Starting phenix.real_space_refine on Wed Mar 5 15:46:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vha_21201/03_2025/6vha_21201.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vha_21201/03_2025/6vha_21201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vha_21201/03_2025/6vha_21201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vha_21201/03_2025/6vha_21201.map" model { file = "/net/cci-nas-00/data/ceres_data/6vha_21201/03_2025/6vha_21201.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vha_21201/03_2025/6vha_21201.cif" } resolution = 4.3 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= 0.001 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 6 5.16 5 C 1521 2.51 5 N 453 2.21 5 O 459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2439 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Restraints were copied for chains: G, F Time building chain proxies: 1.95, per 1000 atoms: 0.80 Number of scatterers: 2439 At special positions: 0 Unit cell: (80.598, 106.05, 31.108, 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 6 16.00 O 459 8.00 N 453 7.00 C 1521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 298.3 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 67.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 275 through 282 removed outlier: 6.993A pdb=" N GLN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE F 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE E 278 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN F 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS E 280 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS F 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE G 277 " --> pdb=" O GLN F 276 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE F 278 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN G 279 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS F 280 " --> pdb=" O ASN G 279 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS G 281 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 285 through 299 removed outlier: 8.876A pdb=" N ASN E 286 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N SER F 289 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLN E 288 " --> pdb=" O SER F 289 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS F 291 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS E 290 " --> pdb=" O CYS F 291 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER F 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLY E 292 " --> pdb=" O SER F 293 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASP F 295 " --> pdb=" O GLY E 292 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS E 294 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE F 297 " --> pdb=" O LYS E 294 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN E 296 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N HIS F 299 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS E 298 " --> pdb=" O HIS F 299 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN F 286 " --> pdb=" O SER G 285 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL G 287 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLN F 288 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER G 289 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS F 290 " --> pdb=" O SER G 289 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER G 293 " --> pdb=" O GLY F 292 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS F 294 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 303 through 310 removed outlier: 6.741A pdb=" N GLY E 304 " --> pdb=" O SER F 305 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLN F 307 " --> pdb=" O GLY E 304 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY F 304 " --> pdb=" O SER G 305 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLN G 307 " --> pdb=" O GLY F 304 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL F 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL G 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE F 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 313 through 321 removed outlier: 6.272A pdb=" N ASP E 314 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS F 317 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER E 316 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR F 319 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP F 314 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LYS G 317 " --> pdb=" O ASP F 314 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER F 316 " --> pdb=" O LYS G 317 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR G 319 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL F 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS G 321 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER F 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 327 through 330 removed outlier: 6.546A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE F 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 336 through 346 removed outlier: 6.800A pdb=" N VAL F 337 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU E 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 339 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS E 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER F 341 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU E 342 " --> pdb=" O SER F 341 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS F 343 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU G 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP F 345 " --> pdb=" O LEU G 344 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N PHE G 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 349 through 362 removed outlier: 6.432A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LEU F 357 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N SER E 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN F 359 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP E 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 361 