Starting phenix.real_space_refine on Tue Sep 24 00:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/09_2024/8q9f_18279.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/09_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_18279/09_2024/8q9f_18279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/09_2024/8q9f_18279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/09_2024/8q9f_18279.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9f_18279/09_2024/8q9f_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 4.53, per 1000 atoms: 0.71 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: 1.54 Conformation dependent library (CDL) restraints added in 486.4 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 51.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'c' and resid 313 through 314 removed outlier: 6.866A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 317 through 322 removed outlier: 6.425A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 325 through 330 removed outlier: 5.881A pdb=" N GLY B 326 " --> pdb=" O ASN c 327 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N HIS c 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 328 " --> pdb=" O HIS c 329 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 336 through 342 Processing sheet with id=AA5, first strand: chain 'c' and resid 345 through 346 removed outlier: 6.596A pdb=" N ASP B 345 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 350 through 357 removed outlier: 6.381A pdb=" N VAL B 350 " --> pdb=" O GLN c 351 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N LYS c 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 352 " --> pdb=" O LYS c 353 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLY c 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE B 354 " --> pdb=" O GLY c 355 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU c 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 356 " --> pdb=" O LEU c 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 360 through 362 removed outlier: 6.386A pdb=" N THR B 361 " --> pdb=" O HIS c 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 369 through 376 removed outlier: 6.219A pdb=" N LYS B 370 " --> pdb=" O ILE c 371 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR c 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU B 372 " --> pdb=" O THR c 373 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N LYS c 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS B 374 " --> pdb=" O LYS c 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.815A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 317 through 330 removed outlier: 6.387A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N GLY D 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N CYS C 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU D 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 10.059A pdb=" N ASN D 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER E 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU C 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.467A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.514A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.391A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.439A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 365 through 366 removed outlier: 4.089A pdb=" N GLY C 365 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 376 removed outlier: 6.322A pdb=" N LYS C 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N THR D 373 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU C 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LYS D 375 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS C 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.87 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: 0.00 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: 3.750 