Starting phenix.real_space_refine on Mon Mar 11 00:35:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/03_2024/8q9f_18279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/03_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_18279/03_2024/8q9f_18279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/03_2024/8q9f_18279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/03_2024/8q9f_18279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/03_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-dev-5265/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: 3.35, per 1000 atoms: 0.52 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: 4.61 Conformation dependent library (CDL) restraints added in 594.1 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: 0.65 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: 2.15 Time building geometry restraints manager: 4.83 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: 2562 13.33 - 26.66: 198 26.66 - 40.00: 74 40.00 - 53.33: 49 53.33 - 66.66: 81 Dihedral angle restraints: 2964 sinusoidal: 1704 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 2961 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: 3.220 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: 0.090 Extract box with map and model: 11.920 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.290 Find NCS groups from input model: 0.280 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:12.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.840 ------------------------------------------------------------------------------- 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 : 0.569 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: 2.6912 time to fit residues: 401.7748 Evaluate side-chains 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.7370 moved from start: 0.3617 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= 0.181 Angle : 0.603 6.159 4254 Z= 0.311 Chirality : 0.048 0.137 480 Planarity : 0.002 0.018 540 Dihedral : 6.810 19.278 420 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: -1.93 (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 0.001 0.000 ARG D 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 117 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 338 GLU cc_start: 0.7599 (tt0) cc_final: 0.7166 (mt-10) REVERT: B 342 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6574 (mp0) REVERT: B 343 LYS cc_start: 0.7896 (mttt) cc_final: 0.7325 (mtmt) REVERT: B 345 ASP cc_start: 0.7973 (t70) cc_final: 0.7649 (t70) REVERT: B 347 LYS cc_start: 0.7579 (mttt) cc_final: 0.7345 (mmtp) REVERT: c 342 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6456 (mp0) REVERT: c 343 LYS cc_start: 0.8097 (mttt) cc_final: 0.7593 (mtmm) REVERT: c 347 LYS cc_start: 0.7653 (mttt) cc_final: 0.7135 (mppt) REVERT: c 349 ARG cc_start: 0.6601 (mtm180) cc_final: 0.5829 (mtt-85) REVERT: c 369 LYS cc_start: 0.7690 (tttt) cc_final: 0.7285 (tppp) REVERT: A 342 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6658 (mp0) REVERT: A 343 LYS cc_start: 0.7849 (mttt) cc_final: 0.7412 (mtmt) REVERT: A 369 LYS cc_start: 0.7960 (tttt) cc_final: 0.7424 (tppp) REVERT: C 311 LYS cc_start: 0.5011 (mtmt) cc_final: 0.4766 (tttm) REVERT: C 320 SER cc_start: 0.7630 (t) cc_final: 0.7363 (p) REVERT: C 331 LYS cc_start: 0.8189 (mttt) cc_final: 0.7983 (mtpp) REVERT: C 347 LYS cc_start: 0.7842 (mttt) cc_final: 0.7563 (mmtp) REVERT: C 369 LYS cc_start: 0.6868 (tttt) cc_final: 0.6402 (ttmp) REVERT: C 372 GLU cc_start: 0.6821 (tt0) cc_final: 0.6377 (mm-30) REVERT: D 311 LYS cc_start: 0.5515 (mtmt) cc_final: 0.5219 (tttp) REVERT: D 324 SER cc_start: 0.7857 (p) cc_final: 