Starting phenix.real_space_refine on Wed Jan 17 22:05:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/01_2024/8q8c_18250.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/01_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_18250/01_2024/8q8c_18250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/01_2024/8q8c_18250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/01_2024/8q8c_18250.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8c_18250/01_2024/8q8c_18250.pdb" } 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-1.21-5211/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: 3.89, per 1000 atoms: 0.59 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: 5.50 Conformation dependent library (CDL) restraints added in 812.8 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: 0.63 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: 2.13 Time building geometry restraints manager: 5.70 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: 2706 15.64 - 31.29: 149 31.29 - 46.93: 21 46.93 - 62.57: 57 62.57 - 78.22: 25 Dihedral angle restraints: 2958 sinusoidal: 1644 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 2955 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 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.559 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.568 1.850 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.568 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.575 1.850 ... (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 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: 3.810 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: 0.100 Extract box with map and model: 11.860 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 26.380 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- 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 : 0.599 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: 2.8240 time to fit residues: 424.7980 Evaluate side-chains 118 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 2.9990 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: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.6511 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3297 Z= 0.274 Angle : 0.587 4.148 4410 Z= 0.308 Chirality : 0.049 0.133 495 Planarity : 0.004 0.032 561 Dihedral : 5.664 13.930 435 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.89 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 329 PHE 0.005 0.001 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 : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7588 (mt) cc_final: 0.7385 (mt) REVERT: A 324 SER cc_start: 0.7143 (p) cc_final: 0.6793 (t) REVERT: A 340 LYS cc_start: 0.7115 (mttt) cc_final: 0.6466 (mttm) REVERT: A 347 LYS cc_start: 0.7074 (mttt) cc_final: 0.6871 (mmtm) REVERT: A 349 ARG cc_start: 0.6491 (mtp85) cc_final: 0.5757 (mtt180) REVERT: A 369 LYS cc_start: 0.6888 (ttmt) cc_final: 0.6449 (ttpt) REVERT: B 311 LYS cc_start: 0.7001 (mttt) cc_final: 0.6591 (mttp) REVERT: B 317 LYS cc_start: 0.6663 (mttt) cc_final: 0.6317 (mttm) REVERT: B 338 GLU cc_start: 0.6296 (mt-10) cc_final: 0.5588 (mt-10) REVERT: B 340 LYS cc_start: 0.6211 (mttt) cc_final: 0.5657 (mtpp) REVERT: B 369 LYS cc_start: 0.6853 (tttt) cc_final: 0.6637 (ttpt) REVERT: B 372 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6485 (mm-30) REVERT: C 315 LEU cc_start: 0.7538 (mt) cc_final: 0.7244 (mp) REVERT: C 340 LYS cc_start: 0.6584 (mttt) cc_final: 0.5999 (mttm) REVERT: C 345 ASP cc_start: 0.6853 (m-30) cc_final: 0.6420 (t0) REVERT: C 349 ARG cc_start: 0.6500 (mtt180) cc_final: 0.4525 (mmp-170) REVERT: C 369 LYS cc_start: 0.6349 (ttmt) cc_final: 0.5935 (ttpt) REVERT: C 372 GLU cc_start: 0.6945 (tt0) cc_final: 0.6661 (mm-30) REVERT: C 373 THR cc_start: 0.7214 (m) cc_final: 0.6722 (p) REVERT: D 311 LYS cc_start: 0.7389 (mttt) cc_final: 0.7099 (mttp) REVERT: D 338 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6117 (mt-10) REVERT: D 340 LYS cc_start: 0.6673 (mttt) cc_final: 0.6087 (mtpt) REVERT: D 369 LYS cc_start: 0.7475 (tttt) cc_final: 0.7209 (ttpt) REVERT: D 375 LYS cc_start: 0.7531 (tttt) cc_final: 0.7104 (tppt) REVERT: E 317 LYS cc_start: 0.6719 (mttt) cc_final: 0.6371 (mttm) REVERT: E 324 SER cc_start: 0.6989 (p) cc_final: 0.6733 (t) REVERT: E 345 ASP cc_start: 0.6822 (m-30) cc_final: 0.6366 (t0) REVERT: E 348 ASP cc_start: 0.7412 (t0) cc_final: 0.7164 (t0) REVERT: E 369 LYS cc_start: 0.6241 (ttmt) cc_final: 0.5831 (ttpt) REVERT: E 372 GLU cc_start: 0.6810 (tt0) cc_final: 0.6442 (tt0) REVERT: F 317 LYS cc_start: 0.6865 (mttt) cc_final: 0.6632 (mttm) REVERT: F 340 LYS cc_start: 0.6248 (mttt) cc_final: 0.5793 (mtpp) REVERT: F 342 GLU cc_start: 0.6191 (pt0) cc_final: 0.5911 (pt0) REVERT: F 349 ARG cc_start: 0.6351 (mtm110) cc_final: 0.5823 (mtt180) REVERT: F 353 LYS cc_start: 0.6545 (tttt) cc_final: 0.6261 (tttp) REVERT: F 369 LYS cc_start: 0.6968 (tttt) cc_final: 0.6354 (ttpt) REVERT: F 371 ILE cc_start: 0.7256 (mt) cc_final: 0.6955 (mm) REVERT: F 372 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6745 (mm-30) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 3.3759 time to fit residues: 399.2687 Evaluate side-chains 110 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.6529 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3297 Z= 0.270 Angle : 0.563 4.011 4410 Z= 0.292 Chirality : 0.051 0.137 495 Planarity : 0.003 0.027 561 Dihedral : 5.365 13.205 435 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.54 % Allowed : 8.06 % Favored : 91.40 % 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: -0.93 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.006 0.002 PHE E 346 TYR 0.011 0.003 TYR B 310 ARG 0.004 0.001 ARG A 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 115 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 113 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: A 347 LYS cc_start: 0.7071 (mttt) cc_final: 0.6858 (mmtm) REVERT: A 349 ARG cc_start: 0.6667 (mtp85) cc_final: 0.5894 (mtt180) REVERT: A 369 LYS cc_start: 0.6887 (ttmt) cc_final: 0.6431 (ttpt) REVERT: B 311 LYS cc_start: 0.7067 (mttt) cc_final: 0.6703 (mttp) REVERT: B 317 LYS cc_start: 0.6717 (mttt) cc_final: 0.6359 (mttm) REVERT: B 338 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5548 (mt-10) REVERT: B 340 LYS cc_start: 0.6197 (mttt) cc_final: 0.5628 (mtpp) REVERT: B 342 GLU cc_start: 0.6144 (pt0) cc_final: 0.5934 (tt0) REVERT: B 369 LYS cc_start: 0.6879 (tttt) cc_final: 0.6617 (ttpt) REVERT: C 315 LEU cc_start: 0.7437 (mt) cc_final: 0.7152 (mp) REVERT: C 340 LYS cc_start: 0.6548 (mttt) cc_final: 0.5968 (mttm) REVERT: C 349 ARG cc_start: 0.6491 (mtt180) cc_final: 0.4555 (mmp-170) REVERT: C 369 LYS cc_start: 0.6393 (ttmt) cc_final: 0.5990 (ttpt) REVERT: C 373 THR cc_start: 0.7230 (m) cc_final: 0.6834 (p) REVERT: D 311 LYS cc_start: 0.7426 (mttt) cc_final: 0.7141 (mttp) REVERT: D 338 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6103 (mt-10) REVERT: D 340 LYS cc_start: 