Starting phenix.real_space_refine on Sat Aug 3 02:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/08_2024/8q8c_18250.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/08_2024/8q8c_18250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/08_2024/8q8c_18250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/08_2024/8q8c_18250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/08_2024/8q8c_18250.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/08_2024/8q8c_18250.cif" } resolution = 1.92 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= 0.003 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2034 2.51 5 N 594 2.21 5 O 612 1.98 5 H 3372 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6618 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1155 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.70, per 1000 atoms: 0.71 Number of scatterers: 6618 At special positions: 0 Unit cell: (134.495, 126.498, 48.709, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 612 8.00 N 594 7.00 C 2034 6.00 H 3372 1.00 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: 4.74 Conformation dependent library (CDL) restraints added in 725.1 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 57.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 309 through 310 removed outlier: 6.499A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.720A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 325 removed outlier: 6.488A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.479A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 346 removed outlier: 6.908A pdb=" N VAL E 337 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU A 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL E 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS A 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER E 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU A 342 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS E 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 10.369A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N GLU E 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N SER C 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N LEU E 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE E 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.354A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.395A pdb=" N ASP C 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR E 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 360 " --> pdb=" O THR E 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 374 removed outlier: 6.480A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.488A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.860A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 325 Processing sheet with id=AB3, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.578A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 337 through 346 removed outlier: 6.569A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER D 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LYS B 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LYS D 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N GLU B 342 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ASP D 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU F 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP B 345 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE F 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 362 removed outlier: 6.898A pdb=" N GLN D 351 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER B 352 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS D 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE B 354 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY D 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N SER B 356 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN B 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER F 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 353 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE F 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY B 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER F 356 " --> pdb=" O GLY B 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 368 through 377 removed outlier: 6.463A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 80 hydrogen bonds defined for protein. 240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 5.