Starting phenix.real_space_refine on Wed Jan 17 20:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/01_2024/8q9f_18279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/01_2024/8q9f_18279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/01_2024/8q9f_18279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/01_2024/8q9f_18279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/01_2024/8q9f_18279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/01_2024/8q9f_18279.pdb" } resolution = 1.91 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= 0.002 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 1956 2.51 5 N 576 2.21 5 O 594 1.98 5 H 3258 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 "c ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 "A ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 6390 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "c" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "A" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "D" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "E" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1065 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 3.45, per 1000 atoms: 0.54 Number of scatterers: 6390 At special positions: 0 Unit cell: (114.139, 126.498, 34.896, 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 594 8.00 N 576 7.00 C 1956 6.00 H 3258 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: 5.09 Conformation dependent library (CDL) restraints added in 698.3 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'c' and resid 313 through 314 removed outlier: 6.866A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 317 through 322 removed outlier: 6.425A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 325 through 330 removed outlier: 5.881A pdb=" N GLY B 326 " --> pdb=" O ASN c 327 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS c 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 328 " --> pdb=" O HIS c 329 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 336 through 342 Processing sheet with id=AA5, first strand: chain 'c' and resid 345 through 346 removed outlier: 6.596A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 350 through 357 removed outlier: 6.381A pdb=" N VAL B 350 " --> pdb=" O GLN c 351 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LYS c 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 352 " --> pdb=" O LYS c 353 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY c 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 354 " --> pdb=" O GLY c 355 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU c 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 356 " --> pdb=" O LEU c 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 360 through 362 removed outlier: 6.386A pdb=" N THR B 361 " --> pdb=" O HIS c 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 369 through 376 removed outlier: 6.219A pdb=" N LYS B 370 " --> pdb=" O ILE c 371 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR c 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU B 372 " --> pdb=" O THR c 373 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LYS c 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS B 374 " --> pdb=" O LYS c 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.815A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 330 removed outlier: 6.387A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY D 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N CYS C 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N ASN D 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER E 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.467A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.514A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.391A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.439A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 365 through 366 removed outlier: 4.089A pdb=" N GLY C 365 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 376 removed outlier: 6.322A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR D 373 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU C 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LYS D 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS C 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3252 1.12 - 1.29: 529 1.29 - 1.47: 1032 1.47 - 1.64: 1619 1.64 - 1.82: 6 Bond restraints: 6438 Sorted by residual: bond pdb=" NE2 HIS D 329 " pdb=" HE2 HIS D 329 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL B 350 " pdb=" H VAL B 350 