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.410 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- 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 : 0.555 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: 2.6607 time to fit residues: 397.0975 Evaluate side-chains 98 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.550 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 342 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6623 (mp0) REVERT: B 343 LYS cc_start: 0.7883 (mttt) cc_final: 0.7331 (mtmt) REVERT: B 345 ASP cc_start: 0.8038 (t70) cc_final: 0.7805 (t70) REVERT: B 347 LYS cc_start: 0.7610 (mttt) cc_final: 0.7262 (mmtt) REVERT: c 342 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6482 (mp0) REVERT: c 343 LYS cc_start: 0.8087 (mttt) cc_final: 0.7589 (mtmm) REVERT: c 347 LYS cc_start: 0.7671 (mttt) cc_final: 0.7396 (mmtm) REVERT: c 349 ARG cc_start: 0.6695 (mtm180) cc_final: 0.5564 (mmp-170) REVERT: c 369 LYS cc_start: 0.7748 (tttt) cc_final: 0.7337 (tppp) REVERT: A 342 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6932 (mp0) REVERT: A 343 LYS cc_start: 0.7759 (mttt) cc_final: 0.7350 (mtmt) REVERT: C 311 LYS cc_start: 0.5085 (mtmt) cc_final: 0.4815 (tttm) REVERT: C 314 ASP cc_start: 0.5416 (t0) cc_final: 0.4984 (t0) REVERT: C 320 SER cc_start: 0.7647 (t) cc_final: 0.7439 (p) REVERT: C 331 LYS cc_start: 0.8220 (mttt) cc_final: 0.8006 (mtpp) REVERT: C 347 LYS cc_start: 0.7845 (mttt) cc_final: 0.7596 (mmtp) REVERT: C 369 LYS cc_start: 0.6888 (tttt) cc_final: 0.6416 (ttmp) REVERT: C 372 GLU cc_start: 0.6875 (tt0) cc_final: 0.6405 (mm-30) REVERT: D 311 LYS cc_start: 0.5638 (mtmt) cc_final: 0.5314 (tttp) REVERT: D 324 SER cc_start: 0.7952 (p) cc_final: 0.7615 (m) REVERT: D 342 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7069 (mt-10) REVERT: D 369 LYS cc_start: 0.7087 (tttt) cc_final: 0.6608 (ttmm) REVERT: D 372 GLU cc_start: 0.7594 (tt0) cc_final: 0.7084 (mm-30) REVERT: D 375 LYS cc_start: 0.5729 (ttpt) cc_final: 0.5281 (ttmm) REVERT: E 311 LYS cc_start: 0.5821 (mtmt) cc_final: 0.5442 (tmtt) REVERT: E 316 SER cc_start: 0.6473 (m) cc_final: 0.5889 (p) REVERT: E 342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7130 (tt0) REVERT: E 347 LYS cc_start: 0.7975 (mttt) cc_final: 0.7709 (mmtp) REVERT: E 369 LYS cc_start: 0.7504 (tttt) cc_final: 0.6878 (ttmt) REVERT: E 372 GLU cc_start: 0.6420 (tt0) cc_final: 0.6124 (mm-30) outliers start: 2 outliers final: 1 residues processed: 111 average time/residue: 3.2333 time to fit residues: 365.7744 Evaluate side-chains 102 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 7.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 E 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3180 Z= 0.205 Angle : 0.590 6.547 4254 Z= 0.308 Chirality : 0.051 0.146 480 Planarity : 0.002 0.016 540 Dihedral : 6.247 19.197 420 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.11 % Allowed : 9.72 % Favored : 89.17 % 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: -2.16 (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 0.004 0.001 HIS E 329 PHE 0.006 0.001 PHE D 346 TYR 0.012 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 114 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 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: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6865 (m) cc_final: 0.6229 (p) REVERT: B 338 GLU cc_start: 0.7587 (tt0) cc_final: 0.7313 (mt-10) REVERT: B 342 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6580 (mp0) REVERT: B 343 LYS cc_start: 0.7937 (mttt) cc_final: 0.7388 (mtmt) REVERT: B 347 LYS cc_start: 0.7600 (mttt) cc_final: 0.7257 (mmtt) REVERT: c 342 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6439 (mp0) REVERT: c 343 LYS cc_start: 0.8179 (mttt) cc_final: 0.7650 (mtmm) REVERT: c 347 LYS cc_start: 0.7645 (mttt) cc_final: 0.7413 (mmtt) REVERT: c 349 ARG cc_start: 0.6679 (mtm180) cc_final: 0.5551 (mmp-170) REVERT: c 369 LYS cc_start: 0.7786 (tttt) cc_final: 0.7445 (tppp) REVERT: A 342 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6664 (mp0) REVERT: A 343 LYS cc_start: 0.7876 (mttt) cc_final: 0.7461 (mtmt) REVERT: A 349 ARG cc_start: 0.6868 (mtm180) cc_final: 0.6413 (mtp180) REVERT: A 369 LYS cc_start: 0.7931 (tttt) cc_final: 0.7398 (tppp) REVERT: C 311 LYS cc_start: 0.5120 (mtmt) cc_final: 0.4850 (tttm) REVERT: C 314 ASP cc_start: 0.5470 (t0) cc_final: 0.5266 (t0) REVERT: C 320 SER cc_start: 0.7652 (t) cc_final: 0.7323 (p) REVERT: C 324 SER cc_start: 0.7749 (p) cc_final: 0.7489 (m) REVERT: C 331 LYS cc_start: 0.8224 (mttt) cc_final: 0.8005 (mtpp) REVERT: C 342 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6765 (tt0) REVERT: C 347 LYS cc_start: 0.7823 (mttt) cc_final: 0.7550 (mmtp) REVERT: C 369 LYS cc_start: 0.6880 (tttt) cc_final: 0.6395 (ttmp) REVERT: C 372 GLU cc_start: 0.6967 (tt0) cc_final: 0.6536 (mm-30) REVERT: D 311 LYS cc_start: 0.5559 (mtmt) cc_final: 0.5234 (tttp) REVERT: D 342 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6960 (tt0) REVERT: D 345 ASP cc_start: 0.7987 (t70) cc_final: 0.7670 (t0) REVERT: D 369 LYS cc_start: 0.6969 (tttt) cc_final: 0.6464 (ttmm) REVERT: D 372 GLU cc_start: 0.7685 (tt0) cc_final: 0.7090 (mm-30) REVERT: D 375 LYS cc_start: 0.5670 (ttpt) cc_final: 0.5251 (ttmm) REVERT: E 311 LYS cc_start: 0.5866 (mtmt) cc_final: 0.5515 (tttm) REVERT: E 342 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7142 (tt0) REVERT: E 347 LYS cc_start: 0.7909 (mttt) cc_final: 0.7646 (mmtp) REVERT: E 369 LYS cc_start: 0.7517 (tttt) cc_final: 0.6891 (ttmt) REVERT: E 372 GLU cc_start: 0.6649 (tt0) cc_final: 0.6413 (mm-30) outliers start: 4 outliers final: 1 residues processed: 110 average time/residue: 3.1539 time to fit residues: 353.7142 Evaluate side-chains 104 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 16 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7400 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3180 Z= 0.149 Angle : 0.524 5.537 4254 Z= 0.269 Chirality : 0.050 0.142 480 Planarity : 0.002 0.018 540 Dihedral : 5.773 19.076 420 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 9.72 % Favored : 89.17 % 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: -2.16 (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 0.003 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 113 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 109 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6744 (m) cc_final: 0.6152 (p) REVERT: B 338 GLU cc_start: 0.7601 (tt0) cc_final: 0.7336 (mt-10) REVERT: B 342 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6572 (mp0) REVERT: B 343 LYS cc_start: 0.7959 (mttt) cc_final: 0.7428 (mtmt) REVERT: B 347 LYS cc_start: 0.7610 (mttt) cc_final: 0.7251 (mmtt) REVERT: c 342 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6386 (mp0) REVERT: c 343 LYS cc_start: 0.8171 (mttt) cc_final: 0.7652 (mtmm) REVERT: c 347 LYS cc_start: 0.7652 (mttt) cc_final: 0.7422 (mmtt) REVERT: c 349 ARG cc_start: 0.6744 (mtm180) cc_final: 0.5567 (mmp-170) REVERT: c 369 LYS cc_start: 0.7815 (tttt) cc_final: 0.7382 (tppp) REVERT: A 342 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6644 (mp0) REVERT: A 343 LYS cc_start: 0.7887 (mttt) cc_final: 0.7475 (mtmt) REVERT: A 349 ARG cc_start: 0.6900 (mtm180) cc_final: 0.6549 (mtp180) REVERT: C 311 LYS cc_start: 0.5084 (mtmt) cc_final: 0.4785 (tttm) REVERT: C 320 SER cc_start: 0.7631 (t) cc_final: 0.7316 (p) REVERT: C 331 LYS cc_start: 0.8218 (mttt) cc_final: 0.7990 (mtpp) REVERT: C 342 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6753 (tt0) REVERT: C 347 LYS cc_start: 0.7808 (mttt) cc_final: 0.7539 (mmtp) REVERT: C 369 LYS cc_start: 0.6913 (tttt) cc_final: 0.6410 (ttmp) REVERT: C 372 GLU cc_start: 0.6994 (tt0) cc_final: 0.6595 (mm-30) REVERT: D 311 LYS cc_start: 0.5564 (mtmt) cc_final: 0.5254 (tttp) REVERT: D 342 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6994 (tt0) REVERT: D 345 ASP cc_start: 0.7850 (t70) cc_final: 0.7626 (t70) REVERT: D 369 LYS cc_start: 0.7043 (tttt) cc_final: 0.6527 (ttmm) REVERT: D 372 GLU cc_start: 0.7649 (tt0) cc_final: 0.7058 (mm-30) REVERT: D 375 LYS cc_start: 0.5756 (ttpt) cc_final: 0.5352 (ttmm) REVERT: E 311 LYS cc_start: 0.5899 (mtmt) cc_final: 0.5625 (ttpt) REVERT: E 314 ASP cc_start: 0.5282 (t70) cc_final: 0.5015 (t70) REVERT: E 316 SER cc_start: 0.6531 (OUTLIER) cc_final: 0.6131 (p) REVERT: E 342 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7174 (tt0) REVERT: E 347 LYS cc_start: 0.7905 (mttt) cc_final: 0.7662 (mmtp) REVERT: E 348 ASP cc_start: 0.7964 (t0) cc_final: 0.7731 (t0) REVERT: E 349 ARG cc_start: 0.6710 (mtm180) cc_final: 0.6375 (mtt180) REVERT: E 369 LYS cc_start: 0.7566 (tttt) cc_final: 0.6942 (ttmt) outliers start: 4 outliers final: 1 residues processed: 109 average time/residue: 3.2625 time to fit residues: 362.3940 Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3180 Z= 0.153 Angle : 0.511 5.438 4254 Z= 0.264 Chirality : 0.049 0.142 480 Planarity : 0.002 0.019 540 Dihedral : 5.584 19.265 420 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.39 % Allowed : 9.72 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.003 0.001 PHE C 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG c 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 0.512 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: 0.6782 (m) cc_final: 0.6325 (p) REVERT: B 338 GLU cc_start: 0.7572 (tt0) cc_final: 0.7335 (mt-10) REVERT: B 342 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6531 (mp0) REVERT: B 343 LYS cc_start: 0.7943 (mttt) cc_final: 0.7434 (mtmt) REVERT: B 347 LYS cc_start: 0.7628 (mttt) cc_final: 0.7263 (mmtt) REVERT: c 342 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6381 (mp0) REVERT: c 343 LYS cc_start: 0.8159 (mttt) cc_final: 0.7649 (mtmm) REVERT: c 347 LYS cc_start: 0.7656 (mttt) cc_final: 0.7438 (mmtt) REVERT: c 349 ARG cc_start: 0.6770 (mtm180) cc_final: 0.5571 (mmp-170) REVERT: c 369 LYS cc_start: 0.7833 (tttt) cc_final: 0.7393 (tppp) REVERT: A 342 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6644 (mp0) REVERT: A 343 LYS cc_start: 0.7894 (mttt) cc_final: 0.7484 (mtmt) REVERT: A 347 LYS cc_start: 0.7681 (mttt) cc_final: 0.7220 (mppt) REVERT: A 349 ARG cc_start: 0.6901 (mtm180) cc_final: 0.6530 (mtp180) REVERT: C 311 LYS cc_start: 0.5116 (mtmt) cc_final: 0.4801 (mttt) REVERT: C 320 SER cc_start: 0.7690 (t) cc_final: 0.7361 (p) REVERT: C 331 LYS cc_start: 0.8218 (mttt) cc_final: 0.7982 (mtpp) REVERT: C 342 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6735 (tt0) REVERT: C 347 LYS cc_start: 0.7791 (mttt) cc_final: 0.7549 (mmtp) REVERT: C 369 LYS cc_start: 0.6905 (tttt) cc_final: 0.6415 (ttmp) REVERT: C 372 GLU cc_start: 0.6992 (tt0) cc_final: 0.6652 (mm-30) REVERT: D 311 LYS cc_start: 0.5592 (mtmt) cc_final: 0.5352 (tttm) REVERT: D 342 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7005 (tt0) REVERT: D 345 ASP cc_start: 0.7805 (t70) cc_final: 0.7554 (t70) REVERT: D 369 LYS cc_start: 0.7028 (tttt) cc_final: 0.6513 (ttmm) REVERT: D 372 GLU cc_start: 0.7669 (tt0) cc_final: 0.7134 (mm-30) REVERT: D 375 LYS cc_start: 0.5778 (ttpt) cc_final: 0.5351 (ttmm) REVERT: E 311 LYS cc_start: 0.5906 (mtmt) cc_final: 0.5669 (ttpt) REVERT: E 314 ASP cc_start: 0.5360 (t70) cc_final: 0.4972 (t70) REVERT: E 316 SER cc_start: 0.6480 (OUTLIER) cc_final: 0.6099 (p) REVERT: E 342 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7160 (tt0) REVERT: E 347 LYS cc_start: 0.7923 (mttt) cc_final: 0.7679 (mmtp) REVERT: E 348 ASP cc_start: 0.7949 (t0) cc_final: 0.7722 (t0) REVERT: E 349 ARG cc_start: 0.6740 (mtm180) cc_final: 0.6380 (mtt180) REVERT: E 369 LYS cc_start: 0.7580 (tttt) cc_final: 0.7050 (ttmp) REVERT: E 372 GLU cc_start: 0.6760 (tt0) cc_final: 0.6527 (tt0) outliers