0.6669 (mttt) cc_final: 0.6090 (mtpt) REVERT: D 369 LYS cc_start: 0.7494 (tttt) cc_final: 0.7241 (ttpt) REVERT: D 375 LYS cc_start: 0.7534 (tttt) cc_final: 0.7120 (tppt) REVERT: E 317 LYS cc_start: 0.6658 (mttt) cc_final: 0.6311 (mttm) REVERT: E 324 SER cc_start: 0.7036 (p) cc_final: 0.6729 (t) REVERT: E 345 ASP cc_start: 0.6868 (m-30) cc_final: 0.6410 (t0) REVERT: E 347 LYS cc_start: 0.7386 (mmtt) cc_final: 0.6951 (mmtt) REVERT: E 369 LYS cc_start: 0.6254 (ttmt) cc_final: 0.5847 (ttpt) REVERT: F 317 LYS cc_start: 0.6885 (mttt) cc_final: 0.6614 (mttm) REVERT: F 324 SER cc_start: 0.7810 (p) cc_final: 0.7608 (t) REVERT: F 340 LYS cc_start: 0.6236 (mttt) cc_final: 0.5770 (mtpp) REVERT: F 342 GLU cc_start: 0.6226 (pt0) cc_final: 0.5901 (pt0) REVERT: F 349 ARG cc_start: 0.6282 (mtm110) cc_final: 0.5761 (mtt180) REVERT: F 353 LYS cc_start: 0.6589 (tttt) cc_final: 0.6324 (tttp) REVERT: F 369 LYS cc_start: 0.6966 (tttt) cc_final: 0.6404 (ttpt) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 3.3109 time to fit residues: 381.4676 Evaluate side-chains 106 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- 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: 0.6528 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3297 Z= 0.182 Angle : 0.500 3.860 4410 Z= 0.256 Chirality : 0.051 0.132 495 Planarity : 0.003 0.024 561 Dihedral : 5.164 12.318 435 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.36 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: -0.92 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.69 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.002 TYR B 310 ARG 0.004 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 108 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7084 (mttt) cc_final: 0.6482 (mttt) REVERT: A 349 ARG cc_start: 0.6729 (mtp85) cc_final: 0.6029 (mtt180) REVERT: A 369 LYS cc_start: 0.6844 (ttmt) cc_final: 0.6371 (ttpt) REVERT: B 338 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5521 (mt-10) REVERT: B 340 LYS cc_start: 0.6252 (mttt) cc_final: 0.5678 (mtpp) REVERT: B 369 LYS cc_start: 0.6874 (tttt) cc_final: 0.6610 (ttpt) REVERT: C 315 LEU cc_start: 0.7429 (mt) cc_final: 0.7148 (mp) REVERT: C 340 LYS cc_start: 0.6508 (mttt) cc_final: 0.5932 (mttm) REVERT: C 345 ASP cc_start: 0.6820 (m-30) cc_final: 0.6422 (t0) REVERT: C 349 ARG cc_start: 0.6564 (mtt180) cc_final: 0.4577 (mmp-170) REVERT: C 369 LYS cc_start: 0.6390 (ttmt) cc_final: 0.5987 (ttpt) REVERT: C 373 THR cc_start: 0.7251 (m) cc_final: 0.6858 (p) REVERT: D 311 LYS cc_start: 0.7441 (mttt) cc_final: 0.7100 (mttp) REVERT: D 338 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6086 (mt-10) REVERT: D 340 LYS cc_start: 0.6714 (mttt) cc_final: 0.6131 (mtpt) REVERT: D 369 LYS cc_start: 0.7499 (tttt) cc_final: 0.7250 (ttpt) REVERT: D 375 LYS cc_start: 0.7551 (tttt) cc_final: 0.7136 (tppt) REVERT: E 317 LYS cc_start: 0.6664 (mttt) cc_final: 0.6298 (mttm) REVERT: E 324 SER cc_start: 0.7007 (p) cc_final: 0.6682 (t) REVERT: E 345 ASP cc_start: 0.6846 (m-30) cc_final: 0.6372 (t0) REVERT: E 347 LYS cc_start: 0.7366 (mmtt) cc_final: 0.6947 (mmtt) REVERT: E 369 LYS cc_start: 0.6267 (ttmt) cc_final: 0.5909 (ttpt) REVERT: F 317 LYS cc_start: 0.6863 (mttt) cc_final: 0.6598 (mttm) REVERT: F 340 LYS cc_start: 0.6262 (mttt) cc_final: 0.5792 (mtpp) REVERT: F 342 GLU cc_start: 0.6208 (pt0) cc_final: 0.5901 (pt0) REVERT: F 349 ARG cc_start: 0.6326 (mtm110) cc_final: 0.5797 (mtt180) REVERT: F 353 LYS cc_start: 0.6597 (tttt) cc_final: 