Starting phenix.real_space_refine on Tue Mar 11 19:42:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n8p_24241/03_2025/7n8p_24241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n8p_24241/03_2025/7n8p_24241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2025/7n8p_24241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2025/7n8p_24241.map" model { file = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2025/7n8p_24241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n8p_24241/03_2025/7n8p_24241.cif" } resolution = 3.42 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= 0.006 sd= 0.043 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 40 5.16 5 C 4438 2.51 5 N 1140 2.21 5 O 1140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6758 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "B" Number of atoms: 3379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3379 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Time building chain proxies: 4.77, per 1000 atoms: 0.71 Number of scatterers: 6758 At special positions: 0 Unit cell: (76.504, 76.504, 114.232, 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 40 16.00 O 1140 8.00 N 1140 7.00 C 4438 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: 1.77 Conformation dependent library (CDL) restraints added in 996.2 milliseconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.996A pdb=" N GLN A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 69 removed outlier: 3.530A pdb=" N ALA A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 69 " --> pdb=" O MET A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.717A pdb=" N LEU A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 80 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.760A pdb=" N GLY A 105 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.172A pdb=" N GLY A 114 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 removed outlier: 3.651A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.528A pdb=" N PHE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 141 Processing helix chain 'A' and resid 148 through 165 removed outlier: 4.047A pdb=" N ILE A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 190 removed outlier: 3.678A pdb=" N ARG A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.645A pdb=" N ILE A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.728A pdb=" N ILE A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 4.153A pdb=" N PHE A 232 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.526A pdb=" N LEU A 252 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 281 removed outlier: 3.531A pdb=" N ILE A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Proline residue: A 267 - end of helix removed outlier: 3.978A pdb=" N ASP A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 304 removed outlier: 4.051A pdb=" N LEU A 293 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N CYS A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.719A pdb=" N PHE A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 379 removed outlier: 3.778A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 395 removed outlier: 4.056A pdb=" N PHE A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 404 through 417 removed outlier: 3.627A pdb=" N GLY A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.535A pdb=" N THR A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 448 through 460 removed outlier: 4.028A pdb=" N ALA A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 26 removed outlier: 4.035A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 69 removed outlier: 3.947A pdb=" N MET B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TRP B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 4.032A pdb=" N SER B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 89 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 97 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.629A pdb=" N GLY B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 132 Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.653A pdb=" N GLY B 141 " --> pdb=" O GLY B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 4.166A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.920A pdb=" N HIS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.668A pdb=" N PHE B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.603A pdb=" N GLY B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 233 removed outlier: 3.752A pdb=" N MET B 228 " --> pdb=" O MET B 224 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE B 232 " --> pdb=" O MET B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.748A pdb=" N LEU B 252 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 281 removed outlier: 3.601A pdb=" N ILE