start: 5 outliers final: 1 residues processed: 106 average time/residue: 3.2304 time to fit residues: 349.3519 Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.7407 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3180 Z= 0.177 Angle : 0.526 5.531 4254 Z= 0.272 Chirality : 0.049 0.143 480 Planarity : 0.002 0.017 540 Dihedral : 5.607 20.099 420 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.11 % Allowed : 9.44 % Favored : 89.44 % 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 329 PHE 0.005 0.001 PHE C 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG B 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 112 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 108 time to evaluate : 0.665 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: 0.6957 (m) cc_final: 0.6382 (p) REVERT: B 342 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6508 (mp0) REVERT: B 343 LYS cc_start: 0.7930 (mttt) cc_final: 0.7429 (mtmt) REVERT: B 347 LYS cc_start: 0.7637 (mttt) cc_final: 0.7203 (mmtp) REVERT: c 342 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6360 (mp0) REVERT: c 343 LYS cc_start: 0.8159 (mttt) cc_final: 0.7638 (mtmm) REVERT: c 349 ARG cc_start: 0.6782 (mtm180) cc_final: 0.5564 (mmp-170) REVERT: c 369 LYS cc_start: 0.7828 (tttt) cc_final: 0.7387 (tppp) REVERT: A 342 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6653 (mp0) REVERT: A 343 LYS cc_start: 0.7892 (mttt) cc_final: 0.7465 (mtmt) REVERT: A 347 LYS cc_start: 0.7699 (mttt) cc_final: 0.7227 (mppt) REVERT: A 349 ARG cc_start: 0.6909 (mtm180) cc_final: 0.6536 (mtp180) REVERT: C 311 LYS cc_start: 0.5134 (mtmt) cc_final: 0.4819 (mttt) REVERT: C 320 SER cc_start: 0.7704 (t) cc_final: 0.7361 (p) REVERT: C 331 LYS cc_start: 0.8204 (mttt) cc_final: 0.7970 (mtpp) REVERT: C 342 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6716 (tt0) REVERT: C 347 LYS cc_start: 0.7799 (mttt) cc_final: 0.7525 (mmtp) REVERT: C 369 LYS cc_start: 0.6889 (tttt) cc_final: 0.6401 (ttmp) REVERT: C 372 GLU cc_start: 0.6982 (tt0) cc_final: 0.6664 (mm-30) REVERT: D 311 LYS cc_start: 0.5634 (mtmt) cc_final: 0.5370 (tttm) REVERT: D 342 GLU cc_start: 0.7481 (mt-10) cc_final: 0.6985 (tt0) REVERT: D 345 ASP cc_start: 0.7943 (t70) cc_final: 0.7524 (t0) REVERT: D 369 LYS cc_start: 0.7021 (tttt) cc_final: 0.6477 (ttmm) REVERT: D 372 GLU cc_start: 0.7654 (tt0) cc_final: 0.7123 (mm-30) REVERT: D 375 LYS cc_start: 0.5656 (ttpt) cc_final: 0.5267 (ttmm) REVERT: E 311 LYS cc_start: 0.5933 (mtmt) cc_final: 0.5692 (ttpt) REVERT: E 316 SER cc_start: 0.6412 (OUTLIER) cc_final: 0.6035 (p) REVERT: E 342 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7145 (tt0) REVERT: E 347 LYS cc_start: 0.7921 (mttt) cc_final: 0.7670 (mmtp) REVERT: E 348 ASP cc_start: 0.7945 (t0) cc_final: 0.7710 (t0) REVERT: E 349 ARG cc_start: 0.6761 (mtm180) cc_final: 0.6402 (mtt180) REVERT: E 369 LYS cc_start: 0.7586 (tttt) cc_final: 0.7067 (ttmp) REVERT: E 372 GLU cc_start: 0.6800 (tt0) cc_final: 0.6544 (tt0) outliers start: 4 outliers final: 0 residues processed: 110 average time/residue: 3.1281 time to fit residues: 351.1898 Evaluate side-chains 104 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN c 351 GLN c 374 HIS A 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4697 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= 0.213 Angle : 0.566 5.764 4254 Z= 0.291 Chirality : 0.050 0.149 480 Planarity : 0.002 0.015 540 Dihedral : 5.728 19.811 420 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.83 % Allowed : 11.39 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.30), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS c 329 PHE 0.005 0.001 PHE C 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG B 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 107 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.7058 (m) cc_final: 0.6517 (p) REVERT: B 342 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6464 (mp0) REVERT: B 343 LYS cc_start: 0.7918 (mttt) cc_final: 0.7422 (mtmt) REVERT: B 347 LYS cc_start: 0.7637 (mttt) cc_final: 0.7266 (mmtt) REVERT: c 342 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6358 (mp0) REVERT: c 343 LYS cc_start: 0.8136 (mttt) cc_final: 0.7615 (mtmt) REVERT: c 349 ARG cc_start: 0.6774 (mtm180) cc_final: 0.5533 (mmp-170) REVERT: c 369 LYS cc_start: 0.7805 (tttt) cc_final: 0.7372 (tppp) REVERT: A 342 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6655 (mp0) REVERT: A 343 LYS cc_start: 0.7883 (mttt) cc_final: 0.7456 (mtmt) REVERT: A 347 LYS cc_start: 0.7725 (mttt) cc_final: 0.7189 (mptt) REVERT: A 349 ARG cc_start: 0.6953 (mtm180) cc_final: 0.6464 (mtp180) REVERT: A 369 LYS cc_start: 0.7918 (tttt) cc_final: 0.7462 (tppp) REVERT: C 311 LYS cc_start: 0.5163 (mtmt) cc_final: 0.4814 (mttt) REVERT: C 320 SER cc_start: 0.7696 (t) cc_final: 0.7369 (p) REVERT: C 331 LYS cc_start: 0.8207 (mttt) cc_final: 0.7972 (mtpp) REVERT: C 342 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6717 (tt0) REVERT: C 369 LYS cc_start: 0.6900 (tttt) cc_final: 0.6420 (ttmp) REVERT: C 372 GLU cc_start: 0.6986 (tt0) cc_final: 0.6646 (mm-30) REVERT: D 311 LYS cc_start: 0.5633 (mtmt) cc_final: 0.5352 (tttm) REVERT: D 342 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6976 (tt0) REVERT: D 345 ASP cc_start: 0.7924 (t70) cc_final: 0.7490 (t0) REVERT: D 369 LYS cc_start: 0.7018 (tttt) cc_final: 0.6462 (ttmm) REVERT: D 372 GLU cc_start: 0.7634 (tt0) cc_final: 0.7058 (mm-30) REVERT: D 375 LYS cc_start: 0.5528 (ttpt) cc_final: 0.5135 (ttmm) REVERT: E 311 LYS cc_start: 0.5967 (mtmt) cc_final: 0.5684 (ttpt) REVERT: E 316 SER cc_start: 0.6278 (OUTLIER) cc_final: 0.5896 (p) REVERT: E 342 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7174 (tt0) REVERT: E 347 LYS cc_start: 0.7945 (mttt) cc_final: 0.7667 (mmtp) REVERT: E 348 ASP cc_start: 0.7931 (t0) cc_final: 0.7680 (t0) REVERT: E 349 ARG cc_start: 0.6745 (mtm180) cc_final: 0.6373 (mtt180) REVERT: E 369 LYS cc_start: 0.7553 (tttt) cc_final: 0.7025 (ttmp) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 3.2046 time to fit residues: 343.2733 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER 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: 7.9990 chunk 3 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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: 0.7405 moved from start: 0.4819 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= 0.150 Angle : 0.516 5.799 4254 Z= 0.262 Chirality : 0.049 0.140 480 Planarity : 0.002 0.017 540 Dihedral : 5.394 20.010 420 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.83 % Allowed : 11.39 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.23), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS c 362 PHE 0.004 0.001 PHE D 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG B 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 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6966 (m) cc_final: 0.6424 (p) REVERT: B 342 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6472 (mp0) REVERT: B 343 LYS cc_start: 0.7955 (mttt) cc_final: 0.7465 (mtmt) REVERT: B 347 LYS cc_start: 0.7608 (mttt) cc_final: 0.7202 (mmtp) REVERT: B 370 LYS cc_start: 0.6715 (mttp) cc_final: 0.6299 (mttt) REVERT: c 342 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6363 (mp0) REVERT: c 343 LYS cc_start: 0.8156 (mttt) cc_final: 0.7647 (mtmt) REVERT: c 349 ARG cc_start: 0.6807 (mtm180) cc_final: 0.5641 (mmp-170) REVERT: c 369 LYS cc_start: 0.7798 (tttt) cc_final: 0.7357 (tppp) REVERT: A 342 GLU cc_start: 0.7499 (mt-10) cc_final: 0.6631 (mp0) REVERT: A 343 LYS cc_start: 0.7871 (mttt) cc_final: 0.7448 (mtmt) REVERT: A 347 LYS cc_start: 0.7698 (mttt) cc_final: 0.7228 (mppt) REVERT: A 349 ARG cc_start: 0.6937 (mtm180) cc_final: 0.6548 (mtp180) REVERT: A 369 LYS cc_start: 0.7964 (tttt) cc_final: 0.7518 (tppp) REVERT: C 311 LYS cc_start: 0.5113 (mtmt) cc_final: 0.4785 (mttt) REVERT: C 320 SER cc_start: 0.7709 (t) cc_final: 0.7368 (p) REVERT: C 331 LYS cc_start: 0.8205 (mttt) cc_final: 0.7968 (mtpp) REVERT: C 342 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6753 (tt0) REVERT: C 369 LYS cc_start: 0.6872 (tttt) cc_final: 0.6390 (ttmp) REVERT: C 372 GLU cc_start: 0.7055 (tt0) cc_final: 0.6730 (mm-30) REVERT: D 311 LYS cc_start: 0.5663 (mtmt) cc_final: 0.5380 (tttm) REVERT: D 342 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6989 (tt0) REVERT: D 345 ASP cc_start: 0.7879 (t70) cc_final: 0.7457 (t0) REVERT: D 369 LYS cc_start: 0.7056 (tttt) cc_final: 0.6496 (ttmm) REVERT: D 372 GLU cc_start: 0.7637 (tt0) cc_final: 0.7077 (mm-30) REVERT: E 311 LYS cc_start: 0.5935 (mtmt) cc_final: 0.5685 (ttpt) REVERT: E 316 SER cc_start: 0.6356 (OUTLIER) cc_final: 0.6027 (p) REVERT: E 342 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7175 (tt0) REVERT: E 347 LYS cc_start: 0.7890 (mttt) cc_final: 0.7661 (mmtp) REVERT: E 348 ASP cc_start: 0.7943 (t0) cc_final: 0.7715 (t0) REVERT: E 349 ARG cc_start: 0.6760 (mtm180) cc_final: 0.6406 (mtt180) REVERT: E 369 LYS cc_start: 0.7574 (tttt) cc_final: 0.7037 (ttmp) outliers start: 3 outliers final: 1 residues processed: 106 average time/residue: 3.0700 time to fit residues: 331.9852 Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER 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: 3.9990 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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: 0.4936 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= 0.132 Angle : 0.502 5.759 4254 Z= 0.251 Chirality : 0.049 0.139 480 Planarity : 0.002 0.019 540 Dihedral : 5.136 19.707 420 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.83 % Allowed : 11.39 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.31), residues: 402 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (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 D 346 TYR 0.005 0.001 TYR c 310 ARG 0.001 0.000 ARG B 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 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.6840 (m) cc_final: 0.6333 (p) REVERT: B 342 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6499 (mp0) REVERT: B 343 LYS cc_start: 0.7975 (mttt) cc_final: 0.7488 (mtmt) REVERT: B 347 LYS cc_start: 0.7593 (mttt) cc_final: 0.7197 (mmtp) REVERT: c 342 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6361 (mp0) REVERT: c 343 LYS cc_start: 0.8171 (mttt) cc_final: 0.7660 (mtmt) REVERT: c 349 ARG cc_start: 0.6840 (mtm180) cc_final: 0.5670 (mmp-170) REVERT: A 342 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6651 (mp0) REVERT: A 343 LYS cc_start: 0.7882 (mttt) cc_final: 0.7446 (mtmt) REVERT: A 347 LYS cc_start: 0.7703 (mttt) cc_final: 0.7224 (mppt) REVERT: A 349 ARG cc_start: 0.6942 (mtm180) cc_final: 0.6547 (mtp180) REVERT: C 311 LYS cc_start: 0.5110 (mtmt) cc_final: 0.4753 (mttt) REVERT: C 320 SER cc_start: 0.7733 (t) cc_final: 0.7359 (p) REVERT: C 331 LYS cc_start: 0.8240 (mttt) cc_final: 0.8000 (mtpp) REVERT: C 342 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6781 (tt0) REVERT: C 369 LYS cc_start: 0.6879 (tttt) cc_final: 0.6402 (ttmp) REVERT: C 372 GLU cc_start: 0.7071 (tt0) cc_final: 0.6746 (mm-30) REVERT: D 311 LYS cc_start: 0.5669 (mtmt) cc_final: 0.5371 (tttp) REVERT: D 342 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7013 (tt0) REVERT: D 345 ASP cc_start: 0.7813 (t70) cc_final: 0.7408 (t0) REVERT: D 369 LYS cc_start: 0.7103 (tttt) cc_final: 0.6542 (ttmm) REVERT: D 372 GLU cc_start: 0.7639 (tt0) cc_final: 0.7123 (mm-30) REVERT: E 311 LYS cc_start: 0.5958 (mtmt) cc_final: 0.5710 (ttpt) REVERT: E 316 SER cc_start: 0.6439 (OUTLIER) cc_final: 0.6118 (p) REVERT: E 342 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7139 (tt0) REVERT: E 347 LYS cc_start: 0.7885 (mttt) cc_final: 0.7673 (mmtp) REVERT: E 349 ARG cc_start: 0.6760 (mtm180) cc_final: 0.6453 (mtt180) REVERT: E 369 LYS cc_start: 0.7558 (tttt) cc_final: 0.7019 (ttmp) outliers start: 3 outliers final: 2 residues processed: 106 average time/residue: 3.1958 time to fit residues: 345.6060 Evaluate side-chains 105 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 376 LEU 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: 7.