0.7597 (m) REVERT: D 340 LYS cc_start: 0.8010 (mttt) cc_final: 0.7616 (mttm) REVERT: D 342 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7040 (mt-10) REVERT: D 345 ASP cc_start: 0.7629 (t0) cc_final: 0.7113 (t0) REVERT: D 369 LYS cc_start: 0.6921 (tttt) cc_final: 0.6431 (ttmm) REVERT: D 372 GLU cc_start: 0.7520 (tt0) cc_final: 0.6955 (mm-30) REVERT: D 375 LYS cc_start: 0.5716 (ttpt) cc_final: 0.5278 (ttmm) REVERT: E 311 LYS cc_start: 0.5749 (mtmt) cc_final: 0.5433 (tttm) REVERT: E 342 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7176 (tt0) REVERT: E 347 LYS cc_start: 0.8001 (mttt) cc_final: 0.7702 (mmtp) REVERT: E 369 LYS cc_start: 0.7531 (tttt) cc_final: 0.6914 (ttmt) REVERT: E 372 GLU cc_start: 0.6392 (tt0) cc_final: 0.6155 (mm-30) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 3.1550 time to fit residues: 369.9195 Evaluate side-chains 97 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 7.9990 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: 3.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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: 0.7410 moved from start: 0.4161 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= 0.235 Angle : 0.611 6.874 4254 Z= 0.318 Chirality : 0.049 0.152 480 Planarity : 0.003 0.015 540 Dihedral : 6.366 19.462 420 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.83 % Allowed : 9.44 % Favored : 89.72 % 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 0.003 0.001 HIS B 329 PHE 0.005 0.002 PHE D 346 TYR 0.012 0.002 TYR C 310 ARG 0.001 0.000 ARG A 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 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6919 (m) cc_final: 0.6278 (p) REVERT: B 338 GLU cc_start: 0.7586 (tt0) cc_final: 0.7319 (mt-10) REVERT: B 342 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6582 (mp0) REVERT: B 343 LYS cc_start: 0.7917 (mttt) cc_final: 0.7357 (mtmt) REVERT: B 345 ASP cc_start: 0.7943 (t70) cc_final: 0.7743 (t70) REVERT: B 347 LYS cc_start: 0.7544 (mttt) cc_final: 0.7189 (mmtt) REVERT: c 342 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6748 (mp0) REVERT: c 343 LYS cc_start: 0.8162 (mttt) cc_final: 0.7629 (mtmm) REVERT: c 347 LYS cc_start: 0.7644 (mttt) cc_final: 0.7367 (mmtt) REVERT: c 349 ARG cc_start: 0.6534 (mtm180) cc_final: 0.5441 (mmp-170) REVERT: A 342 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6659 (mp0) REVERT: A 343 LYS cc_start: 0.7886 (mttt) cc_final: 0.7470 (mtmt) REVERT: A 347 LYS cc_start: 0.7771 (mttt) cc_final: 0.7319 (mppt) REVERT: A 349 ARG cc_start: 0.6875 (mtm180) cc_final: 0.6595 (mtp180) REVERT: A 369 LYS cc_start: 0.7944 (tttt) cc_final: 0.7417 (tppp) REVERT: C 311 LYS cc_start: 0.5162 (mtmt) cc_final: 0.4920 (tttm) REVERT: C 320 SER cc_start: 0.7578 (t) cc_final: 0.7217 (p) REVERT: C 331 LYS cc_start: 0.8188 (mttt) cc_final: 0.7975 (mtpp) REVERT: C 342 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6769 (tt0) REVERT: C 347 LYS cc_start: 0.7799 (mttt) cc_final: 0.7523 (mmtp) REVERT: C 369 LYS cc_start: 0.6919 (tttt) cc_final: 0.6420 (ttmp) REVERT: C 372 GLU cc_start: 0.6872 (tt0) cc_final: 0.6465 (mm-30) REVERT: D 311 LYS cc_start: 0.5502 (mtmt) cc_final: 0.5173 (tttm) REVERT: D 342 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6894 (tt0) REVERT: D 345 ASP cc_start: 0.7648 (t0) cc_final: 0.7114 (t0) REVERT: D 347 LYS cc_start: 0.8031 (mmtp) cc_final: 0.7788 (mmtp) REVERT: D 369 LYS cc_start: 0.6901 (tttt) cc_final: 0.6394 (ttmm) REVERT: D 372 GLU cc_start: 0.7636 (tt0) cc_final: 0.7031 (mm-30) REVERT: D 375 LYS cc_start: 0.5345 (ttpt) cc_final: 0.4961 (ttmm) REVERT: E 311 LYS cc_start: 0.5808 (mtmt) cc_final: 0.5491 (tttm) REVERT: E 342 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7190 (tt0) REVERT: E 347 LYS cc_start: 0.7983 (mttt) cc_final: 0.7685 (mmtp) REVERT: E 369 LYS cc_start: 0.7534 (tttt) cc_final: 0.7006 (ttmp) outliers start: 3 outliers final: 2 residues processed: 108 average time/residue: 3.4118 time to fit residues: 375.8350 Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 100 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 0.8980 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.7395 moved from start: 0.4467 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= 0.134 Angle : 0.510 5.632 4254 Z= 0.263 Chirality : 0.049 0.143 480 Planarity : 0.002 0.020 540 Dihedral : 5.732 19.153 420 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 11.39 % 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: -2.05 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 330 PHE 0.003 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 112 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 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: 0.6792 (m) cc_final: 0.6218 (p) REVERT: B 338 GLU cc_start: 0.7568 (tt0) cc_final: 0.7299 (mt-10) REVERT: B 342 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6480 (mp0) REVERT: B 343 LYS cc_start: 0.7939 (mttt) cc_final: 0.7386 (mtmt) REVERT: B 347 LYS cc_start: 0.7539 (mttt) cc_final: 0.7334 (mmtp) REVERT: c 342 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6369 (mp0) REVERT: c 343 LYS cc_start: 0.8171 (mttt) cc_final: 0.7647 (mtmm) REVERT: c 347 LYS cc_start: 0.7622 (mttt) cc_final: 0.7316 (mmtt) REVERT: c 349 ARG cc_start: 0.6611 (mtm180) cc_final: 0.5485 (mmp-170) REVERT: c 369 LYS cc_start: 0.7765 (tttt) cc_final: 0.7422 (tppp) REVERT: A 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6636 (mp0) REVERT: A 343 LYS cc_start: 0.7898 (mttt) cc_final: 0.7481 (mtmt) REVERT: A 347 LYS cc_start: 0.7746 (mttt) cc_final: 0.7295 (mppt) REVERT: A 349 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6615 (mtp180) REVERT: C 311 LYS cc_start: 0.5096 (mtmt) cc_final: 0.4817 (tttm) REVERT: C 320 SER cc_start: 0.7560 (t) cc_final: 0.7214 (p) REVERT: C 331 LYS cc_start: 0.8196 (mttt) cc_final: 0.7978 (mtpp) REVERT: C 342 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6761 (tt0) REVERT: C 347 LYS cc_start: 0.7801 (mttt) cc_final: 0.7542 (mmtp) REVERT: C 369 LYS cc_start: 0.6878 (tttt) cc_final: 0.6393 (ttmp) REVERT: C 372 GLU cc_start: 0.6850 (tt0) cc_final: 0.6487 (mm-30) REVERT: D 311 LYS cc_start: 0.5588 (mtmt) cc_final: 0.5241 (tttm) REVERT: D 342 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6939 (tt0) REVERT: D 345 ASP cc_start: 0.7657 (t0) cc_final: 0.7112 (t0) REVERT: D 369 LYS cc_start: 0.6956 (tttt) cc_final: 0.6444 (ttmm) REVERT: D 372 GLU cc_start: 0.7577 (tt0) cc_final: 0.6982 (mm-30) REVERT: D 375 LYS cc_start: 0.5702 (ttpt) cc_final: 0.5286 (ttmm) REVERT: E 311 LYS cc_start: 0.5846 (mtmt) cc_final: 0.5591 (ttpt) REVERT: E 316 SER cc_start: 0.6525 (OUTLIER) cc_final: 0.6118 (p) REVERT: E 342 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7206 (tt0) REVERT: E 347 LYS cc_start: 0.7973 (mttt) cc_final: 0.7704 (mmtp) REVERT: E 369 LYS cc_start: 0.7597 (tttt) cc_final: 0.7064 (ttmp) outliers start: 4 outliers final: 1 residues processed: 109 average time/residue: 3.4826 time to fit residues: 387.9253 Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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: 0.5980 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 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 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: 0.7406 moved from start: 0.4577 