0.6328 (tttp) REVERT: F 369 LYS cc_start: 0.6964 (tttt) cc_final: 0.6391 (ttpt) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 3.2579 time to fit residues: 352.2597 Evaluate side-chains 104 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- 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: 0.6523 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3297 Z= 0.120 Angle : 0.455 3.737 4410 Z= 0.230 Chirality : 0.051 0.130 495 Planarity : 0.002 0.019 561 Dihedral : 4.815 10.995 435 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.08 % Allowed : 8.87 % 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: -0.85 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.001 TYR B 310 ARG 0.002 0.000 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 111 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7540 (mt) cc_final: 0.7308 (mp) REVERT: A 340 LYS cc_start: 0.7056 (mttt) cc_final: 0.6449 (mttt) REVERT: A 342 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: A 349 ARG cc_start: 0.6683 (mtp85) cc_final: 0.6011 (mtt180) REVERT: A 369 LYS cc_start: 0.6836 (ttmt) cc_final: 0.6369 (ttpt) REVERT: B 338 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5521 (mt-10) REVERT: B 340 LYS cc_start: 0.6242 (mttt) cc_final: 0.5660 (mtpp) REVERT: B 369 LYS cc_start: 0.6882 (tttt) cc_final: 0.6641 (ttpt) REVERT: C 315 LEU cc_start: 0.7396 (mt) cc_final: 0.7109 (mp) REVERT: C 340 LYS cc_start: 0.6494 (mttt) cc_final: 0.5917 (mttm) REVERT: C 345 ASP cc_start: 0.6820 (m-30) cc_final: 0.6450 (t0) REVERT: C 349 ARG cc_start: 0.6599 (mtt180) cc_final: 0.6178 (mtt180) REVERT: C 369 LYS cc_start: 0.6413 (ttmt) cc_final: 0.6004 (ttpt) REVERT: C 373 THR cc_start: 0.7229 (m) cc_final: 0.6833 (p) REVERT: D 338 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6074 (mt-10) REVERT: D 340 LYS cc_start: 0.6677 (mttt) cc_final: 0.6084 (mtpt) REVERT: D 369 LYS cc_start: 0.7495 (tttt) cc_final: 0.7248 (ttpt) REVERT: D 375 LYS cc_start: 0.7552 (tttt) cc_final: 0.7112 (tppt) REVERT: E 317 LYS cc_start: 0.6628 (mttt) cc_final: 0.6256 (mttp) REVERT: E 324 SER cc_start: 0.6915 (p) cc_final: 0.6614 (t) REVERT: E 345 ASP cc_start: 0.6907 (m-30) cc_final: 0.6405 (t0) REVERT: E 369 LYS cc_start: 0.6285 (ttmt) cc_final: 0.5922 (ttpt) REVERT: F 317 LYS cc_start: 0.6872 (mttt) cc_final: 0.6602 (mttm) REVERT: F 340 LYS cc_start: 0.6271 (mttt) cc_final: 0.5808 (mtpp) REVERT: F 349 ARG cc_start: 0.6411 (mtm110) cc_final: 0.5830 (mtt180) REVERT: F 353 LYS cc_start: 0.6649 (tttt) cc_final: 0.6381 (tttp) REVERT: F 369 LYS cc_start: 0.6929 (tttt) cc_final: 0.6366 (ttpt) outliers start: 4 outliers final: 0 residues processed: 107 average time/residue: 3.2071 time to fit residues: 350.0017 Evaluate side-chains 107 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.6542 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3297 Z= 0.304 Angle : 0.555 3.960 4410 Z= 0.290 Chirality : 0.050 0.134 495 Planarity : 0.004 0.035 561 Dihedral : 5.270 12.520 435 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.99 (0.37), 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 0.004 0.001 HIS D 330 PHE 0.008 0.002 PHE E 346 TYR 0.011 0.002 TYR B 310 ARG 0.004 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 106 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7114 (mttt) cc_final: 0.6513 (mttt) REVERT: A 349 ARG cc_start: 0.6701 (mtp85) cc_final: 0.6054 (mtt180) REVERT: A 369 LYS cc_start: 0.6884 (ttmt) cc_final: 0.6427 (ttpt) REVERT: B 338 GLU cc_start: 