: C 100 PHE cc_start: 0.8117 (t80) cc_final: 0.7268 (m-10) REVERT: C 219 MET cc_start: 0.8454 (mmm) cc_final: 0.8143 (mmp) outliers start: 21 outliers final: 18 residues processed: 161 average time/residue: 0.1953 time to fit residues: 46.0635 Evaluate side-chains 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 10 LEU 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 397 LEU 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 243 LEU Chi-restraints excluded: chain C residue 358 VAL 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: 1.9990 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 46 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.142305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113890 restraints weight = 13319.591| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.62 r_work: 0.3194 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2706 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= 0.175 Angle : 0.585 10.178 13238 Z= 0.289 Chirality : 0.039 0.155 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.037 25.608 1364 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 19.52 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.17), residues: 1024 sheet: None (None), residues: 0 loop : -1.35 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.001 0.000 HIS A 334 PHE 0.027 0.001 PHE A 242 TYR 0.009 0.001 TYR C 387 ARG 0.002 0.000 ARG A 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 179 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 1.084 Fit side-chains REVERT: A 35 PHE cc_start: 0.7948 (m-10) cc_final: 0.7689 (m-10) REVERT: A 51 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8974 (tp) REVERT: A 110 ASN cc_start: 0.8742 (t0) cc_final: 0.8037 (t0) REVERT: A 134 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8542 (tp40) REVERT: A 172 ASN cc_start: 0.9109 (m-40) cc_final: 0.8869 (m110) REVERT: B 8 ARG cc_start: 0.6779 (ppt170) cc_final: 0.6348 (tmm160) REVERT: B 35 PHE cc_start: 0.7312 (m-10) cc_final: 0.7083 (m-10) REVERT: B 295 MET cc_start: 0.8822 (mtp) cc_final: 0.8374 (mtt) REVERT: C 59 LEU cc_start: 0.8122 (mt) cc_final: 0.7515 (pp) REVERT: C 100 PHE cc_start: 0.8113 (t80) cc_final: 0.7217 (m-10) REVERT: C 219 MET cc_start: 0.8460 (mmm) cc_final: 0.8109 (mmp) outliers start: 22 outliers final: 15 residues processed: 169 average time/residue: 0.2029 time to fit residues: 49.9605 Evaluate side-chains 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 286 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 230 LEU 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 358 VAL 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: 0.5980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.140359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113352 restraints weight = 13241.044| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.65 r_work: 0.3158 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9727 Z= 0.229 Angle : 0.628 10.151 13238 Z= 0.310 Chirality : 0.041 0.286 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.116 30.074 1364 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 20.52 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.24), residues: 1272 helix: 1.31 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -1.31 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 16 HIS 0.001 0.000 HIS C 34 PHE 0.030 0.001 PHE A 242 TYR 0.011 0.001 TYR C 387 ARG 0.003 0.000 ARG A 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 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.063 Fit side-chains REVERT: A 35 PHE cc_start: 0.7971 (m-10) cc_final: 0.7732 (m-10) REVERT: A 51 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8974 (tp) REVERT: A 110 ASN cc_start: 0.8729 (t0) cc_final: 0.8087 (t0) REVERT: A 172 ASN cc_start: 0.9096 (m-40) cc_final: 0.8825 (m110) REVERT: B 35 PHE cc_start: 0.7355 (m-10) cc_final: 0.7091 (m-10) REVERT: B 295 MET cc_start: 0.8832 (mtp) cc_final: 0.8382 (mtt) REVERT: B 399 MET cc_start: 0.8005 (mtm) cc_final: 0.7720 (mtm) REVERT: C 100 PHE cc_start: 0.8061 (t80) cc_final: 0.7168 (m-10) REVERT: C 219 MET cc_start: 0.8476 (mmm) cc_final: 0.8147 (mmp) outliers start: 22 outliers final: 18 residues processed: 158 average time/residue: 0.1913 time to fit residues: 44.1977 Evaluate side-chains 163 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 230 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 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3679 r_free = 0.3679 target = 0.141323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114080 restraints weight = 13338.115| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.64 r_work: 0.3174 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2797 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= 0.203 Angle : 0.631 10.210 13238 Z= 0.309 Chirality : 0.040 0.244 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.124 28.983 1364 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 20.92 % Favored : 77.09 % 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: 1.21 (0.24), residues: 1272 helix: 1.34 (0.16), residues: 1019 sheet: None (None), residues: 0 loop : -1.30 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.031 0.001 PHE B 242 TYR 0.010 0.001 TYR C 387 ARG 0.003 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 165 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.999 Fit side-chains REVERT: A 35 PHE cc_start: 0.7941 (m-10) cc_final: 0.7729 (m-10) REVERT: A 51 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8964 (tp) REVERT: A 110 ASN cc_start: 0.8754 (t0) cc_final: 0.8098 (t0) REVERT: A 172 ASN cc_start: 0.9145 (m-40) cc_final: 0.8888 (m110) REVERT: A 222 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6862 (tp40) REVERT: B 8 ARG cc_start: 0.6864 (ppt170) cc_final: 0.6219 (tmm160) REVERT: B 35 PHE cc_start: 0.7338 (m-10) cc_final: 0.7116 (m-10) REVERT: B 295 MET cc_start: 0.8874 (mtp) cc_final: 0.8377 (mtt) REVERT: C 28 PHE cc_start: 0.8571 (t80) cc_final: 0.8359 (t80) REVERT: C 204 MET cc_start: 0.8335 (mmt) cc_final: 0.7966 (mmt) REVERT: C 219 MET cc_start: 0.8534 (mmm) cc_final: 0.8196 (mmp) outliers start: 20 outliers final: 17 residues processed: 155 average time/residue: 0.2033 time to fit residues: 46.2076 Evaluate side-chains 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 222 GLN 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 230 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 353 ILE 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 358 VAL Chi-restraints excluded: chain C residue 389 MET 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: 4.9990 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.140969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112758 restraints weight = 13283.019| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.58 r_work: 0.3188 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9727 Z= 0.213 Angle : 0.627 9.955 13238 Z= 0.310 Chirality : 0.040 0.209 1649 Planarity : 0.005 0.071 1627 Dihedral : 4.138 30.459 1364 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.09 % Allowed : 20.92 % Favored : 76.99 % 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: 1.24 (0.24), residues: 1272 helix: 1.34 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 251 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 0.033 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: 4674.75 seconds wall clock time: 83 minutes 35.92 seconds (5015.92 seconds total)