B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Proline residue: B 267 - end of helix removed outlier: 4.137A pdb=" N ASP B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 308 removed outlier: 3.943A pdb=" N LEU B 293 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 306 " --> pdb=" O CYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 348 removed outlier: 4.099A pdb=" N PHE B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 379 removed outlier: 3.885A pdb=" N LEU B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 377 " --> pdb=" O MET B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 4.543A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 removed outlier: 3.554A pdb=" N ILE B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 438 removed outlier: 3.675A pdb=" N THR B 433 " --> pdb=" O GLY B 429 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 434 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 448 through 460 removed outlier: 3.599A pdb=" N GLN B 456 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 460 " --> pdb=" O GLN B 456 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2133 1.34 - 1.46: 1264 1.46 - 1.57: 3431 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6902 Sorted by residual: bond pdb=" C ILE A 109 " pdb=" N PRO A 110 " ideal model delta sigma weight residual 1.334 1.382 -0.049 8.40e-03 1.42e+04 3.34e+01 bond pdb=" C ALA A 358 " pdb=" N PRO A 359 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.75e+01 bond pdb=" C LEU B 128 " pdb=" N PRO B 129 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.62e+00 bond pdb=" CA ILE B 109 " pdb=" C ILE B 109 " ideal model delta sigma weight residual 1.520 1.535 -0.015 8.80e-03 1.29e+04 2.85e+00 bond pdb=" CG1 ILE A 197 " pdb=" CD1 ILE A 197 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.15e+00 ... (remaining 6897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 9106 2.28 - 4.57: 217 4.57 - 6.85: 35 6.85 - 9.14: 5 9.14 - 11.42: 3 Bond angle restraints: 9366 Sorted by residual: angle pdb=" N LEU A 163 " pdb=" CA LEU A 163 " pdb=" C LEU A 163 " ideal model delta sigma weight residual 114.75 104.28 10.47 1.26e+00 6.30e-01 6.90e+01 angle pdb=" C GLY B 108 " pdb=" N ILE B 109 " pdb=" CA ILE B 109 " ideal model delta sigma weight residual 120.24 124.27 -4.03 6.30e-01 2.52e+00 4.09e+01 angle pdb=" C GLY A 108 " pdb=" N ILE A 109 " pdb=" CA ILE A 109 " ideal model delta sigma weight residual 120.24 122.94 -2.70 6.30e-01 2.52e+00 1.83e+01 angle pdb=" CA LEU A 163 " pdb=" C LEU A 163 " pdb=" N ASP A 164 " ideal model delta sigma weight residual 119.80 114.74 5.06 1.34e+00 5.57e-01 1.42e+01 angle pdb=" C ASN A 318 " pdb=" N LEU A 319 " pdb=" CA LEU A 319 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 ... (remaining 9361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 3525 16.85 - 33.70: 391 33.70 - 50.55: 85 50.55 - 67.40: 7 67.40 - 84.25: 4 Dihedral angle restraints: 4012 sinusoidal: 1524 harmonic: 2488 Sorted by residual: dihedral pdb=" CA LEU A 301 " pdb=" C LEU A 301 " pdb=" N CYS A 302 " pdb=" CA CYS A 302 " ideal model delta harmonic sigma weight residual 180.00 151.80 28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA VAL B 162 " pdb=" C VAL B 162 " pdb=" N LEU B 163 " pdb=" CA LEU B 163 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA PHE A 317 " pdb=" C PHE A 317 " pdb=" N ASN A 318 " pdb=" CA ASN A 318 " ideal model delta harmonic sigma weight residual 180.00 156.45 23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 922 0.065 - 0.131: 162 0.131 - 0.196: 15 0.196 - 0.261: 1 0.261 - 0.327: 2 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CB ILE A 356 " pdb=" CA ILE A 356 " pdb=" CG1 ILE A 356 " pdb=" CG2 ILE A 356 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB VAL A 162 " pdb=" CA VAL A 162 " pdb=" CG1 VAL A 162 " pdb=" CG2 VAL A 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 41 " pdb=" CA VAL A 41 " pdb=" CG1 VAL A 41 " pdb=" CG2 VAL A 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.80e-01 ... (remaining 1099 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 75 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.59e+00 pdb=" N PRO A 76 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 423 " 0.042 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO B 424 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 424 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 424 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 266 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 267 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " -0.032 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1834 2.80 - 3.33: 6031 3.33 - 3.85: 11095 3.85 - 4.38: 13324 4.38 - 4.90: 22660 Nonbonded interactions: 54944 Sorted