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= 0.184 Angle : 0.541 5.837 4254 Z= 0.281 Chirality : 0.049 0.149 480 Planarity : 0.002 0.018 540 Dihedral : 5.811 18.610 420 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % 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: -2.08 (0.31), 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 329 PHE 0.005 0.001 PHE C 346 TYR 0.011 0.002 TYR C 310 ARG 0.001 0.000 ARG D 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 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.561 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: 0.6925 (m) cc_final: 0.6337 (p) REVERT: B 342 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6481 (mp0) REVERT: B 343 LYS cc_start: 0.7894 (mttt) cc_final: 0.7358 (mtmt) REVERT: B 347 LYS cc_start: 0.7572 (mttt) cc_final: 0.7203 (mmtt) REVERT: c 342 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6308 (mp0) REVERT: c 347 LYS cc_start: 0.7603 (mttt) cc_final: 0.7339 (mmtt) REVERT: c 349 ARG cc_start: 0.6615 (mtm180) cc_final: 0.5479 (mmp-170) REVERT: A 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6642 (mp0) REVERT: A 343 LYS cc_start: 0.7898 (mttt) cc_final: 0.7481 (mtmt) REVERT: A 347 LYS cc_start: 0.7778 (mttt) cc_final: 0.7305 (mppt) REVERT: A 349 ARG cc_start: 0.6896 (mtm180) cc_final: 0.6600 (mtp180) REVERT: A 370 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6395 (mmmm) REVERT: C 311 LYS cc_start: 0.5117 (mtmt) cc_final: 0.4775 (mttt) REVERT: C 320 SER cc_start: 0.7680 (t) cc_final: 0.7309 (p) REVERT: C 331 LYS cc_start: 0.8198 (mttt) cc_final: 0.7977 (mtpp) REVERT: C 347 LYS cc_start: 0.7775 (mttt) cc_final: 0.7529 (mmtp) REVERT: C 369 LYS cc_start: 0.6865 (tttt) cc_final: 0.6386 (ttmp) REVERT: C 372 GLU cc_start: 0.6925 (tt0) cc_final: 0.6547 (mm-30) REVERT: D 311 LYS cc_start: 0.5579 (mtmt) cc_final: 0.5326 (tttm) REVERT: D 342 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6949 (tt0) REVERT: D 369 LYS cc_start: 0.6939 (tttt) cc_final: 0.6412 (ttmm) REVERT: D 372 GLU cc_start: 0.7587 (tt0) cc_final: 0.6975 (mm-30) REVERT: D 375 LYS cc_start: 0.5408 (ttpt) cc_final: 0.5026 (ttmm) REVERT: E 311 LYS cc_start: 0.5879 (mtmt) cc_final: 0.5665 (ttpt) REVERT: E 316 SER cc_start: 0.6395 (OUTLIER) cc_final: 0.6003 (p) REVERT: E 342 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7210 (tt0) REVERT: E 347 LYS cc_start: 0.7950 (mttt) cc_final: 0.7674 (mmtp) REVERT: E 369 LYS cc_start: 0.7527 (tttt) cc_final: 0.7010 (ttmp) outliers start: 5 outliers final: 0 residues processed: 109 average time/residue: 3.3254 time to fit residues: 369.8891 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS 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: 6.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3180 Z= 0.151 Angle : 0.523 5.905 4254 Z= 0.267 Chirality : 0.049 0.145 480 Planarity : 0.002 0.019 540 Dihedral : 5.601 20.025 420 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.83 % Allowed : 10.56 % 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: -2.07 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 329 PHE 0.004 0.001 PHE C 346 TYR 0.008 0.001 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 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6885 (m) cc_final: 0.6436 (p) REVERT: B 342 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6470 (mp0) REVERT: B 343 LYS cc_start: 0.7893 (mttt) cc_final: 0.7369 (mtmt) REVERT: B 347 LYS cc_start: 0.7580 (mttt) cc_final: 0.7217 (mmtt) REVERT: B 370 LYS cc_start: 0.6587 (mttp) cc_final: 0.6358 (mttp) REVERT: c 342 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6305 (mp0) REVERT: c 347 LYS cc_start: 0.7619 (mttt) cc_final: 0.7351 (mmtt) REVERT: c 349 ARG cc_start: 0.6629 (mtm180) cc_final: 0.5495 (mmp-170) REVERT: c 369 LYS cc_start: 0.7810 (tttt) cc_final: 0.7372 (tppp) REVERT: c 370 LYS cc_start: 0.6972 (mttp) cc_final: 0.6766 (mttt) REVERT: A 342 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6631 (mp0) REVERT: A 343 LYS cc_start: 0.7875 (mttt) cc_final: 0.7458 (mtmt) REVERT: A 347 LYS cc_start: 0.7755 (mttt) cc_final: 0.7280 (mppt) REVERT: A 349 ARG cc_start: 0.6887 (mtm180) cc_final: 0.6585 (mtp180) REVERT: A 369 LYS cc_start: 0.7923 (tttt) cc_final: 0.7472 (tppp) REVERT: A 370 LYS cc_start: 0.6792 (OUTLIER) cc_final: 0.6588 (mttt) REVERT: C 311 LYS cc_start: 0.5074 (mtmt) cc_final: 0.4733 (mttt) REVERT: C 320 SER cc_start: 0.7632 (t) cc_final: 0.7271 (p) REVERT: C 331 LYS cc_start: 0.8190 (mttt) cc_final: 0.7972 (mtpp) REVERT: C 347 LYS cc_start: 0.7775 (mttt) cc_final: 0.7524 (mmtp) REVERT: C 369 LYS cc_start: 0.6863 (tttt) cc_final: 0.6383 (ttmp) REVERT: C 372 GLU cc_start: 0.6931 (tt0) cc_final: 0.6575 (mm-30) REVERT: D 311 LYS cc_start: 0.5621 (mtmt) cc_final: 0.5366 (tttm) REVERT: D 342 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6980 (tt0) REVERT: D 369 LYS cc_start: 0.6954 (tttt) cc_final: 0.6423 (ttmm) REVERT: D 372 GLU cc_start: 0.7581 (tt0) cc_final: 0.6978 (mm-30) REVERT: D 375 LYS cc_start: 0.5585 (ttpt) cc_final: 0.5182 (ttmm) REVERT: E 311 LYS cc_start: 0.5913 (mtmt) cc_final: 0.5705 (ttpt) REVERT: E 316 SER cc_start: 0.6338 (OUTLIER) cc_final: 0.5959 (p) REVERT: E 342 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7224 (tt0) REVERT: E 347 LYS cc_start: 0.7958 (mttt) cc_final: 0.7680 (mmtp) REVERT: E 369 LYS cc_start: 0.7552 (tttt) cc_final: 0.7037 (ttmp) outliers start: 3 outliers final: 0 residues processed: 106 average time/residue: 3.3753 time to fit residues: 364.9275 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS 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: 7.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7408 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3180 Z= 0.187 Angle : 0.550 5.907 4254 Z= 0.280 Chirality : 0.049 0.149 480 Planarity : 0.002 0.025 540 Dihedral : 5.640 18.944 420 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.11 % Allowed : 10.28 % 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: -2.08 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.24), 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 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 109 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 105 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.7026 (m) cc_final: 0.6482 (p) REVERT: B 342 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6468 (mp0) REVERT: B 343 LYS cc_start: 0.7881 (mttt) cc_final: 0.7362 (mtmt) REVERT: B 347 LYS cc_start: 0.7590 (mttt) cc_final: 0.7217 (mmtt) REVERT: c 342 GLU cc_start: 0.7409 (mt-10) cc_final: 0.6304 (mp0) REVERT: c 347 LYS cc_start: 0.7592 (mttt) cc_final: 0.7321 (mmtt) REVERT: c 349 ARG cc_start: 0.6633 (mtm180) cc_final: 0.5500 (mmp-170) REVERT: c 369 LYS cc_start: 0.7814 (tttt) cc_final: 0.7387 (tppp) REVERT: c 370 LYS cc_start: 0.6982 (mttp) cc_final: 0.6649 (mmtp) REVERT: A 342 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6629 (mp0) REVERT: A 343 LYS cc_start: 0.7882 (mttt) cc_final: 0.7448 (mtmt) REVERT: A 347 LYS cc_start: 0.7786 (mttt) cc_final: 0.7319 (mppt) REVERT: A 349 ARG cc_start: 0.6887 (mtm180) cc_final: 0.6544 (mtp180) REVERT: A 369 LYS cc_start: 0.7954 (tttt) cc_final: 0.7503 (tppp) REVERT: C 311 LYS cc_start: 0.5095 (mtmt) cc_final: 0.4756 (mttt) REVERT: C 320 SER cc_start: 0.7632 (t) cc_final: 0.7244 (p) REVERT: C 331 LYS cc_start: 0.8190 (mttt) cc_final: 0.7972 (mtpp) REVERT: C 347 LYS cc_start: 0.7802 (mttt) cc_final: 0.7524 (mmtp) REVERT: C 369 LYS cc_start: 0.6851 (tttt) cc_final: 0.6385 (ttmp) REVERT: C 372 GLU cc_start: 0.6908 (tt0) cc_final: 0.6567 (mm-30) REVERT: D 311 LYS cc_start: 0.5577 (mtmt) cc_final: 0.5326 (tttm) REVERT: D 342 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7010 (tt0) REVERT: D 345 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7008 (t0) REVERT: D 369 LYS cc_start: 0.6953 (tttt) cc_final: 0.6407 (ttmm) REVERT: D 372 GLU cc_start: 0.7592 (tt0) cc_final: 0.6978 (mm-30) REVERT: E 311 LYS cc_start: 0.5926 (mtmt) cc_final: 0.5714 (ttpt) REVERT: E 314 ASP cc_start: 0.5052 (t70) cc_final: 0.4762 (t70) REVERT: E 316 SER cc_start: 0.6322 (OUTLIER) cc_final: 0.5969 (p) REVERT: E 342 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7231 (tt0) REVERT: E 347 LYS cc_start: 0.7978 (mttt) cc_final: 0.7682 (mmtp) REVERT: E 369 LYS cc_start: 0.7558 (tttt) cc_final: 0.7031 (ttmp) outliers start: 4 outliers final: 1 residues processed: 107 average time/residue: 3.3383 time to fit residues: 364.2094 Evaluate side-chains 106 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 345 ASP 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: 6.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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: 0.7405 moved from start: 0.4862 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= 0.170 Angle : 0.539 6.159 4254 Z= 0.274 Chirality : 0.049 0.146 480 Planarity : 0.002 0.024 540 Dihedral : 5.548 19.805 420 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.83 % Allowed : 10.83 % 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: -2.05 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.24), 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 0.009 0.002 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 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.7004 (m) cc_final: 0.6474 (p) REVERT: B 342 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6461 (mp0) REVERT: B 343 LYS cc_start: 0.7901 (mttt) cc_final: 0.7402 (mtmt) REVERT: B 347 LYS cc_start: 0.7600 (mttt) cc_final: 0.7225 (mmtt) REVERT: c 342 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6283 (mp0) REVERT: c 347 LYS cc_start: 0.7602 (mttt) cc_final: 0.7329 (mmtt) REVERT: c 349 ARG cc_start: 0.6651 (mtm180) cc_final: 0.5503 (mmp-170) REVERT: c 368 ASN cc_start: 0.7439 (m-40) cc_final: 0.7194 (m-40) REVERT: c 369 LYS cc_start: 0.7773 (tttt) cc_final: 0.7350 (tppp) REVERT: c 370 LYS cc_start: 0.7034 (mttp) cc_final: 0.6684 (mmtp) REVERT: A 342 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6631 (mp0) REVERT: A 343 LYS cc_start: 0.7902 (mttt) cc_final: 0.7476 (mtmt) REVERT: A 347 LYS cc_start: 0.7798 (mttt) cc_final: 0.7324 (mppt) REVERT: A 349 ARG cc_start: 0.6898 (mtm180) cc_final: 0.6544 (mtp180) REVERT: A 369 LYS cc_start: 0.8000 (tttt) cc_final: 0.7513 (tppp) REVERT: C 311 LYS cc_start: 0.5101 (mtmt) cc_final: 0.4761 (mttt) REVERT: C 320 SER cc_start: 0.7641 (t) cc_final: 0.7256 (p) REVERT: C 331 LYS cc_start: 0.8188 (mttt) cc_final: 0.7973 (mtpp) REVERT: C 342 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6724 (tt0) REVERT: C 347 LYS cc_start: 0.7751 (mttt) cc_final: 0.7491 (mmtp) REVERT: C 369 LYS cc_start: 0.6835 (tttt) cc_final: 0.6371 (ttmp) REVERT: C 372 GLU cc_start: 0.6896 (tt0) cc_final: 0.6529 (mm-30) REVERT: D 311 LYS cc_start: 0.5569 (mtmt) cc_final: 0.5320 (tttm) REVERT: D 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6969 (tt0) REVERT: D 345 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7005 (t0) REVERT: D 