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7390 moved from start: 0.5014 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= 0.132 Angle : 0.497 5.499 4254 Z= 0.248 Chirality : 0.049 0.140 480 Planarity : 0.002 0.020 540 Dihedral : 5.012 19.484 420 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.56 % Allowed : 11.67 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (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 362 PHE 0.003 0.001 PHE E 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 0.571 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: 0.6751 (m) cc_final: 0.6274 (p) REVERT: B 342 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6492 (mp0) REVERT: B 343 LYS cc_start: 0.7984 (mttt) cc_final: 0.7502 (mtmt) REVERT: B 347 LYS cc_start: 0.7595 (mttt) cc_final: 0.7193 (mmtp) REVERT: c 342 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6365 (mp0) REVERT: c 343 LYS cc_start: 0.8173 (mttt) cc_final: 0.7662 (mtmt) REVERT: c 349 ARG cc_start: 0.6867 (mtm180) cc_final: 0.5685 (mmp-170) REVERT: A 342 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6880 (mp0) REVERT: A 343 LYS cc_start: 0.7880 (mttt) cc_final: 0.7444 (mtmt) REVERT: A 347 LYS cc_start: 0.7694 (mttt) cc_final: 0.7214 (mppt) REVERT: A 349 ARG cc_start: 0.6894 (mtm180) cc_final: 0.6505 (mtp180) REVERT: C 311 LYS cc_start: 0.5117 (mtmt) cc_final: 0.4787 (mttt) REVERT: C 320 SER cc_start: 0.7718 (t) cc_final: 0.7333 (p) REVERT: C 331 LYS cc_start: 0.8246 (mttt) cc_final: 0.8013 (mtpp) REVERT: C 342 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6780 (tt0) REVERT: C 369 LYS cc_start: 0.6878 (tttt) cc_final: 0.6406 (ttmp) REVERT: C 372 GLU cc_start: 0.7084 (tt0) cc_final: 0.6769 (mm-30) REVERT: D 311 LYS cc_start: 0.5672 (mtmt) cc_final: 0.5387 (tttm) REVERT: D 342 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7012 (tt0) REVERT: D 345 ASP cc_start: 0.7797 (t70) cc_final: 0.7411 (t0) REVERT: D 369 LYS cc_start: 0.7086 (tttt) cc_final: 0.6553 (ttmm) REVERT: D 372 GLU cc_start: 0.7609 (tt0) cc_final: 0.7087 (mm-30) REVERT: E 311 LYS cc_start: 0.5957 (mtmt) cc_final: 0.5711 (ttpt) REVERT: E 316 SER cc_start: 0.6370 (m) cc_final: 0.6064 (p) REVERT: E 342 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7126 (tt0) REVERT: E 347 LYS cc_start: 0.7882 (mttt) cc_final: 0.7667 (mmtp) REVERT: E 349 ARG cc_start: 0.6744 (mtm180) cc_final: 0.6468 (mtt180) REVERT: E 369 LYS cc_start: 0.7561 (tttt) cc_final: 0.7018 (ttmp) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 3.1483 time to fit residues: 343.8840 Evaluate side-chains 103 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 3 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 c 374 HIS A 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.197570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.147464 restraints weight = 7010.965| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.46 r_work: 0.4029 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3180 Z= 0.197 Angle : 0.558 6.053 4254 Z= 0.283 Chirality : 0.049 0.148 480 Planarity : 0.002 0.014 540 Dihedral : 5.406 19.640 420 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.56 % Allowed : 11.11 % 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: -2.15 (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 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE C 346 TYR 0.008 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6119.06 seconds wall clock time: 105 minutes 46.60 seconds (6346.60 seconds total)