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER D 352 " pdb=" H SER D 352 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASN C 359 " pdb=" H ASN C 359 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N SER B 324 " pdb=" H SER B 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 6433 not shown) Histogram of bond angle deviations from ideal: 97.00 - 103.47: 31 103.47 - 109.93: 5786 109.93 - 116.40: 2759 116.40 - 122.86: 2577 122.86 - 129.33: 601 Bond angle restraints: 11754 Sorted by residual: angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.42 117.84 -7.42 1.49e+00 4.50e-01 2.48e+01 angle pdb=" OE1 GLN c 351 " pdb=" CD GLN c 351 " pdb=" NE2 GLN c 351 " ideal model delta sigma weight residual 122.60 118.01 4.59 1.00e+00 1.00e+00 2.11e+01 angle pdb=" C LYS D 375 " pdb=" N LEU D 376 " pdb=" CA LEU D 376 " ideal model delta sigma weight residual 123.00 129.15 -6.15 1.38e+00 5.25e-01 1.98e+01 angle pdb=" CA ASN C 327 " pdb=" CB ASN C 327 " pdb=" CG ASN C 327 " ideal model delta sigma weight residual 112.60 117.00 -4.40 1.00e+00 1.00e+00 1.93e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.75 117.09 -6.34 1.46e+00 4.69e-01 1.88e+01 ... (remaining 11749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.33: 2543 13.33 - 26.66: 176 26.66 - 40.00: 57 40.00 - 53.33: 18 53.33 - 66.66: 62 Dihedral angle restraints: 2856 sinusoidal: 1596 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLY C 365 " pdb=" C GLY C 365 " pdb=" N GLY C 366 " pdb=" CA GLY C 366 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA PRO D 364 " pdb=" C PRO D 364 " pdb=" N GLY D 365 " pdb=" CA GLY D 365 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLY E 365 " pdb=" C GLY E 365 " pdb=" N GLY E 366 " pdb=" CA GLY E 366 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 2853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 217 0.059 - 0.117: 176 0.117 - 0.175: 62 0.175 - 0.234: 22 0.234 - 0.292: 3 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA ASN D 327 " pdb=" N ASN D 327 " pdb=" C ASN D 327 " pdb=" CB ASN D 327 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASN E 327 " pdb=" N ASN E 327 " pdb=" C ASN E 327 " pdb=" CB ASN E 327 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA LYS D 343 " pdb=" N LYS D 343 " pdb=" C LYS D 343 " pdb=" CB LYS D 343 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 477 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.151 2.00e-02 2.50e+03 6.29e-02 1.19e+02 pdb=" CG TYR C 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.115 2.00e-02 2.50e+03 pdb=" HD1 TYR C 310 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR C 310 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 TYR C 310 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 TYR C 310 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR c 310 " -0.118 2.00e-02 2.50e+03 4.89e-02 7.19e+01 pdb=" CG TYR c 310 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR c 310 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR c 310 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR c 310 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR c 310 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR c 310 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR c 310 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 TYR c 310 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR c 310 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR c 310 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR c 310 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 365 " 0.039 2.00e-02 2.50e+03 7.13e-02 5.09e+01 pdb=" N GLY E 366 " -0.123 2.00e-02 2.50e+03 pdb=" CA GLY E 366 " 0.034 2.00e-02 2.50e+03 pdb=" H GLY E 366 " 0.050 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 476 2.17 - 2.78: 11065 2.78 - 3.39: 17038 3.39 - 3.99: 22478 3.99 - 4.60: 31699 Nonbonded interactions: 82756 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.564 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.574 1.850 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.594 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.612 1.850 ... (remaining 82751 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'c' } 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: 6.