369 LYS cc_start: 0.6959 (tttt) cc_final: 0.6408 (ttmm) REVERT: D 372 GLU cc_start: 0.7579 (tt0) cc_final: 0.7251 (tt0) REVERT: E 311 LYS cc_start: 0.5922 (mtmt) cc_final: 0.5718 (ttpt) REVERT: E 316 SER cc_start: 0.6312 (OUTLIER) cc_final: 0.5962 (p) REVERT: E 342 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7217 (tt0) REVERT: E 369 LYS cc_start: 0.7588 (tttt) cc_final: 0.7051 (ttmp) outliers start: 3 outliers final: 0 residues processed: 105 average time/residue: 3.2014 time to fit residues: 342.9417 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP 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: 5.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.7398 moved from start: 0.4936 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= 0.143 Angle : 0.512 5.762 4254 Z= 0.258 Chirality : 0.049 0.144 480 Planarity : 0.002 0.016 540 Dihedral : 5.326 19.596 420 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 11.39 % Favored : 88.06 % 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: -1.99 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (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 C 346 TYR 0.009 0.001 TYR D 310 ARG 0.001 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 111 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6974 (m) cc_final: 0.6440 (p) REVERT: B 342 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6511 (mp0) REVERT: B 343 LYS cc_start: 0.7914 (mttt) cc_final: 0.7417 (mtmt) REVERT: B 347 LYS cc_start: 0.7559 (mttt) cc_final: 0.7199 (mmtt) REVERT: c 342 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6296 (mp0) REVERT: c 347 LYS cc_start: 0.7586 (mttt) cc_final: 0.7315 (mmtt) REVERT: c 349 ARG cc_start: 0.6677 (mtm180) cc_final: 0.5524 (mmp-170) REVERT: c 368 ASN cc_start: 0.7449 (m-40) cc_final: 0.7199 (m-40) REVERT: c 369 LYS cc_start: 0.7795 (tttt) cc_final: 0.7371 (tppp) REVERT: A 342 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6641 (mp0) REVERT: A 343 LYS cc_start: 0.7891 (mttt) cc_final: 0.7464 (mtmt) REVERT: A 347 LYS cc_start: 0.7786 (mttt) cc_final: 0.7312 (mppt) REVERT: A 349 ARG cc_start: 0.6902 (mtm180) cc_final: 0.6548 (mtp180) REVERT: C 311 LYS cc_start: 0.5009 (mtmt) cc_final: 0.4741 (tttm) REVERT: C 320 SER cc_start: 0.7605 (t) cc_final: 0.7308 (p) REVERT: C 331 LYS cc_start: 0.8190 (mttt) cc_final: 0.7976 (mtpp) REVERT: C 342 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6733 (tt0) REVERT: C 347 LYS cc_start: 0.7761 (mttt) cc_final: 0.7513 (mmtp) REVERT: C 369 LYS cc_start: 0.6824 (tttt) cc_final: 0.6363 (ttmp) REVERT: C 372 GLU cc_start: 0.6879 (tt0) cc_final: 0.6579 (mm-30) REVERT: D 311 LYS cc_start: 0.5527 (mtmt) cc_final: 0.5202 (tttm) REVERT: D 342 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6986 (tt0) REVERT: D 345 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.6975 (t0) REVERT: D 369 LYS cc_start: 0.6965 (tttt) cc_final: 0.6421 (ttmm) REVERT: D 372 GLU cc_start: 0.7570 (tt0) cc_final: 0.6959 (mm-30) REVERT: E 311 LYS cc_start: 0.5932 (mtmt) cc_final: 0.5649 (ttpt) REVERT: E 316 SER cc_start: 0.6382 (OUTLIER) cc_final: 0.6061 (p) REVERT: E 342 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7188 (tt0) REVERT: E 369 LYS cc_start: 0.7566 (tttt) cc_final: 0.7035 (ttmp) outliers start: 2 outliers final: 0 residues processed: 109 average time/residue: 3.1770 time to fit residues: 353.1293 Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP 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: 8.