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE E 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER F 356 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU G 357 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP F 358 " --> pdb=" O LEU G 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 369 through 379 removed outlier: 6.035A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR F 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLU E 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LYS F 375 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N THR F 377 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU E 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG F 379 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE E 378 " --> pdb=" O ARG F 379 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS F 370 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 373 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLU F 372 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS G 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS F 374 " --> pdb=" O LYS G 375 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR G 377 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU F 376 " --> pdb=" O THR G 377 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG G 379 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N PHE F 378 " --> pdb=" O ARG G 379 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 29 hydrogen bonds defined for protein. 87 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: 0.53 Time building geometry restraints manager: 0.72 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: 813 1.34 - 1.46: 309 1.46 - 1.57: 1344 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2472 Sorted by residual: bond pdb=" CA LYS G 353 " pdb=" CB LYS G 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.69e+00 bond pdb=" CA LYS E 353 " pdb=" CB LYS E 353 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.38e-02 5.25e+03 4.58e+00 bond pdb=" CA LYS F 353 " pdb=" CB LYS F 353 " ideal model delta sigma weight residual 1.529 1.500 0.029 1.38e-02 5.25e+03 4.52e+00 bond pdb=" C LYS G 331 " pdb=" N PRO G 332 " ideal model delta sigma weight residual 1.334 1.296 0.038 2.34e-02 1.83e+03 2.67e+00 bond pdb=" C LYS F 331 " pdb=" N PRO F 332 " ideal model delta sigma weight residual 1.334 1.296 0.038 2.34e-02 1.83e+03 2.66e+00 ... (remaining 2467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 2867 1.38 - 2.77: 363 2.77 - 4.15: 55 4.15 - 5.53: 12 5.53 - 6.92: 6 Bond angle restraints: 3303 Sorted by residual: angle pdb=" C LYS E 347 " pdb=" N ASP E 348 " pdb=" CA ASP E 348 " ideal model delta sigma weight residual 122.17 115.25 6.92 1.54e+00 4.22e-01 2.02e+01 angle pdb=" C LYS G 347 " pdb=" N ASP G 348 " pdb=" CA ASP G 348 " ideal model delta sigma weight residual 122.17 115.28 6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C LYS F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta sigma weight residual 122.17 115.29 6.88 1.54e+00 4.22e-01 2.00e+01 angle pdb=" N ASP E 348 " pdb=" CA ASP E 348 " pdb=" C ASP E 348 " ideal model delta sigma weight residual 112.12 116.70 -4.58 1.34e+00 5.57e-01 1.17e+01 angle pdb=" N ASP F 348 " pdb=" CA ASP F 348 " pdb=" C ASP F 348 " ideal model delta sigma weight residual 112.12 116.69 -4.57 1.34e+00 5.57e-01 1.16e+01 ... (remaining 3298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 1328 16.25 - 32.51: 157 32.51 - 48.76: 27 48.76 - 65.01: 12 65.01 - 81.26: 3 Dihedral angle restraints: 1527 sinusoidal: 642 harmonic: 885 Sorted by residual: dihedral pdb=" CA VAL G 313 " pdb=" C VAL G 313 " pdb=" N ASP G 314 " pdb=" CA ASP G 314 " ideal model delta harmonic sigma weight residual 180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA VAL F 313 " pdb=" C VAL F 313 " pdb=" N ASP F 314 " pdb=" CA ASP F 314 " ideal model delta harmonic sigma weight residual -180.00 -159.26 -20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA VAL E 313 " pdb=" C VAL E 313 " pdb=" N ASP E 314 " pdb=" CA ASP E 314 " ideal model delta harmonic sigma weight residual -180.00 -159.27 -20.73 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 1524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 194 0.035 - 0.071: 108 0.071 - 0.106: 48 0.106 - 0.141: 16 0.141 - 0.177: 6 Chirality restraints: 372 Sorted by residual: chirality pdb=" CB ILE F 277 " pdb=" CA ILE F 277 " pdb=" CG1 ILE F 277 " pdb=" CG2 ILE F 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CB ILE E 277 " pdb=" CA ILE E 277 " pdb=" CG1 ILE E 277 " pdb=" CG2 ILE E 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CB ILE G 277 " pdb=" CA ILE G 277 " pdb=" CG1 ILE G 277 " pdb=" CG2 ILE G 277 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.71e-01 ... (remaining 369 not shown) Planarity restraints: 423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 363 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO G 364 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO G 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 364 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 363 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO F 364 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO F 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 364 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 363 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO E 364 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.029 5.00e-02 4.00e+02 ... (remaining 420 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 782 2.83 - 3.35: 2275 3.35 - 3.87: 4387 3.87 - 4.38: 4326 4.38 - 4.90: 8374 Nonbonded interactions: 20144 Sorted by model distance: nonbonded pdb=" N GLU E 380 " pdb=" OE1 GLU E 380 " model vdw 2.319 3.120 nonbonded pdb=" N GLU F 380 " pdb=" OE1 GLU F 380 " model vdw 2.319 3.120 nonbonded pdb=" N GLU G 380 " pdb=" OE1 GLU G 380 " model vdw 2.319 3.120 nonbonded pdb=" O GLU E 342 " pdb=" CB LYS F 343 " model vdw 2.366 2.752 nonbonded pdb=" O SER G 324 " pdb=" OG SER G 324 " model vdw 2.378 3.040 ... (remaining 20139 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' } 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 group one per residue 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: 0.940 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 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 0.039 2472 Z= 0.489 Angle : 1.025 6.915 3303 Z= 0.590 Chirality : 0.054 0.177 372 Planarity : 0.006 0.052 423 Dihedral : 15.141 81.261 963 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 26.