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.250 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 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 0.036 3180 Z= 0.752 Angle : 1.778 7.419 4254 Z= 1.178 Chirality : 0.089 0.292 480 Planarity : 0.010 0.073 540 Dihedral : 10.301 63.626 1224 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -2.15 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.005 HIS B 330 PHE 0.042 0.020 PHE E 346 TYR 0.133 0.032 TYR C 310 ARG 0.005 0.002 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.586 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: symmetry clash revert: symmetry clash REVERT: B 342 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6573 (mp0) REVERT: c 342 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6497 (mp0) REVERT: c 349 ARG cc_start: 0.6672 (mtm180) cc_final: 0.5592 (mmp-170) REVERT: c 369 LYS cc_start: 0.7589 (tttt) cc_final: 0.7158 (tppp) REVERT: A 320 SER cc_start: 0.7430 (t) cc_final: 0.7135 (p) REVERT: A 342 GLU cc_start: 0.7595 (mt-10) cc_final: 0.6951 (mp0) REVERT: A 349 ARG cc_start: 0.6779 (mtm180) cc_final: 0.6536 (mtm-85) REVERT: A 369 LYS cc_start: 0.8020 (tttt) cc_final: 0.7506 (tppp) REVERT: C 331 LYS cc_start: 0.8233 (mttt) cc_final: 0.8016 (mtpp) REVERT: C 345 ASP cc_start: 0.7641 (t0) cc_final: 0.7400 (m-30) REVERT: C 347 LYS cc_start: 0.7698 (mttt) cc_final: 0.7408 (mmtp) REVERT: C 369 LYS cc_start: 0.6890 (tttt) cc_final: 0.6410 (ttmp) REVERT: C 372 GLU cc_start: 0.6563 (tt0) cc_final: 0.5996 (mm-30) REVERT: D 311 LYS cc_start: 0.5542 (mtmt) cc_final: 0.5222 (tptt) REVERT: D 342 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7073 (mt-10) REVERT: D 345 ASP cc_start: 0.7498 (t0) cc_final: 0.7190 (m-30) REVERT: D 369 LYS cc_start: 0.6873 (tttt) cc_final: 0.6411 (ttmm) REVERT: E 311 LYS cc_start: 0.5755 (mtmt) cc_final: 0.5439 (tptt) REVERT: E 320 SER cc_start: 0.7553 (t) cc_final: 0.7353 (p) REVERT: E 342 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7297 (tt0) REVERT: E 349 ARG cc_start: 0.6780 (mtm180) cc_final: 0.6203 (mtm180) REVERT: E 369 LYS cc_start: 0.7516 (tttt) cc_final: 0.6909 (ttmt) REVERT: E 372 GLU cc_start: 0.6556 (tt0) cc_final: 0.6353 (mm-30) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 2.6257 time to fit residues: 391.9250 Evaluate side-chains 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN B 362 HIS c 351 GLN c 362 HIS A 351 GLN A 362 HIS D 336 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3180 Z= 0.180 Angle : 0.600 5.917 4254 Z= 0.312 Chirality : 0.050 0.141 480 Planarity : 0.002 0.016 540 Dihedral : 6.784 18.971 420 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.56 % Allowed : 9.44 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.003 0.001 PHE D 346 TYR 0.008 0.002 TYR C 310 ARG 0.000 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 0.579 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: B 338 GLU cc_start: 0.7603 (tt0) cc_final: 0.7128 (mt-10) REVERT: B 342 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6630 (mp0) REVERT: B 343 LYS cc_start: 0.7889 (mttt) cc_final: 0.7324 (mtmt) REVERT: B 345 ASP cc_start: 0.7983 (t70) cc_final: 0.7750 (t70) REVERT: B 347 LYS cc_start: 0.7570 (mttt) cc_final: 0.7350 (mmtp) REVERT: c 342 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6469 (mp0) REVERT: c 343 LYS cc_start: 0.8100 (mttt) cc_final: 0.7604 (mtmm) REVERT: c 347 LYS cc_start: 0.7644 (mttt) cc_final: 0.7343 (mmtt) REVERT: c 349 ARG cc_start: 0.6610 (mtm180) cc_final: 0.5838 (mtt-85) REVERT: c 369 LYS cc_start: 0.7679 (tttt) cc_final: 0.7274 (tppp) REVERT: A 342 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6969 (mp0) REVERT: A 343 LYS cc_start: 0.7786 (mttt) cc_final: 0.7365 (mtmt) REVERT: C 311 LYS cc_start: 0.5010 (mtmt) cc_final: 0.4740 (tttm) REVERT: C 320 SER cc_start: 0.7666 (t) cc_final: 0.7409 (p) REVERT: C 331 LYS cc_start: 0.8196 (mttt) cc_final: 0.7992 (mtpp) REVERT: C 347 LYS cc_start: 0.7834 (mttt) cc_final: 0.7604 (mmtp) REVERT: C 369 LYS cc_start: 0.6862 (tttt) cc_final: 0.6394 (ttmp) REVERT: C 372 GLU cc_start: 0.6731 (tt0) cc_final: 0.6337 (mm-30) REVERT: D 311 LYS cc_start: 0.5489 (mtmt) cc_final: 0.5203 (tttp) REVERT: D 324 SER cc_start: 0.7905 (p) cc_final: 0.7615 (m) REVERT: D 342 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7049 (mt-10) REVERT: D 369 LYS cc_start: 0.6929 (tttt) cc_final: 0.6444 (ttmm) REVERT: D 372 GLU cc_start: 0.7513 (tt0) cc_final: 0.6959 (mm-30) REVERT: D 375 LYS cc_start: 0.5725 (ttpt) cc_final: 0.5287 (ttmm) REVERT: E 311 LYS cc_start: 0.5745 (mtmt) cc_final: 0.5407 (tptt) REVERT: E 342 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7179 (tt0) REVERT: E 347 LYS cc_start: 0.7995 (mttt) cc_final: 0.7713 (mmtp) REVERT: E 369 LYS cc_start: 0.7523 (tttt) cc_final: 0.6902 (ttmt) REVERT: E 372 GLU cc_start: 0.6363 (tt0) cc_final: 0.6159 (mm-30) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 3.2474 time to fit