Starting phenix.real_space_refine on Mon Nov 13 15:35:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2023/6vha_21201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2023/6vha_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2023/6vha_21201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2023/6vha_21201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2023/6vha_21201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vha_21201/11_2023/6vha_21201.pdb" } 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 Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 345": "OD1" <-> "OD2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 345": "OD1" <-> "OD2" Residue "G PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 2439 Number of models: 1 Model: "" Number of chains: 3 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} Chain: "F" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "G" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Time building chain proxies: 1.80, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 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: 1.02 Conformation dependent library (CDL) restraints added in 492.7 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: 0.30 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: 0.51 Time building geometry restraints manager: 1.09 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: 102.01 - 107.87: 181 107.87 - 113.73: 1408 113.73 - 119.58: 565 119.58 - 125.44: 1122 125.44 - 131.29: 27 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 2.520 nonbonded pdb=" N GLU F 380 " pdb=" OE1 GLU F 380 " model vdw 2.319 2.520 nonbonded pdb=" N GLU G 380 " pdb=" OE1 GLU G 380 " model vdw 2.319 2.520 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 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.920 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: 3.550 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.820 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.319 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 48 average time/residue: 0.0751 time to fit residues: 4.9486 Evaluate side-chains 13 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3528 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** E 359 ASN E 362 HIS ** E 368 ASN ** 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 359 ASN F 362 HIS ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN G 362 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2472 Z= 0.325 Angle : 0.797 8.069 3303 Z= 0.406 Chirality : 0.053 0.175 372 Planarity : 0.005 0.040 423 Dihedral : 7.357 22.174 327 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % 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: -4.29 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.26), residues: 315 *********************** 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 11 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.334 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0746 time to fit residues: 1.5583 Evaluate side-chains 5 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.304 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 359 ASN F 374 HIS ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 359 ASN G 374 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 2472 Z= 0.573 Angle : 1.094 9.006 3303 Z= 0.573 Chirality : 0.060 0.252 372 Planarity : 0.006 0.043 423 Dihedral : 9.372 30.510 327 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 1.42 % Allowed : 11.70 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -4.74 (0.31), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.24), residues: 315 *********************** 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 fitting. rotamer outliers: 4 poor density : 7 time to evaluate : 0.320 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 11 average time/residue: 0.0724 time to fit residues: 1.5198 Evaluate side-chains 6 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 4 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0268 time to fit residues: 0.5249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ** 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 296 ASN G 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2472 Z= 0.248 Angle : 0.709 6.561 3303 Z= 0.365 Chirality : 0.055 0.261 372 Planarity : 0.004 0.033 423 Dihedral : 7.238 21.713 327 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.33), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.26), residues: 315 *********************** 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 15 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.336 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0892 time to fit residues: 2.1505 Evaluate side-chains 7 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 0.0010 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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** ** G 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5801 moved from start: 0.8048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2472 Z= 0.304 Angle : 0.778 9.705 3303 Z= 0.394 Chirality : 0.054 0.230 372 Planarity : 0.004 0.034 423 Dihedral : 7.320 26.156 327 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -4.46 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.26), residues: 315 *********************** 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 9 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0807 time to fit residues: 1.4203 Evaluate side-chains 7 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5778 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2472 Z= 0.192 Angle : 0.667 8.884 3303 Z= 0.333 Chirality : 0.054 0.236 372 Planarity : 0.004 0.032 423 Dihedral : 6.510 28.600 327 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -4.35 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.31 (0.26), residues: 315 *********************** 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 10 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.377 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0801 time to fit residues: 1.5093 Evaluate side-chains 7 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.2980 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 8 optimal weight: 0.0170 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.0624 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.8551 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= 0.182 Angle : 0.626 5.764 3303 Z= 0.317 Chirality : 0.054 0.248 372 Planarity : 0.003 0.032 423 Dihedral : 6.041 24.145 327 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: -4.36 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.26), residues: 315 *********************** 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 12 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.325 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0770 time to fit residues: 1.6611 Evaluate side-chains 8 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.0670 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.4922 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.8942 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= 0.216 Angle : 0.681 12.781 3303 Z= 0.335 Chirality : 0.052 0.162 372 Planarity : 0.003 0.033 423 Dihedral : 6.258 27.156 327 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: -4.44 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.26), residues: 315 *********************** 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 9 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0639 time to fit residues: 1.2775 Evaluate side-chains 6 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5776 moved from start: 0.9316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2472 Z= 0.244 Angle : 0.689 9.241 3303 Z= 0.348 Chirality : 0.055 0.200 372 Planarity : 0.004 0.033 423 Dihedral : 6.414 26.264 327 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % 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: -4.53 (0.34), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.26), residues: 315 *********************** 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 7 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.337 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0584 time to fit residues: 1.0654 Evaluate side-chains 5 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.332 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.9444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2472 Z= 0.159 Angle : 0.610 6.145 3303 Z= 0.303 Chirality : 0.054 0.218 372 Planarity : 0.003 0.032 423 Dihedral : 5.788 23.097 327 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % 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: -4.37 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.27), residues: 315 ********************** 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 8 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0604 time to fit residues: 1.1836 Evaluate side-chains 5 residues out of total 282 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 20 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.065632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.058751 restraints weight = 24629.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.059201 restraints weight = 19210.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.059767 restraints weight = 16429.985| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.9651 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= 0.180 Angle : 0.631 11.452 3303 Z= 0.311 Chirality : 0.052 0.151 372 Planarity : 0.003 0.032 423 Dihedral : 5.816 22.410 327 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.82 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: -4.37 (0.35), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.27), residues: 315 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1010.38 seconds wall clock time: 19 minutes 5.88 seconds (1145.88 seconds total)