by model distance: nonbonded pdb=" O LEU B 345 " pdb=" OG SER B 349 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR B 94 " pdb=" OG SER B 350 " model vdw 2.291 3.040 nonbonded pdb=" OG SER A 86 " pdb=" O GLY A 141 " model vdw 2.306 3.040 nonbonded pdb=" O VAL B 412 " pdb=" OG1 THR B 416 " model vdw 2.308 3.040 nonbonded pdb=" O LEU B 435 " pdb=" OG1 THR B 439 " model vdw 2.311 3.040 ... (remaining 54939 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.730 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 6902 Z= 0.341 Angle : 0.891 11.422 9366 Z= 0.504 Chirality : 0.051 0.327 1102 Planarity : 0.008 0.073 1176 Dihedral : 14.416 84.252 2440 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.29 % Allowed : 9.44 % Favored : 90.27 % 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: -5.50 (0.20), residues: 896 helix: -3.60 (0.13), residues: 668 sheet: None (None), residues: 0 loop : -2.91 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.003 0.001 HIS B 284 PHE 0.025 0.002 PHE B 219 TYR 0.018 0.002 TYR B 419 ARG 0.002 0.000 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.787 Fit side-chains REVERT: A 167 ARG cc_start: 0.7064 (mtt90) cc_final: 0.6831 (mtm180) REVERT: B 38 MET cc_start: 0.7506 (mmt) cc_final: 0.7300 (mmt) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1853 time to fit residues: 27.2301 Evaluate side-chains 79 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 284 HIS A 418 ASN A 460 GLN B 61 GLN ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.138922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122143 restraints weight = 9729.606| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.74 r_work: 0.3377 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6902 Z= 0.233 Angle : 0.579 9.205 9366 Z= 0.295 Chirality : 0.041 0.139 1102 Planarity : 0.005 0.045 1176 Dihedral : 5.397 35.283 962 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.33 % Allowed : 14.16 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.44 (0.26), residues: 896 helix: -2.16 (0.18), residues: 674 sheet: None (None), residues: 0 loop : -1.94 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 124 HIS 0.002 0.000 HIS B 284 PHE 0.012 0.001 PHE B 208 TYR 0.007 0.001 TYR A 419 ARG 0.003 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.734 Fit side-chains REVERT: A 110 PRO cc_start: 0.9135 (Cg_endo) cc_final: 0.8851 (Cg_exo) REVERT: B 38 MET cc_start: 0.8564 (mmt) cc_final: 0.8252 (mmt) REVERT: B 425 MET cc_start: 0.8944 (mtt) cc_final: 0.8686 (mtp) outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 0.1482 time to fit residues: 19.2073 Evaluate side-chains 76 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.0020 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123948 restraints weight = 9469.605| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.59 r_work: 0.3442 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6902 Z= 0.155 Angle : 0.533 8.025 9366 Z= 0.267 Chirality : 0.039 0.131 1102 Planarity : 0.004 0.041 1176 Dihedral : 4.962 35.526 962 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.33 % Allowed : 15.49 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.38 (0.28), residues: 896 helix: -1.37 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 59 HIS 0.001 0.000 HIS B 175 PHE 0.012 0.001 PHE B 307 TYR 0.017 0.001 TYR B 419 ARG 0.002 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.765 Fit side-chains REVERT: A 110 PRO cc_start: 0.9107 (Cg_endo) cc_final: 0.8813 (Cg_exo) REVERT: A 414 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8285 (mm-30) REVERT: A 421 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8063 (pp) REVERT: B 38 MET cc_start: 0.8556 (mmt) cc_final: 0.8203 (mmt) REVERT: B 419 TYR cc_start: 0.7844 (t80) cc_final: 0.7608 (t80) outliers start: 9 outliers final: 4 residues processed: 88 average time/residue: 0.1325 time to fit residues: 17.7385 Evaluate side-chains 78 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 0.0030 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.142313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.125477 restraints weight = 9917.821| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.75 r_work: 0.3415 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6902 Z= 0.167 Angle : 0.522 7.647 9366 Z= 0.262 Chirality : 0.040 0.134 1102 Planarity : 0.004 0.043 1176 Dihedral : 4.764 34.464 962 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.77 % Allowed : 17.99 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.81 (0.29), residues: 896 helix: -0.95 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.46 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 124 HIS 0.001 0.000 HIS A 284 PHE 0.014 0.001 PHE B 307 TYR 0.010 0.001 TYR B 419 