Starting phenix.real_space_refine on Tue Feb 11 17:32:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9f_18279/02_2025/8q9f_18279.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9f_18279/02_2025/8q9f_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/cci-nas-00/data/ceres_data/8q9f_18279/02_2025/8q9f_18279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9f_18279/02_2025/8q9f_18279.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9f_18279/02_2025/8q9f_18279.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9f_18279/02_2025/8q9f_18279.cif" } 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. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.11, per 1000 atoms: 0.80 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 413.2 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: 1.96 Time building geometry restraints manager: 2.12 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: 0.00 - 2.40: 9775 2.40 - 4.80: 1499 4.80 - 7.20: 451 7.20 - 9.60: 23 9.60 - 12.00: 6 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 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.574 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.612 2.450 ... (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 Time spend for trying shortcut: 0.01 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.620 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.811 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: 2.7930 time to fit residues: 416.9692 Evaluate side-chains 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 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: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 A 351 GLN D 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.202708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.153679 restraints weight = 7026.124| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.42 r_work: 0.4121 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3505 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= 0.168 Angle : 0.611 5.965 4254 Z= 0.318 Chirality : 0.051 0.144 480 Planarity : 0.002 0.013 540 Dihedral : 6.860 18.737 420 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.56 % Allowed : 8.89 % Favored : 90.56 % 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 0.003 0.001 HIS E 362 PHE 0.005 0.001 PHE D 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG C 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 113 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.534 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: B 343 LYS cc_start: 0.8351 (mttt) cc_final: 0.8101 (mtmt) REVERT: c 343 LYS cc_start: 0.8401 (mttt) cc_final: 0.8197 (mtmm) REVERT: c 349 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7134 (mmp-170) REVERT: c 369 LYS cc_start: 0.7678 (tttt) cc_final: 0.7316 (tppp) REVERT: D 342 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7171 (mt-10) REVERT: D 375 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8042 (ttmm) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 3.4018 time to fit residues: 384.5754 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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 22 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4610 r_free = 0.4610 target = 0.195256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.147736 restraints weight = 7272.251| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.41 r_work: 0.4067 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.4004 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3180 Z= 0.173 Angle : 0.584 5.838 4254 Z= 0.299 Chirality : 0.050 0.142 480 Planarity : 0.002 0.018 540 Dihedral : 6.105 18.558 420 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.11 % Allowed : 13.61 % Favored : 85.28 % 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: -2.11 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.004 0.001 PHE D 346 TYR 0.009 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 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.497 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: B 319 THR cc_start: 0.6955 (m) cc_final: 0.6393 (p) REVERT: B 343 LYS cc_start: 0.8419 (mttt) cc_final: 0.8182 (mtmt) REVERT: c 349 ARG cc_start: 0.7377 (mtm180) cc_final: 0.7142 (mmp-170) REVERT: c 369 LYS cc_start: 0.7725 (tttt) cc_final: 0.7419 (tppp) REVERT: A 342 GLU cc_start: 0.7503 (mp0) cc_final: 0.7179 (mp0) REVERT: A 369 LYS cc_start: 0.7784 (tttt) cc_final: 0.7291 (tppp) REVERT: D 345 ASP cc_start: 0.7888 (t70) cc_final: 0.7622 (t0) outliers start: 4 outliers final: 1 residues processed: 102 average time/residue: 3.2161 time to fit residues: 334.6627 Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.192640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.145299 restraints weight = 7271.539| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.41 r_work: 0.4037 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5226 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= 0.191 Angle : 0.572 6.911 4254 Z= 0.295 Chirality : 0.050 0.144 480 Planarity : 0.003 0.021 540 Dihedral : 5.916 18.214 420 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.56 % Allowed : 15.83 % Favored : 83.61 % 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: -2.18 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.004 0.001 PHE C 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG E 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 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.593 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: B 319 THR cc_start: 0.6972 (m) cc_final: 0.6469 (p) REVERT: B 343 LYS cc_start: 0.8404 (mttt) cc_final: 0.8189 (mtmt) REVERT: c 349 ARG cc_start: 0.7436 (mtm180) cc_final: 0.7199 (mmp-170) REVERT: c 369 LYS cc_start: 0.7688 (tttt) cc_final: 0.7415 (tppp) REVERT: A 342 GLU cc_start: 0.7506 (mp0) cc_final: 0.7214 (mp0) REVERT: D 345 ASP cc_start: 0.7857 (t70) cc_final: 0.7631 (t0) outliers start: 2 outliers final: 1 residues processed: 94 average time/residue: 3.4480 time to fit residues: 330.5012 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 374 HIS A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.191765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.148954 restraints weight = 7204.292| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.83 r_work: 0.3988 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.5413 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= 0.201 Angle : 0.577 6.665 4254 Z= 0.296 Chirality : 0.049 0.146 480 Planarity : 0.003 0.024 540 Dihedral : 5.827 19.522 420 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.39 % Allowed : 15.56 % Favored : 83.06 % 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: -2.21 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (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 0.010 0.002 TYR E 310 ARG 0.001 0.000 ARG A 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 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.555 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: 0.7016 (m) cc_final: 0.6561 (p) REVERT: B 343 LYS cc_start: 0.8425 (mttt) cc_final: 0.8169 (mtmt) REVERT: B 347 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8200 (mmtp) REVERT: c 349 ARG cc_start: 0.7494 (mtm180) cc_final: 0.7119 (mmp-170) REVERT: c 369 LYS cc_start: 0.7754 (tttt) cc_final: 0.7347 (tppp) REVERT: A 342 GLU cc_start: 0.7631 (mp0) cc_final: 0.7285 (mp0) REVERT: A 368 ASN cc_start: 0.7501 (m110) cc_final: 0.7190 (m-40) REVERT: D 345 ASP cc_start: 0.8048 (t70) cc_final: 0.7796 (t0) outliers start: 5 outliers final: 1 residues processed: 95 average time/residue: 3.1705 time to fit residues: 307.4966 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 11 optimal weight: 0.2980 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.191139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143429 restraints weight = 7146.625| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 1.39 r_work: 0.4011 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5458 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= 0.195 Angle : 0.560 5.420 4254 Z= 0.287 Chirality : 0.050 0.144 480 Planarity : 0.003 0.028 540 Dihedral : 5.748 19.719 420 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.39 % Allowed : 15.28 % Favored : 83.33 % 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: -2.21 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (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 0.009 0.002 TYR C 310 ARG 0.002 0.000 ARG A 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 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 93 time to evaluate : 0.574 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: 0.7049 (m) cc_final: 0.6600 (p) REVERT: B 343 LYS cc_start: 0.8404 (mttt) cc_final: 0.8185 (mtmt) REVERT: c 349 ARG cc_start: 0.7453 (mtm180) cc_final: 0.7158 (mmp-170) REVERT: c 369 LYS cc_start: 0.7713 (tttt) cc_final: 0.7314 (tppp) REVERT: A 342 GLU cc_start: 0.7540 (mp0) cc_final: 0.7244 (mp0) REVERT: A 368 ASN cc_start: 0.7456 (m110) cc_final: 0.7151 (m-40) REVERT: D 345 ASP cc_start: 0.7934 (t70) cc_final: 0.7684 (t0) outliers start: 5 outliers final: 0 residues processed: 95 average time/residue: 3.1555 time to fit residues: 306.0433 Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 overall best weight: 1.2542 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.193184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.146118 restraints weight = 7182.453| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.39 r_work: 0.4043 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3979 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3180 Z= 0.168 Angle : 0.557 5.715 4254 Z= 0.278 Chirality : 0.050 0.142 480 Planarity : 0.002 0.027 540 Dihedral : 5.565 20.201 420 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.11 % Allowed : 15.83 % Favored : 83.06 % 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: -2.17 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.23), 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 0.007 0.001 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 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6986 (m) cc_final: 0.6580 (p) REVERT: B 343 LYS cc_start: 0.8442 (mttt) cc_final: 0.8233 (mtmt) REVERT: c 349 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7165 (mmp-170) REVERT: c 369 LYS cc_start: 0.7705 (tttt) cc_final: 0.7302 (tppp) REVERT: A 342 GLU cc_start: 0.7521 (mp0) cc_final: 0.7246 (mp0) REVERT: A 368 ASN cc_start: 0.7414 (m110) cc_final: 0.7139 (m-40) REVERT: A 369 LYS cc_start: 0.7757 (tttt) cc_final: 0.7303 (tppp) REVERT: D 345 ASP cc_start: 0.7864 (t70) cc_final: 0.7606 (t0) outliers start: 4 outliers final: 0 residues processed: 98 average time/residue: 3.1649 time to fit residues: 316.7276 Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 0.0270 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 2.1242 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.191692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.143587 restraints weight = 