0.6204 (mt-10) cc_final: 0.5527 (mt-10) REVERT: B 340 LYS cc_start: 0.6219 (mttt) cc_final: 0.5640 (mtpp) REVERT: B 369 LYS cc_start: 0.6866 (tttt) cc_final: 0.6617 (ttpt) REVERT: C 315 LEU cc_start: 0.7391 (mt) cc_final: 0.7110 (mp) REVERT: C 340 LYS cc_start: 0.6532 (mttt) cc_final: 0.5969 (mttm) REVERT: C 349 ARG cc_start: 0.6522 (mtt180) cc_final: 0.4641 (mmp-170) REVERT: C 369 LYS cc_start: 0.6470 (ttmt) cc_final: 0.6078 (ttpt) REVERT: C 373 THR cc_start: 0.7257 (m) cc_final: 0.6873 (p) REVERT: D 338 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6069 (mt-10) REVERT: D 340 LYS cc_start: 0.6692 (mttt) cc_final: 0.6130 (mtpt) REVERT: D 369 LYS cc_start: 0.7513 (tttt) cc_final: 0.7221 (ttpt) REVERT: D 375 LYS cc_start: 0.7559 (tttt) cc_final: 0.7117 (tppt) REVERT: E 317 LYS cc_start: 0.6658 (mttt) cc_final: 0.6306 (mttp) REVERT: E 324 SER cc_start: 0.7069 (p) cc_final: 0.6741 (t) REVERT: E 345 ASP cc_start: 0.6885 (m-30) cc_final: 0.6434 (t0) REVERT: E 369 LYS cc_start: 0.6285 (ttmt) cc_final: 0.5932 (ttpt) REVERT: F 317 LYS cc_start: 0.6869 (mttt) cc_final: 0.6605 (mttm) REVERT: F 340 LYS cc_start: 0.6265 (mttt) cc_final: 0.5787 (mtpp) REVERT: F 342 GLU cc_start: 0.6155 (pt0) cc_final: 0.5908 (pt0) REVERT: F 349 ARG cc_start: 0.6275 (mtm110) cc_final: 0.5798 (mtt180) REVERT: F 353 LYS cc_start: 0.6584 (tttt) cc_final: 0.6306 (tttp) REVERT: F 369 LYS cc_start: 0.6933 (tttt) cc_final: 0.6353 (ttpt) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 2.9703 time to fit residues: 314.9627 Evaluate side-chains 103 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 0.0030 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 overall best weight: 1.8596 ------------------------------------------------------------------------------- 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: 0.6533 moved from start: 0.3349 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= 0.167 Angle : 0.488 3.787 4410 Z= 0.251 Chirality : 0.051 0.133 495 Planarity : 0.003 0.035 561 Dihedral : 5.037 11.715 435 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -0.99 (0.37), 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 0.001 HIS D 330 PHE 0.004 0.001 PHE E 346 TYR 0.008 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: 2 poor density : 105 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7534 (mt) cc_final: 0.7293 (mp) REVERT: A 340 LYS cc_start: 0.7097 (mttt) cc_final: 0.6491 (mttt) REVERT: A 347 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7471 (mmtp) REVERT: A 349 ARG cc_start: 0.6707 (mtp85) cc_final: 0.6030 (mtt180) REVERT: A 369 LYS cc_start: 0.6895 (ttmt) cc_final: 0.6441 (ttpt) REVERT: B 338 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5515 (mt-10) REVERT: B 340 LYS cc_start: 0.6241 (mttt) cc_final: 0.5654 (mtpp) REVERT: B 369 LYS cc_start: 0.6856 (tttt) cc_final: 0.6619 (ttpt) REVERT: C 315 LEU cc_start: 0.7391 (mt) cc_final: 0.7102 (mp) REVERT: C 340 LYS cc_start: 0.6505 (mttt) cc_final: 0.5942 (mttm) REVERT: C 345 ASP cc_start: 0.6800 (m-30) cc_final: 0.6413 (t0) REVERT: C 349 ARG cc_start: 0.6572 (mtt180) cc_final: 0.6185 (mtt180) REVERT: C 369 LYS cc_start: 0.6494 (ttmt) cc_final: 0.6097 (ttpt) REVERT: C 373 THR cc_start: 0.7248 (m) cc_final: 0.6863 (p) REVERT: D 338 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6060 (mt-10) REVERT: D 340 LYS cc_start: 0.6669 (mttt) cc_final: 0.6110 (mtpt) REVERT: D 369 LYS cc_start: 0.7528 (tttt) cc_final: 0.7218 (ttpt) REVERT: D 375 LYS cc_start: 