residues: 377.3827 Evaluate side-chains 97 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 351 GLN A 351 GLN E 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3180 Z= 0.231 Angle : 0.610 6.608 4254 Z= 0.318 Chirality : 0.050 0.147 480 Planarity : 0.003 0.014 540 Dihedral : 6.355 18.952 420 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.83 % Allowed : 10.28 % Favored : 88.89 % 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: -2.09 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.005 0.002 PHE C 346 TYR 0.013 0.002 TYR C 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6891 (m) cc_final: 0.6250 (p) REVERT: B 338 GLU cc_start: 0.7586 (tt0) cc_final: 0.7328 (mt-10) REVERT: B 342 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6585 (mp0) REVERT: B 343 LYS cc_start: 0.7929 (mttt) cc_final: 0.7374 (mtmt) REVERT: B 345 ASP cc_start: 0.7954 (t70) cc_final: 0.7733 (t70) REVERT: B 347 LYS cc_start: 0.7531 (mttt) cc_final: 0.7324 (mmtp) REVERT: c 342 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6766 (mp0) REVERT: c 343 LYS cc_start: 0.8160 (mttt) cc_final: 0.7631 (mtmm) REVERT: c 347 LYS cc_start: 0.7644 (mttt) cc_final: 0.7330 (mmtt) REVERT: c 349 ARG cc_start: 0.6538 (mtm180) cc_final: 0.5436 (mmp-170) REVERT: A 342 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6670 (mp0) REVERT: A 343 LYS cc_start: 0.7886 (mttt) cc_final: 0.7469 (mtmt) REVERT: A 347 LYS cc_start: 0.7719 (mttt) cc_final: 0.7257 (mppt) REVERT: A 349 ARG cc_start: 0.6848 (mtm180) cc_final: 0.6583 (mtp180) REVERT: A 369 LYS cc_start: 0.7951 (tttt) cc_final: 0.7420 (tppp) REVERT: C 311 LYS cc_start: 0.5158 (mtmt) cc_final: 0.4907 (tttm) REVERT: C 320 SER cc_start: 0.7573 (t) cc_final: 0.7222 (p) REVERT: C 331 LYS cc_start: 0.8192 (mttt) cc_final: 0.7977 (mtpp) REVERT: C 342 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6772 (tt0) REVERT: C 347 LYS cc_start: 0.7822 (mttt) cc_final: 0.7542 (mmtp) REVERT: C 369 LYS cc_start: 0.6892 (tttt) cc_final: 0.6396 (ttmp) REVERT: C 372 GLU cc_start: 0.6916 (tt0) cc_final: 0.6495 (mm-30) REVERT: D 311 LYS cc_start: 0.5532 (mtmt) cc_final: 0.5210 (tttp) REVERT: D 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6920 (tt0) REVERT: D 345 ASP cc_start: 0.7982 (t70) cc_final: 0.7667 (t0) REVERT: D 369 LYS cc_start: 0.6919 (tttt) cc_final: 0.6412 (ttmm) REVERT: D 372 GLU cc_start: 0.7595 (tt0) cc_final: 0.6946 (mm-30) REVERT: D 375 LYS cc_start: 0.5395 (ttpt) cc_final: 0.5001 (ttmm) REVERT: E 311 LYS cc_start: 0.5785 (mtmt) cc_final: 0.5463 (tttm) REVERT: E 342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7172 (tt0) REVERT: E 347 LYS cc_start: 0.7966 (mttt) cc_final: 0.7682 (mmtp) REVERT: E 369 LYS cc_start: 0.7537 (tttt) cc_final: 0.7005 (ttmp) outliers start: 3 outliers final: 2 residues processed: 107 average time/residue: 3.2317 time to fit residues: 353.0527 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 374 HIS A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3180 Z= 0.156 Angle : 0.539 5.718 4254 Z= 0.277 Chirality : 0.049 0.144 480 Planarity : 0.002 0.019 540 Dihedral : 5.873 18.981 420 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.83 % Allowed : 11.67 % Favored : 87.50 % 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: -2.09 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.001 PHE C 346 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6802 (m) cc_final: 0.6217 (p) REVERT: B 338 GLU cc_start: 0.7577 (tt0) cc_final: 0.7340 (mt-10) REVERT: B 342 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6525 (mp0) REVERT: B 343 LYS cc_start: 0.7934 (mttt) cc_final: 0.7382 (mtmt) REVERT: B 347 LYS cc_start: 0.7537 (mttt) cc_final: 0.7330 (mmtp) REVERT: c 342 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6387 (mp0) REVERT: c 343 LYS cc_start: 0.8168 (mttt) cc_final: 0.7645 (mtmm) REVERT: c 347 LYS cc_start: 0.7629 (mttt) cc_final: 0.7322 (mmtt) REVERT: c 349 ARG cc_start: 0.6600 (mtm180) cc_final: 0.5482 (mmp-170) REVERT: c 369 LYS cc_start: 0.7778 (tttt) cc_final: 0.7352 (tppp) REVERT: A 342 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6669 (mp0) REVERT: A 343 LYS cc_start: 0.7904 (mttt) cc_final: 0.7491 (mtmt) REVERT: A 347 LYS cc_start: 0.7763 (mttt) cc_final: 0.7315 (mppt) REVERT: A 349 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6623 (mtp180) REVERT: C 311 LYS cc_start: 0.5006 (mtmt) cc_final: 0.4712 (tttm) REVERT: C 320 SER cc_start: 0.7557 (t) cc_final: 0.7218 (p) REVERT: C 331 LYS cc_start: 0.8195 (mttt) cc_final: 0.7975 (mtpp) REVERT: C 342 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6746 (tt0) REVERT: C 347 LYS cc_start: 0.7792 (mttt) cc_final: 0.7518 (mmtp) REVERT: C 369 LYS cc_start: 0.6896 (tttt) cc_final: 0.6411 (ttmp) REVERT: C 372 GLU cc_start: 0.6804 (tt0) cc_final: 0.6461 (mm-30) REVERT: D 311 LYS cc_start: 0.5529 (mtmt) cc_final: 0.5204 (tttp) REVERT: D 342 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6936 (tt0) REVERT: D 345 ASP cc_start: 0.7953 (t70) cc_final: 0.7608 (t70) REVERT: D 369 LYS cc_start: 0.6945 (tttt) cc_final: 0.6428 (ttmm) REVERT: D 372 GLU cc_start: 0.7599 (tt0) cc_final: 0.6986 (mm-30) REVERT: D 375 LYS cc_start: 0.5638 (ttpt) cc_final: 0.5253 (ttmm) REVERT: E 311 LYS cc_start: 0.5873 (mtmt) cc_final: 0.5572 (ttpt) REVERT: E 342 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7212 (tt0) REVERT: E 347 LYS cc_start: 0.7973 (mttt) cc_final: 0.7701 (mmtp) REVERT: E 369 LYS cc_start: 0.7580 (tttt) cc_final: 0.7046 (ttmp) outliers start: 3 outliers final: 2 residues processed: 108 average time/residue: 3.3551 time to fit residues: 369.2862 Evaluate side-chains 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 374 HIS A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3180 Z= 0.220 Angle : 0.565 6.007 4254 Z= 0.294 Chirality : 0.049 0.152 480 Planarity : 0.002 0.017 540 Dihedral : 5.967 18.446 420 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.11 % Allowed : 11.11 % Favored : 87.78 % 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: -2.12 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 329 PHE 0.005 0.001 PHE C 346 TYR 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6981 (m) cc_final: 0.6377 (p) REVERT: B 338 GLU cc_start: 0.7577 (tt0) cc_final: 0.7373 (mt-10) REVERT: B 342 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6509 (mp0) REVERT: B 343 LYS cc_start: 0.7898 (mttt) cc_final: 0.7367 (mtmt) REVERT: B 347 LYS cc_start: 0.7591 (mttt) cc_final: 0.7217 (mmtt) REVERT: c 342 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6277 (mp0) REVERT: c 347 LYS cc_start: 0.7604 (mttt) cc_final: 0.7338 (mmtt) REVERT: c 349 ARG cc_start: 0.6580 (mtm180) cc_final: 0.5463 (mmp-170) REVERT: c 369 LYS cc_start: 0.7787 (tttt) cc_final: 0.7354 (tppp) REVERT: A 342 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6661 (mp0) REVERT: A 343 LYS cc_start: 0.7871 (mttt) cc_final: 0.7459 (mtmt) REVERT: A 347 LYS cc_start: 0.7791 (mttt) cc_final: 0.7315 (mppt) REVERT: A 349 ARG cc_start: 0.6888 (mtm180) cc_final: 0.6580 (mtp180) REVERT: C 311 LYS cc_start: 0.5198 (mtmt) cc_final: 0.4859 (mttt) REVERT: C 320 SER cc_start: 0.7639 (t) cc_final: 0.7274 (p) REVERT: C 331 LYS cc_start: 0.8192 (mttt) cc_final: 0.7970 (mtpp) REVERT: C 347 LYS cc_start: 0.7738 (mttt) cc_final: 0.7463 (mmtp) REVERT: C 369 LYS cc_start: 0.6885 (tttt) cc_final: 0.6407 (ttmp) REVERT: C 372 GLU cc_start: 0.6925 (tt0) cc_final: 0.6528 (mm-30) REVERT: D 311 LYS cc_start: 0.5537 (mtmt) cc_final: 0.5287 (tttm) REVERT: D 342 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6976 (tt0) REVERT: D 345 ASP cc_start: 0.7910 (t70) cc_final: 0.7503 (t0) REVERT: D 369 LYS cc_start: 0.6951 (tttt) cc_final: 0.6417 (ttmm) REVERT: D 372 GLU cc_start: 0.7605 (tt0) cc_final: 0.7000 (mm-30) REVERT: D 375 LYS cc_start: 0.5358 (ttpt) cc_final: 0.4978 (ttmm) REVERT: E 311 LYS cc_start: 0.5881 (mtmt) cc_final: 0.5662 (ttpt) REVERT: E 316 SER cc_start: 0.6355 (OUTLIER) cc_final: 0.5946 (p) REVERT: E 342 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7220 (tt0) REVERT: E 347 LYS cc_start: 0.7955 (mttt) cc_final: 0.7672 (mmtp) REVERT: E 369 LYS cc_start: 0.7530 (tttt) cc_final: 0.7017 (ttmp) outliers start: 4 outliers final: 0 residues processed: 108 average time/residue: 3.2176 time to fit residues: 354.7878 Evaluate side-chains 99 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 374 HIS A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3180 Z= 0.205 Angle : 0.563 6.209 4254 Z= 0.290 Chirality : 0.049 0.149 480 Planarity : 0.003 0.025 540 Dihedral : 5.895 19.928 420 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.56 % Allowed : 10.56 % Favored : 88.89 % 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: -2.14 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 329 PHE 0.005 0.001 PHE C 346 TYR 0.010 0.002 TYR C 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6989 (m) cc_final: 0.6410 (p) REVERT: B 342 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6473 (mp0) REVERT: B 343 LYS cc_start: 0.7873 (mttt) cc_final: 0.7353 (mtmt) REVERT: B 347 LYS cc_start: 0.7612 (mttt) cc_final: 0.7234 (mmtt) REVERT: B 370 LYS cc_start: 0.6610 (mttp) cc_final: 0.6399 (mttp) REVERT: c 342 