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3366 1.12 - 1.29: 546 1.29 - 1.47: 1092 1.47 - 1.64: 1659 1.64 - 1.82: 6 Bond restraints: 6669 Sorted by residual: bond pdb=" N ILE F 360 " pdb=" H ILE F 360 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE1 HIS D 362 " pdb=" HE1 HIS D 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS D 353 " pdb=" H LYS D 353 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CZ PHE F 378 " pdb=" HZ PHE F 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ILE D 360 " pdb=" H ILE D 360 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 6664 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.05: 26 103.05 - 109.89: 5892 109.89 - 116.73: 2996 116.73 - 123.56: 2748 123.56 - 130.40: 506 Bond angle restraints: 12168 Sorted by residual: angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 118.43 -5.83 1.00e+00 1.00e+00 3.40e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.13 5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.80e+01 angle pdb=" N PRO F 312 " pdb=" CA PRO F 312 " pdb=" CB PRO F 312 " ideal model delta sigma weight residual 103.25 107.20 -3.95 8.80e-01 1.29e+00 2.01e+01 ... (remaining 12163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 2739 15.64 - 31.29: 169 31.29 - 46.93: 48 46.93 - 62.57: 91 62.57 - 78.22: 25 Dihedral angle restraints: 3072 sinusoidal: 1758 harmonic: 1314 Sorted by residual: dihedral pdb=" CA GLU F 372 " pdb=" C GLU F 372 " pdb=" N THR F 373 " pdb=" CA THR F 373 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA THR E 319 " pdb=" C THR E 319 " pdb=" N SER E 320 " pdb=" CA SER E 320 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA THR C 319 " pdb=" C THR C 319 " pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 3069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 235 0.059 - 0.118: 198 0.118 - 0.177: 58 0.177 - 0.236: 3 0.236 - 0.295: 1 Chirality restraints: 495 Sorted by residual: chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA GLU B 342 " pdb=" N GLU B 342 " pdb=" C GLU B 342 " pdb=" CB GLU B 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 492 not shown) Planarity restraints: 966 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 336 " -0.062 2.00e-02 2.50e+03 5.63e-02 4.76e+01 pdb=" CD GLN C 336 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN C 336 " 0.038 2.00e-02 2.50e+03 pdb=" NE2 GLN C 336 " 0.045 2.00e-02 2.50e+03 pdb="HE21 GLN C 336 " 0.045 2.00e-02 2.50e+03 pdb="HE22 GLN C 336 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 330 " 0.070 2.00e-02 2.50e+03 4.53e-02 4.62e+01 pdb=" CG HIS E 330 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS E 330 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 HIS E 330 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 HIS E 330 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS E 330 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 HIS E 330 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS E 330 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 HIS E 330 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 362 " -0.071 2.00e-02 2.50e+03 4.36e-02 4.27e+01 pdb=" CG HIS B 362 " 0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS B 362 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS B 362 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS B 362 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS B 362 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 HIS B 362 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS B 362 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 HIS B 362 " -0.054 2.00e-02 2.50e+03 ... (remaining 963 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 481 2.16 - 2.77: 10878 2.77 - 3.38: 17307 3.38 - 3.99: 23620 3.99 - 4.60: 32257 Nonbonded interactions: 84543 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.559 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.568 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.575 2.450 ... (remaining 84538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 308 through 375) selection = chain 'C' selection = (chain 'D' and resid 308 through 375) selection = chain 'E' selection = (chain 'F' and resid 308 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.270 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.011 0.039 3297 Z= 0.754 Angle : 1.664 6.272 4410 Z= 1.109 Chirality : 0.077 0.295 495 Planarity : 0.008 0.038 561 Dihedral : 10.695 78.218 1263 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.27 % Allowed : 1.61 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.34), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS F 362 PHE 0.048 0.015 PHE D 378 TYR 0.035 0.012 TYR B 310 ARG 0.009 0.002 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7638 (mt) cc_final: 0.7382 (mt) REVERT: A 317 LYS cc_start: 0.7328 (mttt) cc_final: 0.6972 (mttp) REVERT: A 324 SER cc_start: 0.7139 (p) cc_final: 0.6938 (t) REVERT: A 342 GLU cc_start: 0.6579 (tt0) cc_final: 0.5870 (tm-30) REVERT: A 343 LYS cc_start: 0.7171 (mttt) cc_final: 0.6962 (mttt) REVERT: A 369 LYS cc_start: 0.6792 (ttmt) cc_final: 0.6313 (ttpt) REVERT: B 311 LYS cc_start: 0.7137 (mttt) cc_final: 0.6707 (mttp) REVERT: B 317 LYS cc_start: 0.6616 (mttt) cc_final: 0.6264 (mttm) REVERT: B 336 GLN cc_start: 0.6722 (tt0) cc_final: 0.6320 (tt0) REVERT: B 340 LYS cc_start: 0.6200 (mttt) cc_final: 0.5699 (mtpp) REVERT: B 345 ASP cc_start: 0.6847 (t0) cc_final: 0.6639 (t70) REVERT: B 369 LYS cc_start: 0.6862 (tttt) cc_final: 0.6602 (ttpt) REVERT: B 372 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6420 (mm-30) REVERT: C 311 LYS cc_start: 0.6874 (mtmt) cc_final: 0.6099 (mttm) REVERT: C 342 GLU cc_start: 0.6017 (tt0) cc_final: 0.5717 (tt0) REVERT: C 345 ASP cc_start: 0.6946 (m-30) cc_final: 0.6487 (t0) REVERT: C 351 GLN cc_start: 0.6850 (mt0) cc_final: 0.6647 (mt0) REVERT: C 369 LYS cc_start: 0.6336 (ttmt) cc_final: 0.5909 (ttpt) REVERT: C 372 GLU cc_start: 0.6975 (tt0) cc_final: 0.6673 (mm-30) REVERT: C 373 THR cc_start: 0.7260 (m) cc_final: 0.6743 (p) REVERT: D 311 LYS cc_start: 0.7440 (mttt) cc_final: 0.7176 (mttp) REVERT: D 338 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6249 (mt-10) REVERT: D 340 LYS cc_start: 0.6745 (mttt) cc_final: 0.6160 (mtpt) REVERT: D 369 LYS cc_start: 0.7477 (tttt) cc_final: 0.7174 (ttpt) REVERT: D 375 LYS cc_start: 0.7491 (tttt) cc_final: 0.7034 (tppt) REVERT: E 317 LYS cc_start: 0.6681 (mttt) cc_final: 0.6346 (mttp) REVERT: E 324 SER cc_start: 0.7159 (p) cc_final: 0.6950 (t) REVERT: E 342 GLU cc_start: 0.6120 (tt0) cc_final: 0.5344 (tm-30) REVERT: E 343 LYS cc_start: 0.6946 (mttt) cc_final: 0.6641 (mttt) REVERT: E 345 ASP cc_start: 0.6993 (m-30) cc_final: 0.6620 (m-30) REVERT: E 347 LYS cc_start: 0.6949 (mttt) cc_final: 0.6723 (mmtt) REVERT: E 369 LYS cc_start: 0.6188 (ttmt) cc_final: 0.5803 (ttpt) REVERT: E 372 GLU cc_start: 0.6736 (tt0) cc_final: 0.6400 (tt0) REVERT: F 317 LYS cc_start: 0.6739 (mttt) cc_final: 0.6486 (mttm) REVERT: F 338 GLU cc_start: 0.5326 (mm-30) cc_final: 0.5124 (mt-10) REVERT: F 340 LYS cc_start: 0.6289 (mttt) cc_final: 0.5819 (mtpp) REVERT: F 342 GLU cc_start: 0.6299 (pt0) cc_final: 0.6019 (pt0) REVERT: F 349 ARG cc_start: 0.6240 (mtm110) cc_final: 0.5643 (mtt180) REVERT: F 353 LYS cc_start: 0.6663 (tttt) cc_final: 0.6309 (tttp) REVERT: F 356 SER cc_start: 0.7183 (m) cc_final: 0.6936 (t) REVERT: F 369 LYS cc_start: 0.6934 (tttt) cc_final: 0.6375 (ttpt) REVERT: F 371 ILE cc_start: 0.7214 (mt) cc_final: 0.6970 (mm) REVERT: F 372 GLU cc_start: 0.7017 (mt-10) cc_final: 0.6670 (mm-30) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 2.7463 time to fit residues: 412.6587 Evaluate side-chains 118 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN D 327 ASN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3297 Z= 0.339 Angle : 0.612 4.346 4410 Z= 0.321 Chirality : 0.050 0.129 495 Planarity : 0.004 0.034 561 Dihedral : 5.693 14.700 435 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 329 PHE 0.006 0.002 PHE D 346 TYR 0.008 0.002 TYR B 310 ARG 0.004 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7578 (mt) cc_final: 0.7346 (mt) REVERT: A 324 SER cc_start: 0.7220 (p) cc_final: 0.6999 (m) REVERT: A 340 LYS cc_start: 0.7070 (mttt) cc_final: 0.6590 (mttm) REVERT: A 349 ARG cc_start: 0.6546 (mtp85) cc_final: 0.5965 (mtt180) REVERT: A 369 LYS cc_start: 0.6889 (ttmt) cc_final: 0.6454 (ttpt) REVERT: B 311 LYS cc_start: 0.7064 (mttt) cc_final: 0.6682 (mttp) REVERT: B 317 LYS cc_start: 0.6633 (mttt) cc_final: 0.6290 (mttm) REVERT: B 338 GLU cc_start: 0.6355 (mt-10) cc_final: 0.5603 (mt-10) REVERT: B 340 LYS cc_start: 0.6271 (mttt) cc_final: 0.5701 (mtpp) REVERT: B 369 LYS cc_start: 0.6924 (tttt) cc_final: 0.6686 (ttpt) REVERT: B 372 GLU cc_start: 0.6656 (mt-10) cc_final: 0.6446 (mm-30) REVERT: C 315 LEU cc_start: 0.7499 (mt) cc_final: 0.7199 (mp) REVERT: C 340 LYS cc_start: 0.6661 (mttt) cc_final: 0.6072 (mttm) REVERT: C 345 ASP cc_start: 0.6939 (m-30) cc_final: 0.6507 (t0) REVERT: C 349 ARG cc_start: 0.6568 (mtt180) cc_final: 0.4610 (mmp-170) REVERT: C 369 LYS cc_start: 0.6410 (ttmt) cc_final: 0.5994 (ttpt) REVERT: C 372 GLU cc_start: 0.6927 (tt0) cc_final: 0.6646 (mm-30) REVERT: C 373 THR cc_start: 0.7302 (m) cc_final: 0.6837 (p) REVERT: D 311 LYS cc_start: 0.7418 (mttt) cc_final: 0.7117 (mttp) REVERT: D 338 GLU cc_start: 0.6854 (mt-10) cc_final: 0.6076 (mt-10) REVERT: D 340 LYS cc_start: 0.6662 (mttt) cc_final: 0.6070 (mtpt) REVERT: D 369 LYS cc_start: 0.7489 (tttt) cc_final: 0.7220 (ttpt) REVERT: D 375 LYS cc_start: 0.7513 (tttt) cc_final: 0.7110 (tppt) REVERT: E 317 LYS cc_start: 0.6738 (mttt) cc_final: 0.6391 (mttm) REVERT: E 324 SER cc_start: 0.7034 (p) cc_final: 0.6748 (t) REVERT: E 345 ASP cc_start: 0.6816 (m-30) cc_final: 0.6369 (t0) REVERT: E 347 LYS cc_start: 0.6951 (mttt) cc_final: 0.6741 (mmtt) REVERT: E 369 LYS cc_start: 0.6230 (ttmt) cc_final: 0.5825 (ttpt) REVERT: E 372 GLU cc_start: 0.6843 (tt0) cc_final: 0.6522 (tt0) REVERT: F 317 LYS cc_start: 0.6887 (mttt) cc_final: 0.6590 (mttm) REVERT: F 340 LYS cc_start: 0.6252 (mttt) cc_final: 0.5799 (mtpp) REVERT: F 342 GLU cc_start: 0.6202 (pt0) cc_final: 0.5893 (pt0) REVERT: F 349 ARG cc_start: 0.6373 (mtm110) cc_final: 0.5833 (mtt180) REVERT: F 353 LYS cc_start: 0.6589 (tttt) cc_final: 0.6301 (tttp) REVERT: F 369 LYS cc_start: 0.6961 (tttt) cc_final: 0.6431 (ttpt) REVERT: F 372 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6771 (mm-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 3.2904 time to fit residues: 389.0736 Evaluate side-chains 111 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3297 Z= 0.187 Angle : 0.522 4.499 4410 Z= 0.269 Chirality : 0.052 0.135 495 Planarity : 0.003 0.027 561 Dihedral : 5.211 13.078 435 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.54 % Allowed : 7.53 % Favored : 91.94 % 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: -0.91 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE B 346 TYR 0.009 0.002 TYR B 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7025 (mttt) cc_final: 0.6404 (mttm) REVERT: A 342 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.6253 (tt0) REVERT: A 349 ARG cc_start: 0.6659 (mtp85) cc_final: 0.6055 (mtt180) REVERT: A 369 LYS cc_start: 0.6925 (ttmt) cc_final: 0.6508 (ttpt) REVERT: B 311 LYS cc_start: 0.7123 (mttt) cc_final: 0.6706 (mttp) REVERT: B 317 LYS cc_start: 0.6677 (mttt) cc_final: 0.6321 (mttm) REVERT: B 338 GLU cc_start: 0.6283 (mt-10) cc_final: 0.5618 (mt-10) REVERT: B 340 LYS cc_start: 0.6296 (mttt) cc_final: 0.5722 (mtpp) REVERT: B 369 LYS cc_start: 0.6927 (tttt) cc_final: 0.6713 (ttpt) REVERT: C 315 LEU cc_start: 0.7499 (mt) cc_final: 0.7233 (mp) REVERT: C 340 LYS cc_start: 0.6656 (mttt) cc_final: 0.6087 (mttm) REVERT: C 345 ASP cc_start: 0.6955 (m-30) cc_final: 0.6532 (t0) REVERT: C 349 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6292 (mtt180) REVERT: C 369 LYS cc_start: 0.6469 (ttmt) cc_final: 0.6044 (ttpt) REVERT: C 372 GLU cc_start: 0.6896 (tt0) cc_final: 0.6594 (mm-30) REVERT: C 373 THR cc_start: 0.7314 (m) cc_final: 0.6889 (p) REVERT: D 311 LYS cc_start: 0.7434 (mttt) cc_final: 0.7153 (mttp) REVERT: D 338 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6030 (mt-10) REVERT: D 340 LYS cc_start: 0.6640 (mttt) cc_final: 0.6044 (mtpt) REVERT: D 369 LYS cc_start: 0.7469 (tttt) cc_final: 0.7187 (ttpt) REVERT: D 375 LYS cc_start: 0.7512 (tttt) cc_final: 0.7094 (tppt) REVERT: E 317 LYS cc_start: 0.6705 (mttt) cc_final: 0.6348 (mttp) REVERT: E 324 SER cc_start: 0.7033 (p) cc_final: 0.6687 (t) REVERT: E 345 ASP cc_start: 0.6859 (m-30) cc_final: 0.6403 (t0) REVERT: E 369 LYS cc_start: 0.6254 (ttmt) cc_final: 0.5829 (ttpt) REVERT: E 372 GLU cc_start: 0.6898 (tt0) cc_final: 0.6615 (tt0) REVERT: F 317 LYS cc_start: 0.6883 (mttt) cc_final: 0.6584 (mttm) REVERT: F 340 LYS cc_start: 0.6240 (mttt) cc_final: 0.5772 (mtpp) REVERT: F 342 GLU cc_start: 0.6211 (pt0) cc_final: 0.5886 (pt0) REVERT: F 349 ARG cc_start: 0.6416 (mtm110) cc_final: 0.5926 (mtp85) REVERT: F 353 LYS cc_start: 0.6669 (tttt) cc_final: 0.6376 (tttp) REVERT: F 369 LYS cc_start: 0.6959 (tttt) cc_final: 0.6348 (ttpt) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 3.4023 time to fit residues: 398.7419 Evaluate side-chains 108 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3297 Z= 0.189 Angle : 0.503 4.385 4410 Z= 0.258 Chirality : 0.052 0.133 495 Planarity : 0.003 0.024 561 Dihedral : 5.101 13.210 435 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 9.68 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.005 0.001 PHE E 346 TYR 0.007 0.002 TYR B 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ARG cc_start: 0.6668 (mtp85) cc_final: 0.6130 (mtt180) REVERT: A 369 LYS cc_start: 0.6885 (ttmt) cc_final: 0.6408 (ttpt) REVERT: B 311 LYS cc_start: 0.7103 (mttt) cc_final: 0.6692 (mttp) REVERT: B 338 GLU cc_start: 0.6275 (mt-10) cc_final: 0.5614 (mt-10) REVERT: B 340 LYS cc_start: 0.6327 (mttt) cc_final: 0.5756 (mtpp) REVERT: B 345 ASP cc_start: 0.6954 (t0) cc_final: 0.6669 (t70) REVERT: B 369 LYS cc_start: 0.6923 (tttt) cc_final: 0.6689 (ttpt) REVERT: C 315 LEU cc_start: 0.7486 (mt) cc_final: 0.7231 (mp) REVERT: C 340 LYS cc_start: 0.6673 (mttt) cc_final: 0.6113 (mttt) REVERT: C 345 ASP cc_start: 0.6947 (m-30) cc_final: 0.6534 (t0) REVERT: C 348 ASP cc_start: 