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 2.13 % Allowed : 10.64 % Favored : 87.23 % 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: -4.78 (0.33), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 374 PHE 0.003 0.001 PHE E 378 TYR 0.004 0.002 TYR E 310 ARG 0.001 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.281 Fit side-chains REVERT: E 285 SER cc_start: 0.8035 (t) cc_final: 0.7808 (t) REVERT: F 325 LEU cc_start: 0.9497 (mp) cc_final: 0.9098 (tp) REVERT: G 319 THR cc_start: 0.8383 (m) cc_final: 0.8105 (p) REVERT: G 325 LEU cc_start: 0.8703 (mp) cc_final: 0.8448 (tp) outliers start: 6 outliers final: 0 residues processed: 48 average time/residue: 0.0769 time to fit residues: 5.0683 Evaluate side-chains 15 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 HIS E 362 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.066573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.057042 restraints weight = 23336.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.057602 restraints weight = 19358.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.058056 restraints weight = 16913.262| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2472 Z= 0.311 Angle : 0.764 5.060 3303 Z= 0.400 Chirality : 0.055 0.218 372 Planarity : 0.005 0.039 423 Dihedral : 7.276 21.662 327 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.31 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 374 PHE 0.009 0.002 PHE E 378 TYR 0.008 0.002 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.280 Fit side-chains REVERT: F 325 LEU cc_start: 0.9351 (mp) cc_final: 0.9044 (tp) REVERT: G 278 ILE cc_start: 0.7926 (mm) cc_final: 0.7674 (mm) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0596 time to fit residues: 1.5609 Evaluate side-chains 8 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 HIS ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.064982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.055704 restraints weight = 24132.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.056305 restraints weight = 19945.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.056782 restraints weight = 17151.783| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2472 Z= 0.243 Angle : 0.677 6.152 3303 Z= 0.344 Chirality : 0.051 0.148 372 Planarity : 0.004 0.034 423 Dihedral : 6.539 19.282 327 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % 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: -4.27 (0.33), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS F 330 PHE 0.005 0.001 PHE F 346 TYR 0.005 0.002 TYR E 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.318 Fit side-chains REVERT: F 325 LEU cc_start: 0.9298 (mp) cc_final: 0.9066 (tp) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0773 time to fit residues: 1.6752 Evaluate side-chains 6 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN E 374 HIS ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.067211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.058711 restraints weight = 24686.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.059375 restraints weight = 19359.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.059880 restraints weight = 16123.825| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.6900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2472 Z= 0.349 Angle : 0.787 5.476 3303 Z= 0.406 Chirality : 0.052 0.174 372 Planarity : 0.004 0.032 423 Dihedral : 7.467 26.053 327 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.35 % Allowed : 6.03 % Favored : 93.62 % 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: -4.49 (0.32), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.24), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 374 PHE 0.011 0.002 PHE E 378 TYR 0.007 0.003 TYR F 310 ARG 0.002 0.000 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.305 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.0817 time to fit residues: 1.7087 Evaluate side-chains 7 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.066767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.058898 restraints weight = 24619.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.059322 restraints weight = 19751.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.059955 restraints weight = 16526.226| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 2472 Z= 0.373 Angle : 0.857 12.073 3303 Z= 0.428 Chirality : 0.055 0.230 372 Planarity : 0.004 0.032 423 Dihedral : 7.836 25.111 327 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % 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: -4.65 (0.32), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.24), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS F 329 PHE 0.008 0.002 PHE G 346 TYR 0.008 0.003 TYR F 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0485 time to fit residues: 0.9047 Evaluate side-chains 4 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.067327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.059586 restraints weight = 24050.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.060200 restraints weight = 18723.