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6264 (mp0) REVERT: c 347 LYS cc_start: 0.7611 (mttt) cc_final: 0.7344 (mmtt) REVERT: c 349 ARG cc_start: 0.6601 (mtm180) cc_final: 0.5476 (mmp-170) REVERT: c 369 LYS cc_start: 0.7792 (tttt) cc_final: 0.7351 (tppp) REVERT: A 342 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6676 (mp0) REVERT: A 343 LYS cc_start: 0.7878 (mttt) cc_final: 0.7473 (mtmt) REVERT: A 347 LYS cc_start: 0.7783 (mttt) cc_final: 0.7258 (mptt) REVERT: A 349 ARG cc_start: 0.6897 (mtm180) cc_final: 0.6476 (mtp180) REVERT: A 369 LYS cc_start: 0.7961 (tttt) cc_final: 0.7473 (tppp) REVERT: C 311 LYS cc_start: 0.5174 (mtmt) cc_final: 0.4832 (mttt) REVERT: C 320 SER cc_start: 0.7634 (t) cc_final: 0.7278 (p) REVERT: C 331 LYS cc_start: 0.8189 (mttt) cc_final: 0.7967 (mtpp) REVERT: C 347 LYS cc_start: 0.7756 (mttt) cc_final: 0.7480 (mmtp) REVERT: C 369 LYS cc_start: 0.6873 (tttt) cc_final: 0.6397 (ttmp) REVERT: C 372 GLU cc_start: 0.6905 (tt0) cc_final: 0.6544 (mm-30) REVERT: D 311 LYS cc_start: 0.5538 (mtmt) cc_final: 0.5296 (tttm) REVERT: D 342 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6985 (tt0) REVERT: D 345 ASP cc_start: 0.7919 (t70) cc_final: 0.7507 (t0) REVERT: D 369 LYS cc_start: 0.6966 (tttt) cc_final: 0.6418 (ttmm) REVERT: D 372 GLU cc_start: 0.7578 (tt0) cc_final: 0.6958 (mm-30) REVERT: D 375 LYS cc_start: 0.5421 (ttpt) cc_final: 0.5071 (ttmm) REVERT: E 311 LYS cc_start: 0.5915 (mtmt) cc_final: 0.5693 (ttpt) REVERT: E 316 SER cc_start: 0.6343 (OUTLIER) cc_final: 0.5924 (p) REVERT: E 342 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7225 (tt0) REVERT: E 347 LYS cc_start: 0.7971 (mttt) cc_final: 0.7683 (mmtp) REVERT: E 369 LYS cc_start: 0.7530 (tttt) cc_final: 0.7000 (ttmp) outliers start: 2 outliers final: 0 residues processed: 107 average time/residue: 3.2859 time to fit residues: 358.8499 Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 374 HIS A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3180 Z= 0.217 Angle : 0.576 6.444 4254 Z= 0.296 Chirality : 0.049 0.153 480 Planarity : 0.003 0.029 540 Dihedral : 5.864 19.486 420 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.28 % Allowed : 11.11 % Favored : 88.61 % 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: -2.12 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 329 PHE 0.005 0.001 PHE C 346 TYR 0.011 0.002 TYR C 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.7033 (m) cc_final: 0.6466 (p) REVERT: B 342 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6459 (mp0) REVERT: B 343 LYS cc_start: 0.7872 (mttt) cc_final: 0.7350 (mtmt) REVERT: B 347 LYS cc_start: 0.7604 (mttt) cc_final: 0.7227 (mmtt) REVERT: B 370 LYS cc_start: 0.6613 (mttp) cc_final: 0.6410 (mttt) REVERT: c 342 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6259 (mp0) REVERT: c 347 LYS cc_start: 0.7607 (mttt) cc_final: 0.7338 (mmtt) REVERT: c 349 ARG cc_start: 0.6632 (mtm180) cc_final: 0.5482 (mmp-170) REVERT: c 369 LYS cc_start: 0.7794 (tttt) cc_final: 0.7361 (tppp) REVERT: c 370 LYS cc_start: 0.6981 (mttp) cc_final: 0.6684 (mmtp) REVERT: A 342 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6653 (mp0) REVERT: A 343 LYS cc_start: 0.7880 (mttt) cc_final: 0.7460 (mtmt) REVERT: A 347 LYS cc_start: 0.7798 (mttt) cc_final: 0.7317 (mptt) REVERT: A 349 ARG cc_start: 0.6912 (mtm180) cc_final: 0.6542 (mtp180) REVERT: A 369 LYS cc_start: 0.8004 (tttt) cc_final: 0.7485 (tppp) REVERT: C 311 LYS cc_start: 0.5149 (mtmt) cc_final: 0.4892 (tttm) REVERT: C 320 SER cc_start: 0.7663 (t) cc_final: 0.7291 (p) REVERT: C 331 LYS cc_start: 0.8197 (mttt) cc_final: 0.7973 (mtpp) REVERT: C 347 LYS cc_start: 0.7701 (mttt) cc_final: 0.7465 (mmtp) REVERT: C 369 LYS cc_start: 0.6839 (tttt) cc_final: 0.6374 (ttmp) REVERT: C 372 GLU cc_start: 0.6935 (tt0) cc_final: 0.6527 (mm-30) REVERT: D 311 LYS cc_start: 0.5534 (mtmt) cc_final: 0.5195 (tttm) REVERT: D 342 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7005 (tt0) REVERT: D 345 ASP cc_start: 0.7888 (t70) cc_final: 0.7469 (t0) REVERT: D 369 LYS cc_start: 0.6969 (tttt) cc_final: 0.6409 (ttmm) REVERT: D 372 GLU cc_start: 0.7598 (tt0) cc_final: 0.7283 (tt0) REVERT: E 311 LYS cc_start: 0.5889 (mtmt) cc_final: 0.5647 (ttpt) REVERT: E 314 ASP cc_start: 0.4942 (t70) cc_final: 0.4632 (t70) REVERT: E 316 SER cc_start: 0.6324 (OUTLIER) cc_final: 0.5946 (p) REVERT: E 342 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7256 (tt0) REVERT: E 347 LYS cc_start: 0.7983 (mttt) cc_final: 0.7673 (mmtp) REVERT: E 369 LYS cc_start: 0.7541 (tttt) cc_final: 0.7000 (ttmp) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 