0.7521 (t0) cc_final: 0.7169 (t0) REVERT: C 349 ARG cc_start: 0.6625 (mtt180) cc_final: 0.4627 (mmp-170) REVERT: C 369 LYS cc_start: 0.6469 (ttmt) cc_final: 0.6061 (ttpt) REVERT: C 372 GLU cc_start: 0.6926 (tt0) cc_final: 0.6516 (mm-30) REVERT: C 373 THR cc_start: 0.7314 (m) cc_final: 0.6904 (p) REVERT: D 311 LYS cc_start: 0.7461 (mttt) cc_final: 0.7166 (mttp) REVERT: D 338 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6004 (mt-10) REVERT: D 340 LYS cc_start: 0.6670 (mttt) cc_final: 0.6075 (mtpt) REVERT: D 369 LYS cc_start: 0.7475 (tttt) cc_final: 0.7205 (ttpt) REVERT: D 375 LYS cc_start: 0.7507 (tttt) cc_final: 0.7057 (tppt) REVERT: E 317 LYS cc_start: 0.6718 (mttt) cc_final: 0.6343 (mttp) REVERT: E 324 SER cc_start: 0.7037 (p) cc_final: 0.6685 (t) REVERT: E 345 ASP cc_start: 0.6890 (m-30) cc_final: 0.6451 (t0) REVERT: E 369 LYS cc_start: 0.6252 (ttmt) cc_final: 0.5885 (ttpt) REVERT: E 372 GLU cc_start: 0.6959 (tt0) cc_final: 0.6651 (tt0) REVERT: F 317 LYS cc_start: 0.6865 (mttt) cc_final: 0.6602 (mttm) REVERT: F 340 LYS cc_start: 0.6240 (mttt) cc_final: 0.5773 (mtpp) REVERT: F 342 GLU cc_start: 0.6179 (pt0) cc_final: 0.5906 (pt0) REVERT: F 349 ARG cc_start: 0.6422 (mtm110) cc_final: 0.5942 (mtt180) REVERT: F 353 LYS cc_start: 0.6653 (tttt) cc_final: 0.6395 (tttp) REVERT: F 369 LYS cc_start: 0.6982 (tttt) cc_final: 0.6346 (ttpt) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 3.4633 time to fit residues: 377.7349 Evaluate side-chains 103 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3297 Z= 0.126 Angle : 0.463 4.346 4410 Z= 0.235 Chirality : 0.052 0.132 495 Planarity : 0.002 0.021 561 Dihedral : 4.862 12.490 435 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.81 % Allowed : 9.14 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.72 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.005 0.001 PHE A 346 TYR 0.006 0.001 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.6999 (mttt) cc_final: 0.6595 (mttm) REVERT: A 345 ASP cc_start: 0.7385 (m-30) cc_final: 0.7154 (t0) REVERT: A 349 ARG cc_start: 0.6699 (mtp85) cc_final: 0.6007 (mtt180) REVERT: A 369 LYS cc_start: 0.6871 (ttmt) cc_final: 0.6388 (ttpt) REVERT: B 311 LYS cc_start: 0.7088 (mttt) cc_final: 0.6745 (mttp) REVERT: B 338 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5950 (mt-10) REVERT: B 340 LYS cc_start: 0.6341 (mttt) cc_final: 0.5766 (mtpp) REVERT: B 345 ASP cc_start: 0.6955 (t0) cc_final: 0.6643 (t70) REVERT: B 369 LYS cc_start: 0.6969 (tttt) cc_final: 0.6744 (ttpt) REVERT: C 315 LEU cc_start: 0.7493 (mt) cc_final: 0.7235 (mp) REVERT: C 340 LYS cc_start: 0.6677 (mttt) cc_final: 0.6128 (mttt) REVERT: C 345 ASP cc_start: 0.6973 (m-30) cc_final: 0.6578 (t0) REVERT: C 348 ASP cc_start: 0.7473 (t0) cc_final: 0.7138 (t0) REVERT: C 349 ARG cc_start: 0.6686 (mtt180) cc_final: 0.4698 (mmp-170) REVERT: C 369 LYS cc_start: 0.6541 (ttmt) cc_final: 0.6137 (ttpt) REVERT: C 372 GLU cc_start: 0.6895 (tt0) cc_final: 0.6504 (mm-30) REVERT: C 373 THR cc_start: 0.7323 (m) cc_final: 0.6921 (p) REVERT: D 311 LYS cc_start: 0.7471 (mttt) cc_final: 0.7190 (mttp) REVERT: D 338 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6180 (mt-10) REVERT: D 340 LYS cc_start: 0.6689 (mttt) cc_final: 0.6103 (mtpt) REVERT: D 369 LYS cc_start: 0.7458 (tttt) cc_final: 0.7177 (ttpt) REVERT: D 372 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: D 375 LYS cc_start: 0.7487 (tttt) cc_final: 0.7047 (tppt) REVERT: E 317 LYS cc_start: 0.6729 (mttt) cc_final: 0.6353 (mttp) REVERT: E 324 SER cc_start: 0.6971 (p) cc_final: 0.6644 (t) REVERT: E 345 ASP cc_start: 0.6845 (m-30) cc_final: 0.6314 (t0) REVERT: E 369 LYS cc_start: 0.6275 (ttmt) cc_final: 0.5903 (ttpt) REVERT: E 372 GLU cc_start: 0.6962 (tt0) cc_final: 0.6653 (tt0) REVERT: F 317 LYS cc_start: 0.6854 (mttt) cc_final: 0.6585 (mttm) REVERT: F 340 LYS cc_start: 0.6272 (mttt) cc_final: 0.5790 (mtpp) REVERT: F 342 GLU cc_start: 0.6223 (pt0) cc_final: 0.5936 (pt0) REVERT: F 349 ARG cc_start: 0.6431 (mtm110) cc_final: 0.5946 (mtp85) REVERT: F 353 LYS cc_start: 0.6696 (tttt) cc_final: 0.6423 (tttp) REVERT: F 369 LYS cc_start: 0.6943 (tttt) cc_final: 0.6299 (ttpt) outliers start: 3 outliers final: 0 residues processed: 106 average time/residue: 3.3002 time to fit residues: 356.7392 Evaluate side-chains 105 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 27 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3297 Z= 0.275 Angle : 0.537 3.964 4410 Z= 0.280 Chirality : 0.051 0.133 495 Planarity : 0.003 0.025 561 Dihedral : 5.197 13.452 435 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.08 % Allowed : 8.60 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 330 PHE 0.006 0.002 PHE E 346 TYR 