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.060662 restraints weight = 15731.878| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.8297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2472 Z= 0.191 Angle : 0.677 11.110 3303 Z= 0.332 Chirality : 0.054 0.188 372 Planarity : 0.004 0.029 423 Dihedral : 6.532 26.317 327 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -4.43 (0.33), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 299 PHE 0.016 0.002 PHE F 346 TYR 0.006 0.002 TYR F 310 ARG 0.004 0.001 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.302 Fit side-chains REVERT: E 325 LEU cc_start: 0.8850 (pp) cc_final: 0.8586 (tp) REVERT: E 344 LEU cc_start: 0.9272 (mt) cc_final: 0.8905 (mp) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0689 time to fit residues: 1.2712 Evaluate side-chains 6 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** 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 = 0.3927 r_free = 0.3927 target = 0.066292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.058717 restraints weight = 25732.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.059100 restraints weight = 19698.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.059783 restraints weight = 16797.884| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.8940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2472 Z= 0.296 Angle : 0.745 9.423 3303 Z= 0.377 Chirality : 0.054 0.195 372 Planarity : 0.004 0.029 423 Dihedral : 7.082 26.998 327 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.02 % Favored : 86.98 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -4.59 (0.32), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 330 PHE 0.008 0.002 PHE E 378 TYR 0.008 0.003 TYR F 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.298 Fit side-chains REVERT: E 344 LEU cc_start: 0.9265 (mt) cc_final: 0.8825 (mp) outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0550 time to fit residues: 0.9204 Evaluate side-chains 5 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 0.0870 chunk 21 optimal weight: 6.9990 chunk 29 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.066774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.059344 restraints weight = 24911.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.059973 restraints weight = 19654.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.060382 restraints weight = 16482.970| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.9006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2472 Z= 0.146 Angle : 0.629 6.499 3303 Z= 0.309 Chirality : 0.055 0.279 372 Planarity : 0.003 0.031 423 Dihedral : 5.976 23.782 327 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.35 % Allowed : 1.77 % Favored : 97.87 % 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: -4.34 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 330 PHE 0.004 0.001 PHE F 346 TYR 0.005 0.001 TYR F 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: E 344 LEU cc_start: 0.9286 (mt) cc_final: 0.8922 (mp) outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.0670 time to fit residues: 1.4635 Evaluate side-chains 8 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** 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 = 0.3914 r_free = 0.3914 target = 0.066191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.058980 restraints weight = 24896.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.059563 restraints weight = 19456.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.059945 restraints weight = 16092.945| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.9289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2472 Z= 0.215 Angle : 0.665 10.672 3303 Z= 0.328 Chirality : 0.053 0.252 372 Planarity : 0.003 0.031 423 Dihedral : 6.258 24.259 327 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -4.42 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 330 PHE 0.006 0.001 PHE E 378 TYR 0.007 0.002 TYR F 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.287 Fit side-chains REVERT: E 344 LEU cc_start: 0.9303 (mt) cc_final: 0.8874 (mp) REVERT: F 315 LEU cc_start: 0.8490 (pp) cc_final: 0.7762 (tp) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0566 time to fit residues: 1.1369 Evaluate side-chains 8 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.066225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.059089 restraints weight = 24791.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.059763 restraints weight = 19212.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.060115 restraints weight = 15817.849| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.9728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2472 Z= 0.226 Angle : 0.655 5.097 3303 Z= 0.330 Chirality : 0.054 0.244 372 Planarity : 0.003 0.031 423 Dihedral : 6.291 23.886 327 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.48 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 330 PHE 0.006 0.002 PHE F 378 TYR 0.006 0.002 TYR F 310 ARG 0.001 0.000 ARG G 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.316 Fit side-chains REVERT: E 344 LEU cc_start: 0.9309 (mt) cc_final: 0.8873 (mp) REVERT: F 315 LEU cc_start: 0.8533 (pp) cc_final: 0.7867 (tp) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0594 time to fit residues: 1.0550 Evaluate side-chains 6 residues out of total 282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** 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 = 0.3913 r_free = 0.3913 target = 0.066848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.059700 restraints weight = 24040.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.060299 restraints weight = 18980.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.060750 restraints weight = 15782.789| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.9814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2472 Z= 0.142 Angle : 0.581 5.583 3303 Z= 0.287 Chirality : 0.054 0.229 372 Planarity : 0.003 0.032 423 Dihedral : 5.497 19.308 327 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.28 (0.36), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.27), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 330 PHE 0.004 0.001 PHE E 346 TYR 0.005 0.001 TYR F 310 ARG 0.002 0.000 ARG G 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1264.88 seconds wall clock time: 22 minutes 43.27 seconds (1363.27 seconds total)