3.2255 time to fit residues: 342.1835 Evaluate side-chains 101 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN A 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3180 Z= 0.139 Angle : 0.516 6.107 4254 Z= 0.259 Chirality : 0.049 0.139 480 Planarity : 0.002 0.022 540 Dihedral : 5.424 20.100 420 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.28 % Allowed : 11.39 % Favored : 88.33 % 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: -2.01 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.004 0.001 PHE C 346 TYR 0.005 0.001 TYR c 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6875 (m) cc_final: 0.6348 (p) REVERT: B 342 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6450 (mp0) REVERT: B 343 LYS cc_start: 0.7910 (mttt) cc_final: 0.7415 (mtmt) REVERT: B 347 LYS cc_start: 0.7556 (mttt) cc_final: 0.7194 (mmtt) REVERT: c 338 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7226 (mp0) REVERT: c 342 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6292 (mp0) REVERT: c 347 LYS cc_start: 0.7566 (mttt) cc_final: 0.7300 (mmtt) REVERT: c 349 ARG cc_start: 0.6678 (mtm180) cc_final: 0.5531 (mmp-170) REVERT: c 369 LYS cc_start: 0.7778 (tttt) cc_final: 0.7348 (tppp) REVERT: A 342 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6631 (mp0) REVERT: A 343 LYS cc_start: 0.7883 (mttt) cc_final: 0.7458 (mtmt) REVERT: A 347 LYS cc_start: 0.7763 (mttt) cc_final: 0.7284 (mppt) REVERT: A 349 ARG cc_start: 0.6907 (mtm180) cc_final: 0.6555 (mtp180) REVERT: A 369 LYS cc_start: 0.8001 (tttt) cc_final: 0.7474 (tppp) REVERT: C 311 LYS cc_start: 0.4989 (mtmt) cc_final: 0.4720 (tttm) REVERT: C 320 SER cc_start: 0.7648 (t) cc_final: 0.7272 (p) REVERT: C 331 LYS cc_start: 0.8185 (mttt) cc_final: 0.7958 (mtpp) REVERT: C 342 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6738 (tt0) REVERT: C 347 LYS cc_start: 0.7722 (mttt) cc_final: 0.7464 (mmtp) REVERT: C 369 LYS cc_start: 0.6832 (tttt) cc_final: 0.6360 (ttmp) REVERT: C 372 GLU cc_start: 0.6915 (tt0) cc_final: 0.6546 (mm-30) REVERT: D 311 LYS cc_start: 0.5520 (mtmt) cc_final: 0.5196 (tttm) REVERT: D 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6996 (tt0) REVERT: D 345 ASP cc_start: 0.7882 (t70) cc_final: 0.7490 (t0) REVERT: D 369 LYS cc_start: 0.6997 (tttt) cc_final: 0.6437 (ttmm) REVERT: D 372 GLU cc_start: 0.7549 (tt0) cc_final: 0.7259 (tt0) REVERT: E 311 LYS cc_start: 0.5933 (mtmt) cc_final: 0.5673 (ttpt) REVERT: E 314 ASP cc_start: 0.4946 (t70) cc_final: 0.4662 (t70) REVERT: E 316 SER cc_start: 0.6359 (OUTLIER) cc_final: 0.6030 (p) REVERT: E 342 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7224 (tt0) REVERT: E 369 LYS cc_start: 0.7565 (tttt) cc_final: 0.7027 (ttmp) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 3.4055 time to fit residues: 361.3183 Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 368 ASN A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3180 Z= 0.128 Angle : 0.493 5.859 4254 Z= 0.247 Chirality : 0.049 0.140 480 Planarity : 0.002 0.029 540 Dihedral : 5.128 19.175 420 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.28 % Allowed : 11.94 % Favored : 87.78 % 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: -1.96 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 362 PHE 0.004 0.001 PHE C 346 TYR 0.006 0.001 TYR E 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6767 (m) cc_final: 0.6362 (p) REVERT: B 342 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6448 (mp0) REVERT: B 343 LYS cc_start: 0.7905 (mttt) cc_final: 0.7410 (mtmt) REVERT: B 347 LYS cc_start: 0.7546 (mttt) cc_final: 0.7138 (mmtp) REVERT: c 338 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7225 (mp0) REVERT: c 342 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6281 (mp0) REVERT: c 347 LYS cc_start: 0.7562 (mttt) cc_final: 0.7328 (mmtt) REVERT: c 349 ARG cc_start: 0.6713 (mtm180) cc_final: 0.5546 (mmp-170) REVERT: c 369 LYS cc_start: 0.7777 (tttt) cc_final: 0.7375 (tppp) REVERT: A 342 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6651 (mp0) REVERT: A 343 LYS cc_start: 0.7892 (mttt) cc_final: 0.7465 (mtmt) REVERT: A 347 LYS cc_start: 0.7755 (mttt) cc_final: 0.7232 (mppt) REVERT: A 349 ARG cc_start: 0.6922 (mtm180) cc_final: 0.6555 (mtp180) REVERT: C 311 LYS cc_start: 0.5003 (mtmt) cc_final: 0.4749 (tttm) REVERT: C 320 SER cc_start: 0.7516 (t) cc_final: 0.7243 (p) REVERT: C 331 LYS cc_start: 0.8213 (mttt) cc_final: 0.7981 (mtpp) REVERT: C 342 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6753 (tt0) REVERT: C 347 LYS cc_start: 0.7692 (mttt) cc_final: 0.7481 (mmtp) REVERT: C 369 LYS cc_start: 0.6828 (tttt) cc_final: 0.6367 (ttmp) REVERT: C 372 GLU cc_start: 0.6878 (tt0) cc_final: 0.6574 (mm-30) REVERT: D 311 LYS cc_start: 0.5529 (mtmt) cc_final: 0.5202 (tttm) REVERT: D 342 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6986 (tt0) REVERT: D 345 ASP cc_start: 0.7830 (t70) cc_final: 0.7457 (t0) REVERT: D 369 LYS cc_start: 0.6970 (tttt) cc_final: 0.6421 (ttmm) REVERT: D 372 GLU cc_start: 0.7524 (tt0) cc_final: 0.6953 (mm-30) REVERT: E 311 LYS cc_start: 0.5893 (mtmt) cc_final: 0.5610 (ttpt) REVERT: E 316 SER cc_start: 0.6399 (OUTLIER) cc_final: 0.6071 (p) REVERT: E 340 LYS cc_start: 0.8265 (mttt) cc_final: 0.8057 (mttm) REVERT: E 342 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7198 (tt0) REVERT: E 345 ASP cc_start: 0.8058 (t70) cc_final: 0.7183 (t70) REVERT: E 347 LYS cc_start: 0.8012 (mttt) cc_final: 0.7722 (mmtp) REVERT: E 369 LYS cc_start: 0.7562 (tttt) cc_final: 0.7019 (ttmp) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 3.2434 time to fit residues: 350.5490 Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN A 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3180 Z= 0.160 Angle : 0.539 6.420 4254 Z= 0.269 Chirality : 0.049 0.147 480 Planarity : 0.002 0.018 540 Dihedral : 5.328 19.925 420 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.28 % Allowed : 12.50 % Favored : 87.22 % 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: -1.96 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.005 0.001 PHE C 346 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6933 (m) cc_final: 0.6419 (p) REVERT: B 342 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6453 (mp0) REVERT: B 343 LYS cc_start: 0.7895 (mttt) cc_final: 0.7406 (mtmt) REVERT: B 347 LYS cc_start: 0.7592 (mttt) cc_final: 0.7170 (mmtp) REVERT: c 338 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7236 (mp0) REVERT: c 342 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6280 (mp0) REVERT: c 347 LYS cc_start: 0.7568 (mttt) cc_final: 0.7330 (mmtt) REVERT: c 349 ARG cc_start: 0.6702 (mtm180) cc_final: 0.5527 (mmp-170) REVERT: c 369 LYS cc_start: 0.7783 (tttt) cc_final: 0.7361 (tppp) REVERT: A 342 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6630 (mp0) REVERT: A 343 LYS cc_start: 0.7889 (mttt) cc_final: 0.7465 (mtmt) REVERT: A 347 LYS cc_start: 0.7776 (mttt) cc_final: 0.7302 (mppt) REVERT: A 349 ARG cc_start: 0.6919 (mtm180) cc_final: 0.6519 (mtp180) REVERT: C 311 LYS cc_start: 0.5017 (mtmt) cc_final: 0.4751 (tttm) REVERT: C 320 SER cc_start: 0.7625 (t) cc_final: 0.7303 (p) REVERT: C 331 LYS cc_start: 0.8194 (mttt) cc_final: 0.7965 (mtpp) REVERT: C 342 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6737 (tt0) REVERT: C 347 LYS cc_start: 0.7727 (mttt) cc_final: 0.7477 (mmtp) REVERT: C 369 LYS cc_start: 0.6810 (tttt) cc_final: 0.6343 (ttmp) REVERT: C 372 GLU cc_start: 0.6884 (tt0) cc_final: 0.6593 (mm-30) REVERT: D 311 LYS cc_start: 0.5530 (mtmt) cc_final: 0.5203 (tttm) REVERT: D 342 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6964 (tt0) REVERT: D 345 ASP cc_start: 0.7872 (t70) cc_final: 0.7499 (t0) REVERT: D 369 LYS cc_start: 0.6954 (tttt) cc_final: 0.6390 (ttmm) REVERT: D 372 GLU cc_start: 0.7546 (tt0) cc_final: 0.6949 (mm-30) REVERT: E 311 LYS cc_start: 0.5882 (mtmt) cc_final: 0.5607 (ttpt) REVERT: E 314 ASP cc_start: 0.5158 (t70) cc_final: 0.4900 (t70) REVERT: E 316 SER cc_start: 0.6359 (OUTLIER) cc_final: 0.6018 (p) REVERT: E 342 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7221 (tt0) REVERT: E 369 LYS cc_start: 0.7583 (tttt) cc_final: 0.7050 (ttmp) outliers start: 1 outliers final: 0 residues processed: 101 average time/residue: 3.2396 time to fit residues: 333.6763 Evaluate side-chains 100 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN A 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.196890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.147293 restraints weight = 7011.391| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.47 r_work: 0.4051 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3986 rms_B_bonded: 2.02 restraints_weight: 0.2500 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3180 Z= 0.136 Angle : 0.502 6.164 4254 Z= 0.251 Chirality : 0.049 0.139 480 Planarity : 0.002 0.017 540 Dihedral : 5.127 19.480 420 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.28 % Allowed : 12.50 % Favored : 87.22 % 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: -1.96 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE D 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6189.60 seconds wall clock time: 108 minutes 50.26 seconds (6530.26 seconds total)