0.010 0.002 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7037 (mttt) cc_final: 0.6345 (mttm) REVERT: A 349 ARG cc_start: 0.6722 (mtp85) cc_final: 0.6012 (mtt180) REVERT: A 369 LYS cc_start: 0.6846 (ttmt) cc_final: 0.6370 (ttpt) REVERT: B 311 LYS cc_start: 0.7081 (mttt) cc_final: 0.6721 (mttp) REVERT: B 338 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5621 (mt-10) REVERT: B 340 LYS cc_start: 0.6308 (mttt) cc_final: 0.5729 (mtpp) REVERT: B 369 LYS cc_start: 0.6919 (tttt) cc_final: 0.6676 (ttpt) REVERT: C 315 LEU cc_start: 0.7487 (mt) cc_final: 0.7226 (mp) REVERT: C 340 LYS cc_start: 0.6638 (mttt) cc_final: 0.6104 (mttt) REVERT: C 348 ASP cc_start: 0.7403 (t0) cc_final: 0.7109 (t0) REVERT: C 349 ARG cc_start: 0.6630 (mtt180) cc_final: 0.4655 (mmp-170) REVERT: C 369 LYS cc_start: 0.6454 (ttmt) cc_final: 0.6053 (ttpt) REVERT: C 373 THR cc_start: 0.7345 (m) cc_final: 0.6979 (p) REVERT: D 338 GLU cc_start: 0.6827 (mt-10) cc_final: 0.6071 (mt-10) REVERT: D 340 LYS cc_start: 0.6707 (mttt) cc_final: 0.6129 (mtpt) REVERT: D 369 LYS cc_start: 0.7517 (tttt) cc_final: 0.7277 (ttpt) REVERT: D 372 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: D 375 LYS cc_start: 0.7528 (tttt) cc_final: 0.7076 (tppt) REVERT: E 317 LYS cc_start: 0.6672 (mttt) cc_final: 0.6317 (mttp) REVERT: E 324 SER cc_start: 0.7058 (p) cc_final: 0.6713 (t) REVERT: E 345 ASP cc_start: 0.6905 (m-30) cc_final: 0.6428 (t0) REVERT: E 369 LYS cc_start: 0.6264 (ttmt) cc_final: 0.5912 (ttpt) REVERT: F 317 LYS cc_start: 0.6858 (mttt) cc_final: 0.6594 (mttm) REVERT: F 340 LYS cc_start: 0.6279 (mttt) cc_final: 0.5789 (mtpp) REVERT: F 342 GLU cc_start: 0.6302 (pt0) cc_final: 0.6052 (pt0) REVERT: F 349 ARG cc_start: 0.6301 (mtm110) cc_final: 0.5777 (mtt180) REVERT: F 353 LYS cc_start: 0.6657 (tttt) cc_final: 0.6374 (tttp) REVERT: F 369 LYS cc_start: 0.6948 (tttt) cc_final: 0.6378 (ttpt) outliers start: 4 outliers final: 0 residues processed: 106 average time/residue: 3.2740 time to fit residues: 353.9385 Evaluate side-chains 105 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3297 Z= 0.175 Angle : 0.489 3.933 4410 Z= 0.253 Chirality : 0.052 0.136 495 Planarity : 0.003 0.023 561 Dihedral : 5.043 13.237 435 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.81 % Allowed : 9.41 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.78 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE E 346 TYR 0.007 0.002 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7021 (mttt) cc_final: 0.6416 (mttt) REVERT: A 345 ASP cc_start: 0.7414 (m-30) cc_final: 0.7183 (t0) REVERT: A 349 ARG cc_start: 0.6716 (mtp85) cc_final: 0.6017 (mtt180) REVERT: A 369 LYS cc_start: 0.6877 (ttmt) cc_final: 0.6412 (ttpt) REVERT: B 311 LYS cc_start: 0.7084 (mttt) cc_final: 0.6701 (mttp) REVERT: B 338 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5947 (mt-10) REVERT: B 340 LYS cc_start: 0.6319 (mttt) cc_final: 0.5739 (mtpp) REVERT: B 345 ASP cc_start: 0.6955 (t0) cc_final: 0.6671 (t70) REVERT: B 349 ARG cc_start: 0.6581 (mtt180) cc_final: 0.6369 (mtt-85) REVERT: B 369 LYS cc_start: 0.6992 (tttt) cc_final: 0.6752 (ttpt) REVERT: C 315 LEU cc_start: 0.7476 (mt) cc_final: 0.7223 (mp) REVERT: C 340 LYS cc_start: 0.6656 (mttt) cc_final: 0.6114 (mttt) REVERT: C 348 ASP cc_start: 0.7431 (t0) cc_final: 0.7123 (t0) REVERT: C 349 ARG cc_start: 0.6654 (mtt180) cc_final: 0.4674 (mmp-170) REVERT: C 369 LYS cc_start: 0.6519 (ttmt) cc_final: 0.6116 (ttpt) REVERT: C 373 THR cc_start: 0.7318 (m) cc_final: 0.6959 (p) REVERT: D 338 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6181 (mt-10) REVERT: D 340 LYS cc_start: 0.6716 (mttt) cc_final: 0.6144 (mtpt) REVERT: D 369 LYS cc_start: 0.7511 (tttt) cc_final: 0.7197 (ttpt) REVERT: D 372 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: D 375 LYS cc_start: 0.7481 (tttt) cc_final: 0.7036 (tppt) REVERT: E 317 LYS cc_start: 0.6703 (mttt) cc_final: 0.6330 (mttp) REVERT: E 324 SER cc_start: 0.7054 (p) cc_final: 0.6681 (t) REVERT: E 345 ASP cc_start: 0.6892 (m-30) cc_final: 0.6378 (t0) REVERT: E 369 LYS cc_start: 0.6279 (ttmt) cc_final: 0.5919 (ttpt) REVERT: F 317 LYS cc_start: 0.6866 (mttt) cc_final: 0.6598 (mttm) REVERT: F 340 LYS cc_start: 0.6290 (mttt) cc_final: 0.5789 (mtpp) REVERT: F 342 GLU cc_start: 0.6265 (pt0) cc_final: 0.5988 (pt0) REVERT: F 349 ARG cc_start: 0.6433 (mtm110) cc_final: 0.5867 (mtt180) REVERT: F 353 LYS cc_start: 0.6728 (tttt) cc_final: 0.6437 (tttp) REVERT: F 369 LYS cc_start: 0.6916 (tttt) cc_final: 0.6332 (ttpt) outliers start: 3 outliers final: 0 residues processed: 104 average time/residue: 3.3026 time to fit residues: 350.0764 Evaluate side-chains 103 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 