0.7554 (tttt) cc_final: 0.7141 (tppt) REVERT: E 317 LYS cc_start: 0.6636 (mttt) cc_final: 0.6258 (mttm) REVERT: E 324 SER cc_start: 0.7026 (p) cc_final: 0.6683 (t) REVERT: E 345 ASP cc_start: 0.6878 (m-30) cc_final: 0.6374 (t0) REVERT: E 349 ARG cc_start: 0.6423 (mtp85) cc_final: 0.6162 (mtp85) REVERT: E 369 LYS cc_start: 0.6288 (ttmt) cc_final: 0.5930 (ttpt) REVERT: F 317 LYS cc_start: 0.6865 (mttt) cc_final: 0.6601 (mttm) REVERT: F 340 LYS cc_start: 0.6284 (mttt) cc_final: 0.5801 (mtpp) REVERT: F 349 ARG cc_start: 0.6339 (mtm110) cc_final: 0.5840 (mtt180) REVERT: F 353 LYS cc_start: 0.6650 (tttt) cc_final: 0.6369 (tttp) REVERT: F 369 LYS cc_start: 0.6909 (tttt) cc_final: 0.6318 (ttpt) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 3.2378 time to fit residues: 346.6864 Evaluate side-chains 105 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- 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: 0.6528 moved from start: 0.3381 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= 0.141 Angle : 0.465 3.708 4410 Z= 0.237 Chirality : 0.051 0.131 495 Planarity : 0.003 0.020 561 Dihedral : 4.858 11.223 435 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 1.06 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: -0.94 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (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 0.002 0.001 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 109 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7533 (mt) cc_final: 0.7293 (mp) REVERT: A 340 LYS cc_start: 0.7087 (mttt) cc_final: 0.6482 (mttt) REVERT: A 347 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7508 (mmtp) REVERT: A 349 ARG cc_start: 0.6700 (mtp85) cc_final: 0.6025 (mtt180) REVERT: A 369 LYS cc_start: 0.6892 (ttmt) cc_final: 0.6436 (ttpt) REVERT: B 311 LYS cc_start: 0.7065 (mttt) cc_final: 0.6708 (mttp) REVERT: B 338 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5506 (mt-10) REVERT: B 340 LYS cc_start: 0.6254 (mttt) cc_final: 0.5661 (mtpp) REVERT: B 369 LYS cc_start: 0.6847 (tttt) cc_final: 0.6617 (ttpt) REVERT: C 315 LEU cc_start: 0.7389 (mt) cc_final: 0.7103 (mp) REVERT: C 340 LYS cc_start: 0.6520 (mttt) cc_final: 0.5962 (mttm) REVERT: C 345 ASP cc_start: 0.6822 (m-30) cc_final: 0.6448 (t0) REVERT: C 349 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6215 (mtt180) REVERT: C 369 LYS cc_start: 0.6483 (ttmt) cc_final: 0.6085 (ttpt) REVERT: C 373 THR cc_start: 0.7246 (m) cc_final: 0.6859 (p) REVERT: D 338 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6050 (mt-10) REVERT: D 340 LYS cc_start: 0.6695 (mttt) cc_final: 0.6129 (mtpt) REVERT: D 369 LYS cc_start: 0.7502 (tttt) cc_final: 0.7199 (ttpt) REVERT: D 372 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: D 375 LYS cc_start: 0.7576 (tttt) cc_final: 0.7130 (tppt) REVERT: E 317 LYS cc_start: 0.6619 (mttt) cc_final: 0.6245 (mttp) REVERT: E 324 SER cc_start: 0.6957 (p) cc_final: 0.6639 (t) REVERT: E 345 ASP cc_start: 0.6911 (m-30) cc_final: 0.6425 (t0) REVERT: E 349 ARG cc_start: 0.6446 (mtp85) cc_final: 0.6200 (mtp85) REVERT: E 369 LYS cc_start: 0.6291 (ttmt) cc_final: 0.5933 (ttpt) REVERT: F 317 LYS cc_start: 0.6870 (mttt) cc_final: 0.6599 (mttm) REVERT: F 340 LYS cc_start: 0.6316 (mttt) cc_final: 0.5819 (mtpp) REVERT: F 349 ARG cc_start: 0.6368 (mtm110) cc_final: 0.5863 (mtt180) REVERT: F 353 LYS cc_start: 0.6668 (tttt) cc_final: 0.6386 (tttp) REVERT: F 369 LYS cc_start: 0.6916 (tttt) cc_final: 0.6267 (ttpt) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 3.2662 time to fit residues: 356.5951 Evaluate side-chains 109 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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: 0.6534 moved from start: 0.3397 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= 0.178 Angle : 0.483 3.754 4410 Z= 0.249 Chirality : 0.050 0.133 495 Planarity : 0.003 0.021 561 Dihedral : 4.959 11.472 435 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.54 % Allowed : 9.41 % 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: -0.97 (0.37), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (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 D 378 TYR 0.008 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 108 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7529 (mt) cc_final: 0.7287 (mp) REVERT: A 340 LYS cc_start: 0.7101 (mttt) cc_final: 0.6504 (mttt) REVERT: A 347 LYS cc_start: 0.7702 (mmtm) cc_final: 0.7497 (mmtp) REVERT: A 349 ARG cc_start: 0.6707 (mtp85) cc_final: 0.6080 (mtt180) REVERT: A 369 LYS cc_start: 0.6886 (ttmt) cc_final: 0.6434 (ttpt) REVERT: B 311 LYS cc_start: 0.7045 (mttt) cc_final: 0.6680 (mttp) REVERT: B 338 GLU cc_start: 0.6209 (mt-10) cc_final: 0.5509 (mt-10) REVERT: B 340 LYS cc_start: 0.6247 (mttt) cc_final: 0.5653 (mtpp) REVERT: B 369 LYS cc_start: 0.6846 (tttt) cc_final: 0.6611 (ttpt) REVERT: C 315 LEU cc_start: 0.7389 (mt) cc_final: 0.7101 (mp) REVERT: C 340 LYS cc_start: 0.6533 (mttt) cc_final: 0.5973 (mttm) REVERT: C 345 ASP cc_start: 0.6813 (m-30) cc_final: 0.6429 (t0) REVERT: C 349 ARG cc_start: 0.6593 (mtt180) cc_final: 0.6213 (mtt180) REVERT: C 369 LYS cc_start: 0.6482 (ttmt) cc_final: 0.6095 (ttpt) REVERT: C 373 THR cc_start: 0.7256 (m) cc_final: 0.6871 (p) REVERT: D 338 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6039 (mt-10) REVERT: D 340 LYS cc_start: 0.6657 (mttt) cc_final: 0.6095 (mtpt) REVERT: D 369 LYS cc_start: 0.7510 (tttt) cc_final: 0.7219 (ttpt) REVERT: D 372 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6666 (tt0) REVERT: D 375 LYS cc_start: 0.7558 (tttt) cc_final: 0.7120 (tppt) REVERT: E 317 LYS cc_start: 0.6651 (mttt) cc_final: 0.6297 (mttp) REVERT: E 324 SER cc_start: 0.7017 (p) cc_final: 0.6663 (t) REVERT: E 342 GLU cc_start: 0.6252 (tt0) cc_final: 0.5372 (tm-30) REVERT: E 345 ASP cc_start: 0.6880 (m-30) cc_final: 0.6407 (t0) REVERT: E 349 ARG cc_start: 0.6437 (mtp85) cc_final: 0.6207 (mtp85) REVERT: E 369 LYS cc_start: 0.6286 (ttmt) cc_final: 0.5928 (ttpt) REVERT: F 317 LYS cc_start: 0.6867 (mttt) cc_final: 0.6596 (mttm) REVERT: F 340 LYS cc_start: 0.6300 (mttt) cc_final: 0.5812 (mtpp) REVERT: F 349 ARG cc_start: 0.6343 (mtm110) cc_final: 0.5853 (mtt180) REVERT: F 353 LYS cc_start: 0.6673 (tttt) cc_final: 0.6388 (tttp) REVERT: F 369 LYS cc_start: 0.6919 (tttt) cc_final: 0.6260 (ttpt) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 3.2466 time to fit residues: 350.9002 Evaluate side-chains 108 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.0040 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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: 0.6532 moved from start: 0.3430 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= 0.184 Angle : 0.488 3.769 4410 Z= 0.251 Chirality : 0.050 0.134 495 Planarity : 0.003 0.021 561 Dihedral : 4.989 11.570 435 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 9.41 % 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: -0.97 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.006 