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.703 Fit side-chains REVERT: A 110 PRO cc_start: 0.9089 (Cg_endo) cc_final: 0.8793 (Cg_exo) REVERT: A 414 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8108 (mm-30) REVERT: A 421 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8026 (pp) REVERT: B 38 MET cc_start: 0.8624 (mmt) cc_final: 0.8265 (mmt) REVERT: B 136 LEU cc_start: 0.7847 (tp) cc_final: 0.7619 (tp) REVERT: B 419 TYR cc_start: 0.8037 (t80) cc_final: 0.7605 (t80) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 0.1360 time to fit residues: 18.9127 Evaluate side-chains 88 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.143109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.126372 restraints weight = 9726.802| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.73 r_work: 0.3434 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6902 Z= 0.160 Angle : 0.517 7.217 9366 Z= 0.258 Chirality : 0.039 0.134 1102 Planarity : 0.004 0.043 1176 Dihedral : 4.633 34.877 962 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.36 % Allowed : 17.85 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.44 (0.29), residues: 896 helix: -0.68 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.33 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 253 HIS 0.001 0.000 HIS A 284 PHE 0.016 0.001 PHE A 379 TYR 0.007 0.001 TYR B 94 ARG 0.006 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.692 Fit side-chains REVERT: A 110 PRO cc_start: 0.9022 (Cg_endo) cc_final: 0.8701 (Cg_exo) REVERT: A 111 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8185 (tm-30) REVERT: A 414 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8011 (mm-30) REVERT: A 421 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8018 (pp) REVERT: B 38 MET cc_start: 0.8585 (mmt) cc_final: 0.8168 (mmt) REVERT: B 136 LEU cc_start: 0.7816 (tp) cc_final: 0.7615 (tp) REVERT: B 223 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7825 (mt) REVERT: B 419 TYR cc_start: 0.7984 (t80) cc_final: 0.7535 (t80) outliers start: 16 outliers final: 9 residues processed: 96 average time/residue: 0.1375 time to fit residues: 19.6306 Evaluate side-chains 87 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.142012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.125137 restraints weight = 9796.483| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.75 r_work: 0.3412 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6902 Z= 0.187 Angle : 0.532 9.905 9366 Z= 0.263 Chirality : 0.040 0.135 1102 Planarity : 0.004 0.044 1176 Dihedral : 4.607 33.971 962 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.95 % Allowed : 18.58 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.27 (0.30), residues: 896 helix: -0.56 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.24 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 124 HIS 0.001 0.000 HIS A 284 PHE 0.016 0.001 PHE A 379 TYR 0.006 0.001 TYR B 255 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.773 Fit side-chains REVERT: A 414 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8243 (mm-30) REVERT: A 421 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8093 (pp) REVERT: A 461 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7987 (pp) REVERT: B 38 MET cc_start: 0.8610 (mmt) cc_final: 0.8167 (mmt) REVERT: B 136 LEU cc_start: 0.7861 (tp) cc_final: 0.7650 (tp) outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 0.1291 time to fit residues: 19.1294 Evaluate side-chains 90 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122434 restraints weight = 9831.773| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.76 r_work: 0.3377 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6902 Z= 0.249 Angle : 0.571 9.727 9366 Z= 0.281 Chirality : 0.041 0.157 1102 Planarity : 0.004 0.046 1176 Dihedral : 4.695 32.795 962 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.51 % Allowed : 19.03 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.28 (0.29), residues: 896 helix: -0.57 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.24 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 124 HIS 0.001 0.000 HIS A 70 PHE 0.015 0.001 PHE A 379 TYR 0.027 0.001 TYR B 419 ARG 0.003 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.751 Fit side-chains REVERT: A 421 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8186 (pp) REVERT: A 461 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7903 (pp) REVERT: B 38 MET cc_start: 0.8650 (mmt) cc_final: 0.8213 (mmt) outliers start: 17 outliers final: 11 residues processed: 92 average time/residue: 0.1334 time to fit residues: 18.7381 Evaluate side-chains 88 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 388 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.138158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122523 