7182.173| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.43 r_work: 0.4013 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5633 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= 0.210 Angle : 0.589 5.788 4254 Z= 0.299 Chirality : 0.050 0.149 480 Planarity : 0.002 0.020 540 Dihedral : 5.697 19.862 420 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.11 % Allowed : 15.56 % Favored : 83.33 % 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: -2.21 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE C 346 TYR 0.010 0.002 TYR C 310 ARG 0.002 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 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.538 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: B 319 THR cc_start: 0.7146 (m) cc_final: 0.6714 (p) REVERT: B 343 LYS cc_start: 0.8432 (mttt) cc_final: 0.8220 (mtmt) REVERT: B 370 LYS cc_start: 0.7120 (mttp) cc_final: 0.6668 (mttt) REVERT: c 349 ARG cc_start: 0.7523 (mtm180) cc_final: 0.7165 (mmp-170) REVERT: c 369 LYS cc_start: 0.7708 (tttt) cc_final: 0.7296 (tppp) REVERT: A 342 GLU cc_start: 0.7543 (mp0) cc_final: 0.7247 (mp0) REVERT: A 368 ASN cc_start: 0.7495 (m110) cc_final: 0.7224 (m-40) REVERT: A 369 LYS cc_start: 0.7763 (tttt) cc_final: 0.7300 (tppp) REVERT: D 345 ASP cc_start: 0.7910 (t70) cc_final: 0.7659 (t0) outliers start: 4 outliers final: 2 residues processed: 96 average time/residue: 3.1821 time to fit residues: 313.0265 Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 376 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.192525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.144329 restraints weight = 7191.254| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 1.40 r_work: 0.4018 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 1.97 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5663 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= 0.190 Angle : 0.584 6.077 4254 Z= 0.291 Chirality : 0.049 0.143 480 Planarity : 0.002 0.021 540 Dihedral : 5.588 20.536 420 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.56 % Allowed : 16.67 % Favored : 82.78 % 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: -2.20 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (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 0.003 0.000 ARG A 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 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.7141 (m) cc_final: 0.6715 (p) REVERT: B 343 LYS cc_start: 0.8402 (mttt) cc_final: 0.8198 (mtmt) REVERT: B 370 LYS cc_start: 0.7176 (mttp) cc_final: 0.6752 (mttt) REVERT: c 349 ARG cc_start: 0.7505 (mtm180) cc_final: 0.7156 (mmp-170) REVERT: c 369 LYS cc_start: 0.7662 (tttt) cc_final: 0.7293 (tppp) REVERT: A 342 GLU cc_start: 0.7552 (mp0) cc_final: 0.7268 (mp0) REVERT: A 368 ASN cc_start: 0.7509 (m110) cc_final: 0.7235 (m-40) REVERT: A 369 LYS cc_start: 0.7786 (tttt) cc_final: 0.7417 (tppp) REVERT: D 345 ASP cc_start: 0.7910 (t70) cc_final: 0.7656 (t0) outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 3.2165 time to fit residues: 311.9333 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.194314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152135 restraints weight = 7293.195| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.86 r_work: 0.4035 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5780 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= 0.159 Angle : 0.563 6.251 4254 Z= 0.278 Chirality : 0.049 0.140 480 Planarity : 0.002 0.018 540 Dihedral : 5.385 20.296 420 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 16.94 % Favored : 82.50 % 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: -2.18 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.23), 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 0.005 0.001 TYR C 310 ARG 0.002 0.000 ARG A 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 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.541 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: B 319 THR cc_start: 0.7046 (m) cc_final: 0.6626 (p) REVERT: B 343 LYS cc_start: 0.8499 (mttt) cc_final: 0.8258 (mtmt) REVERT: c 349 ARG cc_start: 0.7541 (mtm180) cc_final: 0.7118 (mmp-170) REVERT: A 342 GLU cc_start: 0.7572 (mp0) cc_final: 0.7279 (mp0) REVERT: A 368 ASN cc_start: 0.7487 (m110) cc_final: 0.7201 (m-40) REVERT: A 369 LYS cc_start: 0.7777 (tttt) cc_final: 0.7391 (tppp) REVERT: D 345 ASP cc_start: 0.7906 (t70) cc_final: 0.7663 (t0) REVERT: E 345 ASP cc_start: 0.8099 (t70) cc_final: 0.7786 (t70) outliers start: 2 outliers final: 2 residues processed: 93 average time/residue: 3.0637 time to fit residues: 290.9850 Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 376 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.194279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.146600 restraints weight = 7367.926| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.39 r_work: 0.4052 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5807 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= 0.158 Angle : 0.559 6.197 4254 Z= 0.278 Chirality : 0.049 0.142 480 Planarity : 0.002 0.022 540 Dihedral : 5.288 20.116 420 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.56 % Allowed : 17.22 % Favored : 82.22 % 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: -2.19 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.24), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE C 346 TYR 0.006 0.001 TYR C 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9873.10 seconds wall clock time: 173 minutes 25.76 seconds (10405.76 seconds total)