0.001 PHE D 378 TYR 0.008 0.002 TYR B 310 ARG 0.003 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 107 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.7527 (mt) cc_final: 0.7288 (mp) REVERT: A 340 LYS cc_start: 0.7079 (mttt) cc_final: 0.6493 (mttt) REVERT: A 349 ARG cc_start: 0.6714 (mtp85) cc_final: 0.6092 (mtt180) REVERT: A 369 LYS cc_start: 0.6890 (ttmt) cc_final: 0.6443 (ttpt) REVERT: B 311 LYS cc_start: 0.7050 (mttt) cc_final: 0.6682 (mttp) REVERT: B 338 GLU cc_start: 0.6205 (mt-10) cc_final: 0.5506 (mt-10) REVERT: B 340 LYS cc_start: 0.6245 (mttt) cc_final: 0.5649 (mtpp) REVERT: B 369 LYS cc_start: 0.6838 (tttt) cc_final: 0.6610 (ttpt) REVERT: C 315 LEU cc_start: 0.7377 (mt) cc_final: 0.7089 (mp) REVERT: C 340 LYS cc_start: 0.6543 (mttt) cc_final: 0.5980 (mttm) REVERT: C 345 ASP cc_start: 0.6827 (m-30) cc_final: 0.6432 (t0) REVERT: C 349 ARG cc_start: 0.6575 (mtt180) cc_final: 0.6196 (mtt180) REVERT: C 369 LYS cc_start: 0.6473 (ttmt) cc_final: 0.6086 (ttpt) REVERT: C 373 THR cc_start: 0.7262 (m) cc_final: 0.6872 (p) REVERT: D 338 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6037 (mt-10) REVERT: D 340 LYS cc_start: 0.6652 (mttt) cc_final: 0.6090 (mtpt) REVERT: D 369 LYS cc_start: 0.7526 (tttt) cc_final: 0.7228 (ttpt) REVERT: D 372 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6620 (tt0) REVERT: D 375 LYS cc_start: 0.7536 (tttt) cc_final: 0.7104 (tppt) REVERT: E 317 LYS cc_start: 0.6655 (mttt) cc_final: 0.6301 (mttp) REVERT: E 324 SER cc_start: 0.7025 (p) cc_final: 0.6672 (t) REVERT: E 342 GLU cc_start: 0.6214 (tt0) cc_final: 0.5362 (tm-30) REVERT: E 345 ASP cc_start: 0.6883 (m-30) cc_final: 0.6392 (t0) REVERT: E 347 LYS cc_start: 0.7333 (mmtt) cc_final: 0.7080 (mmtm) REVERT: E 349 ARG cc_start: 0.6444 (mtp85) cc_final: 0.6224 (mtp85) REVERT: E 369 LYS cc_start: 0.6295 (ttmt) cc_final: 0.5931 (ttpt) REVERT: F 317 LYS cc_start: 0.6863 (mttt) cc_final: 0.6591 (mttm) REVERT: F 340 LYS cc_start: 0.6307 (mttt) cc_final: 0.5813 (mtpp) REVERT: F 349 ARG cc_start: 0.6339 (mtm110) cc_final: 0.5830 (mtt180) REVERT: F 353 LYS cc_start: 0.6649 (tttt) cc_final: 0.6359 (tttp) REVERT: F 369 LYS cc_start: 0.6922 (tttt) cc_final: 0.6254 (ttpt) outliers start: 2 outliers final: 1 residues processed: 105 average time/residue: 3.2648 time to fit residues: 349.6050 Evaluate side-chains 107 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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: 0.0670 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.0270 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.152819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.139147 restraints weight = 8601.894| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 0.86 r_work: 0.3876 rms_B_bonded: 0.90 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 1.59 restraints_weight: 0.2500 r_work: 0.3662 rms_B_bonded: 4.46 restraints_weight: 0.1250 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3297 Z= 0.124 Angle : 0.457 4.264 4410 Z= 0.231 Chirality : 0.051 0.131 495 Planarity : 0.003 0.033 561 Dihedral : 4.711 10.862 435 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.54 % Allowed : 10.22 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.38), residues: 417 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.005 0.001 PHE D 378 TYR 0.005 0.001 TYR B 310 ARG 0.003 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6435.16 seconds wall clock time: 112 minutes 58.28 seconds (6778.28 seconds total)