0.0020 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 0.7966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3297 Z= 0.120 Angle : 0.450 3.724 4410 Z= 0.229 Chirality : 0.052 0.131 495 Planarity : 0.002 0.020 561 Dihedral : 4.732 12.259 435 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.54 % Allowed : 9.68 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.004 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7564 (mt) cc_final: 0.7278 (mp) REVERT: A 340 LYS cc_start: 0.6979 (mttt) cc_final: 0.6365 (mttt) REVERT: A 345 ASP cc_start: 0.7317 (m-30) cc_final: 0.7096 (t0) REVERT: A 347 LYS cc_start: 0.7652 (mmtm) cc_final: 0.7421 (mmtp) REVERT: A 349 ARG cc_start: 0.6723 (mtp85) cc_final: 0.5987 (mtt180) REVERT: A 369 LYS cc_start: 0.6890 (ttmt) cc_final: 0.6436 (ttpt) REVERT: B 311 LYS cc_start: 0.7106 (mttt) cc_final: 0.6728 (mttp) REVERT: B 338 GLU cc_start: 0.6355 (mt-10) cc_final: 0.5865 (mt-10) REVERT: B 340 LYS cc_start: 0.6366 (mttt) cc_final: 0.5778 (mtpp) REVERT: B 345 ASP cc_start: 0.6968 (t0) cc_final: 0.6665 (t70) REVERT: B 369 LYS cc_start: 0.6995 (tttt) cc_final: 0.6773 (ttpt) REVERT: C 315 LEU cc_start: 0.7475 (mt) cc_final: 0.7230 (mp) REVERT: C 340 LYS cc_start: 0.6735 (mttt) cc_final: 0.6177 (mttt) REVERT: C 345 ASP cc_start: 0.6936 (m-30) cc_final: 0.6543 (t0) REVERT: C 348 ASP cc_start: 0.7430 (t0) cc_final: 0.7120 (t0) REVERT: C 349 ARG cc_start: 0.6693 (mtt180) cc_final: 0.4740 (mmp-170) REVERT: C 369 LYS cc_start: 0.6599 (ttmt) cc_final: 0.6199 (ttpt) REVERT: C 373 THR cc_start: 0.7321 (m) cc_final: 0.6967 (p) REVERT: D 338 GLU cc_start: 0.6672 (mt-10) cc_final: 0.6100 (mt-10) REVERT: D 340 LYS cc_start: 0.6689 (mttt) cc_final: 0.6107 (mtpt) REVERT: D 351 GLN cc_start: 0.7362 (mt0) cc_final: 0.7093 (mt0) REVERT: D 369 LYS cc_start: 0.7470 (tttt) cc_final: 0.7132 (ttpt) REVERT: D 372 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6739 (tt0) REVERT: D 375 LYS cc_start: 0.7459 (tttt) cc_final: 0.7119 (ttpt) REVERT: E 317 LYS cc_start: 0.6746 (mttt) cc_final: 0.6360 (mttp) REVERT: E 324 SER cc_start: 0.6909 (p) cc_final: 0.6623 (t) REVERT: E 342 GLU cc_start: 0.6303 (tt0) cc_final: 0.5433 (tm-30) REVERT: E 345 ASP cc_start: 0.6861 (m-30) cc_final: 0.6319 (t0) REVERT: E 369 LYS cc_start: 0.6260 (ttmt) cc_final: 0.5899 (ttpt) REVERT: F 317 LYS cc_start: 0.6869 (mttt) cc_final: 0.6596 (mttm) REVERT: F 336 GLN cc_start: 0.6666 (tt0) cc_final: 0.6389 (tt0) REVERT: F 340 LYS cc_start: 0.6297 (mttt) cc_final: 0.5798 (mtpp) REVERT: F 342 GLU cc_start: 0.6215 (pt0) cc_final: 0.5944 (pt0) REVERT: F 349 ARG cc_start: 0.6231 (mtm110) cc_final: 0.5715 (mtt180) REVERT: F 353 LYS cc_start: 0.6748 (tttt) cc_final: 0.6457 (tttp) REVERT: F 369 LYS cc_start: 0.6901 (tttt) cc_final: 0.6302 (ttpt) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 3.1925 time to fit residues: 354.9878 Evaluate side-chains 106 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3297 Z= 0.173 Angle : 0.477 3.751 4410 Z= 0.245 Chirality : 0.051 0.131 495 Planarity : 0.003 0.022 561 Dihedral : 4.897 12.356 435 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.54 % Allowed : 9.68 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 330 PHE 0.004 0.001 PHE D 378 TYR 0.007 0.002 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7562 (mt) cc_final: 0.7287 (mp) REVERT: A 340 LYS cc_start: 0.7029 (mttt) cc_final: 0.6421 (mttt) REVERT: A 345 ASP cc_start: 0.7404 (m-30) cc_final: 0.7183 (t0) REVERT: A 349 ARG cc_start: 0.6689 (mtp85) cc_final: 0.6015 (mtt180) REVERT: A 369 LYS cc_start: 0.6866 (ttmt) cc_final: 0.6405 (ttpt) REVERT: B 311 LYS cc_start: 0.7095 (mttt) cc_final: 0.6715 (mttp) REVERT: B 338 GLU cc_start: 0.6318 (mt-10) cc_final: 0.5771 (mt-10) REVERT: B 345 ASP cc_start: 0.6970 (t0) cc_final: 0.6676 (t70) REVERT: B 369 LYS cc_start: 0.6993 (tttt) cc_final: 0.6765 (ttpt) REVERT: C 315 LEU cc_start: 0.7475 (mt) cc_final: 0.7226 (mp) REVERT: C 340 LYS cc_start: 0.6681 (mttt) cc_final: 0.6136 (mttt) REVERT: C 345 ASP cc_start: 0.6910 (m-30) cc_final: 0.6496 (t0) REVERT: C 349 ARG cc_start: 0.6690 (mtt180) cc_final: 0.4705 (mmp-170) REVERT: C 369 LYS cc_start: 0.6472 (ttmt) cc_final: 0.6069 (ttpt) REVERT: C 373 THR cc_start: 0.7324 (m) cc_final: 0.6969 (p) REVERT: D 338 GLU cc_start: 0.6731 (mt-10) cc_final: 0.6099 (mt-10) REVERT: D 340 LYS cc_start: 0.6728 (mttt) cc_final: 0.6145 (mtpt) REVERT: D 351 GLN cc_start: 0.7365 (mt0) cc_final: 0.7095 (mt0) REVERT: D 369 LYS cc_start: 0.7510 (tttt) cc_final: 0.7194 (ttpt) REVERT: D 372 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6628 (tt0) REVERT: D 375 LYS cc_start: 0.7434 (tttt) cc_final: 0.6994 (tppt) REVERT: E 317 LYS cc_start: 0.6715 (mttt) cc_final: 0.6335 (mttp) REVERT: E 324 SER cc_start: 0.7015 (p) cc_final: 0.6664 (t) REVERT: E 345 ASP cc_start: 0.6881 (m-30) cc_final: 0.6330 (t0) REVERT: E 369 LYS cc_start: 0.6273 (ttmt) cc_final: 0.5913 (ttpt) REVERT: F 317 LYS cc_start: 0.6862 (mttt) cc_final: 0.6591 (mttm) REVERT: F 340 LYS cc_start: 0.6313 (mttt) cc_final: 0.5813 (mtpp) REVERT: F 342 GLU cc_start: 0.6272 (pt0) cc_final: 0.6005 (pt0) REVERT: F 349 ARG cc_start: 0.6345 (mtm110) cc_final: 0.5845 (mtt180) REVERT: F 353 LYS cc_start: 0.6748 (tttt) cc_final: 0.6451 (tttp) REVERT: F 369 LYS cc_start: 0.6906 (tttt) cc_final: 0.6297 (ttpt) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 3.2383 time to fit residues: 346.7562 Evaluate side-chains 107 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN D 307 GLN F 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3297 Z= 0.151 Angle : 0.469 3.785 4410 Z= 0.241 Chirality : 0.052 0.134 495 Planarity : 0.002 0.022 561 Dihedral : 4.857 12.297 435 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.54 % Allowed : 9.95 % Favored : 89.52 % 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: -1.01 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.76 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 329 PHE 0.004 0.001 PHE D 378 TYR 0.006 0.002 TYR B 310 ARG 0.002 0.001 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7561 (mt) cc_final: 0.7290 (mp) REVERT: A 340 LYS cc_start: 0.7031 (mttt) cc_final: 0.6416 (mttt) REVERT: A 345 ASP cc_start: 0.7358 (m-30) cc_final: 0.7151 (t0) REVERT: A 347 LYS cc_start: 0.7675 (mmtm) cc_final: 0.5718 (pmtt) REVERT: A 349 ARG cc_start: 0.6690 (mtp85) cc_final: 0.6052 (mtt180) REVERT: A 369 LYS cc_start: 0.6877 (ttmt) cc_final: 0.6418 (ttpt) REVERT: B 311 LYS cc_start: 0.7088 (mttt) cc_final: 0.6705 (mttp) REVERT: B 338 GLU cc_start: 0.6333 (mt-10) cc_final: 0.5816 (mt-10) REVERT: B 345 ASP cc_start: 0.6968 (t0) cc_final: 0.6681 (t70) REVERT: B 369 LYS cc_start: 0.6991 (tttt) cc_final: 0.6738 (ttpt) REVERT: C 315 LEU cc_start: 0.7477 (mt) cc_final: 0.7226 (mp) REVERT: C 340 LYS cc_start: 0.6671 (mttt) cc_final: 0.6130 (mttt) REVERT: C 345 ASP cc_start: 0.6950 (m-30) cc_final: 0.6523 (t0) REVERT: C 349 ARG cc_start: 0.6676 (mtt180) cc_final: 0.4706 (mmp-170) REVERT: C 369 LYS cc_start: 0.6535 (ttmt) cc_final: 0.6150 (ttpt) REVERT: C 373 THR cc_start: 0.7341 (m) cc_final: 0.6980 (p) REVERT: D 338 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6089 (mt-10) REVERT: D 340 LYS cc_start: 0.6704 (mttt) cc_final: 0.6125 (mtpt) REVERT: D 369 LYS cc_start: 0.7499 (tttt) cc_final: 0.7191 (ttpt) REVERT: D 372 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6632 (tt0) REVERT: D 375 LYS cc_start: 0.7430 (tttt) cc_final: 0.7086 (ttpt) REVERT: E 317 LYS cc_start: 0.6712 (mttt) cc_final: 0.6325 (mttp) REVERT: E 324 SER cc_start: 0.7006 (p) cc_final: 0.6663 (t) REVERT: E 342 GLU cc_start: 0.6218 (tt0) cc_final: 0.5416 (tm-30) REVERT: E 345 ASP cc_start: 0.6892 (m-30) cc_final: 0.6333 (t0) REVERT: E 369 LYS cc_start: 0.6279 (ttmt) cc_final: 0.5915 (ttpt) REVERT: F 317 LYS cc_start: 0.6869 (mttt) cc_final: 0.6600 (mttm) REVERT: F 336 GLN cc_start: 0.6715 (tt0) cc_final: 0.6448 (tt0) REVERT: F 340 LYS cc_start: 0.6316 (mttt) cc_final: 0.5814 (mtpp) REVERT: F 342 GLU cc_start: 0.6213 (pt0) cc_final: 0.5960 (pt0) REVERT: F 349 ARG cc_start: 0.6354 (mtm110) cc_final: 0.5846 (mtt180) REVERT: F 353 LYS cc_start: 0.6744 (tttt) cc_final: 0.6444 (tttp) REVERT: F 369 LYS cc_start: 0.6905 (tttt) cc_final: 0.6282 (ttpt) outliers start: 2 outliers final: 1 residues processed: 104 average time/residue: 3.2201 time to fit residues: 341.5260 Evaluate side-chains 105 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain F residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.0470 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.154569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.141018 restraints weight = 8638.443| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.85 r_work: 0.3907 rms_B_bonded: 0.89 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.3697 rms_B_bonded: 4.46 restraints_weight: 0.1250 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3297 Z= 0.142 Angle : 0.465 3.744 4410 Z= 0.238 Chirality : 0.052 0.132 495 Planarity : 0.003 0.036 561 Dihedral : 4.814 12.155 435 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 10.48 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.74 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.004 0.001 PHE D 378 TYR 0.006 0.001 TYR B 310 ARG 0.004 0.001 ARG F 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6388.11 seconds wall clock time: 111 minutes 54.23 seconds (6714.23 seconds total)