restraints weight = 9447.070| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.59 r_work: 0.3422 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6902 Z= 0.182 Angle : 0.547 9.406 9366 Z= 0.269 Chirality : 0.040 0.158 1102 Planarity : 0.004 0.046 1176 Dihedral : 4.604 33.971 962 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.36 % Allowed : 19.62 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.06 (0.30), residues: 896 helix: -0.39 (0.21), residues: 674 sheet: None (None), residues: 0 loop : -1.22 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 124 HIS 0.001 0.000 HIS A 284 PHE 0.012 0.001 PHE A 379 TYR 0.022 0.001 TYR B 419 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 461 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7859 (pp) REVERT: B 38 MET cc_start: 0.8599 (mmt) cc_final: 0.8164 (mmt) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 0.1377 time to fit residues: 19.7634 Evaluate side-chains 85 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 2 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 0.0470 chunk 59 optimal weight: 0.9980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.140105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.124477 restraints weight = 9545.776| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.61 r_work: 0.3449 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6902 Z= 0.163 Angle : 0.550 9.820 9366 Z= 0.268 Chirality : 0.040 0.153 1102 Planarity : 0.004 0.044 1176 Dihedral : 4.347 34.266 960 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.77 % Allowed : 20.35 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.74 (0.30), residues: 896 helix: -0.14 (0.21), residues: 670 sheet: None (None), residues: 0 loop : -1.20 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 253 HIS 0.001 0.000 HIS A 284 PHE 0.021 0.001 PHE B 307 TYR 0.015 0.001 TYR B 419 ARG 0.004 0.000 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.766 Fit side-chains REVERT: A 461 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7834 (pp) REVERT: B 38 MET cc_start: 0.8544 (mmt) cc_final: 0.8163 (mmt) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1359 time to fit residues: 18.7318 Evaluate side-chains 85 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.0770 chunk 81 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.124862 restraints weight = 9523.687| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.60 r_work: 0.3449 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6902 Z= 0.166 Angle : 0.558 10.756 9366 Z= 0.274 Chirality : 0.040 0.154 1102 Planarity : 0.004 0.046 1176 Dihedral : 4.297 33.313 960 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.92 % Allowed : 20.21 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.56 (0.30), residues: 896 helix: 0.02 (0.21), residues: 670 sheet: None (None), residues: 0 loop : -1.21 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 253 HIS 0.001 0.000 HIS A 284 PHE 0.025 0.001 PHE B 307 TYR 0.012 0.001 TYR B 419 ARG 0.005 0.000 ARG B 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.701 Fit side-chains REVERT: A 461 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7812 (pp) REVERT: B 38 MET cc_start: 0.8512 (mmt) cc_final: 0.8091 (mmt) REVERT: B 74 ASN cc_start: 0.8633 (t0) cc_final: 0.8358 (t0) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.1365 time to fit residues: 18.4134 Evaluate side-chains 86 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 328 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 434 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 79 optimal weight: 0.2980 chunk 88 optimal weight: 0.0040 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 72 optimal weight: 0.0870 chunk 60 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.2570 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.147433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.130367 restraints weight = 9767.034| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.79 r_work: 0.3472 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6902 Z= 0.144 Angle : 0.546 11.183 9366 Z= 0.267 Chirality : 0.040 0.155 1102 Planarity : 0.004 0.045 1176 Dihedral : 4.180 33.667 960 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.77 % Allowed : 20.50 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.32 (0.30), residues: 896 helix: 0.27 (0.22), residues: 670 sheet: None (None), residues: 0 loop : -1.42 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 253 HIS 0.001 0.000 HIS A 284 PHE 0.023 0.001 PHE B 307 TYR 0.009 0.001 TYR A 419 ARG 0.006 0.000 ARG B 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3006.17 seconds wall clock time: 52 minutes 19.08 seconds (3139.08 seconds total)