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7399 moved from start: 0.4980 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= 0.154 Angle : 0.534 6.521 4254 Z= 0.266 Chirality : 0.049 0.146 480 Planarity : 0.002 0.017 540 Dihedral : 5.302 19.911 420 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.56 % Allowed : 11.94 % 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: -1.99 (0.32), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.004 0.001 PHE C 346 TYR 0.009 0.001 TYR D 310 ARG 0.001 0.000 ARG D 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 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6963 (m) cc_final: 0.6449 (p) REVERT: B 342 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6509 (mp0) REVERT: B 343 LYS cc_start: 0.7909 (mttt) cc_final: 0.7414 (mtmt) REVERT: B 347 LYS cc_start: 0.7574 (mttt) cc_final: 0.7218 (mmtt) REVERT: c 342 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6313 (mp0) REVERT: c 347 LYS cc_start: 0.7586 (mttt) cc_final: 0.7312 (mmtt) REVERT: c 349 ARG cc_start: 0.6687 (mtm180) cc_final: 0.5527 (mmp-170) REVERT: c 368 ASN cc_start: 0.7460 (m-40) cc_final: 0.7213 (m-40) REVERT: c 369 LYS cc_start: 0.7796 (tttt) cc_final: 0.7371 (tppp) REVERT: A 342 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6638 (mp0) REVERT: A 343 LYS cc_start: 0.7895 (mttt) cc_final: 0.7463 (mtmt) REVERT: A 347 LYS cc_start: 0.7782 (mttt) cc_final: 0.7307 (mppt) REVERT: A 349 ARG cc_start: 0.6911 (mtm180) cc_final: 0.6527 (mtp180) REVERT: C 311 LYS cc_start: 0.5043 (mtmt) cc_final: 0.4771 (tttm) REVERT: C 320 SER cc_start: 0.7630 (t) cc_final: 0.7325 (p) REVERT: C 331 LYS cc_start: 0.8198 (mttt) cc_final: 0.7982 (mtpp) REVERT: C 342 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6732 (tt0) REVERT: C 347 LYS cc_start: 0.7742 (mttt) cc_final: 0.7487 (mmtp) REVERT: C 369 LYS cc_start: 0.6822 (tttt) cc_final: 0.6361 (ttmp) REVERT: C 372 GLU cc_start: 0.6884 (tt0) cc_final: 0.6593 (mm-30) REVERT: D 311 LYS cc_start: 0.5508 (mtmt) cc_final: 0.5163 (tttm) REVERT: D 342 GLU cc_start: 0.7466 (mt-10) cc_final: 0.6981 (tt0) REVERT: D 345 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.6973 (t0) REVERT: D 369 LYS cc_start: 0.6965 (tttt) cc_final: 0.6416 (ttmm) REVERT: D 372 GLU cc_start: 0.7550 (tt0) cc_final: 0.6945 (mm-30) REVERT: E 311 LYS cc_start: 0.5935 (mtmt) cc_final: 0.5655 (ttpt) REVERT: E 314 ASP cc_start: 0.5222 (t70) cc_final: 0.4967 (t70) REVERT: E 316 SER cc_start: 0.6340 (OUTLIER) cc_final: 0.6010 (p) REVERT: E 342 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7182 (tt0) REVERT: E 369 LYS cc_start: 0.7569 (tttt) cc_final: 0.7041 (ttmp) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 3.2279 time to fit residues: 348.8765 Evaluate side-chains 106 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 345 ASP 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: 6.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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 = 0.4573 r_free = 0.4573 target = 0.194383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.144447 restraints weight = 7001.030| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.47 r_work: 0.4016 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4984 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= 0.196 Angle : 0.552 6.409 4254 Z= 0.281 Chirality : 0.049 0.150 480 Planarity : 0.002 0.018 540 Dihedral : 5.505 20.188 420 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.56 % Allowed : 11.94 % 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: -2.05 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.24), 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 0.009 0.002 TYR D 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: 6217.06 seconds wall clock time: 109 minutes 9.35 seconds (6549.35 seconds total)