Starting phenix.real_space_refine on Wed Feb 12 16:21:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6e_13227/02_2025/7p6e_13227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6e_13227/02_2025/7p6e_13227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2025/7p6e_13227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2025/7p6e_13227.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2025/7p6e_13227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2025/7p6e_13227.cif" } resolution = 3.4 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 5050 2.51 5 N 1500 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8090 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F, I, J, Q, R Time building chain proxies: 3.02, per 1000 atoms: 0.37 Number of scatterers: 8090 At special positions: 0 Unit cell: (182.85, 120.75, 40.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1520 8.00 N 1500 7.00 C 5050 6.00 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: 1.84 Conformation dependent library (CDL) restraints added in 900.0 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1900 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 275 through 279 removed outlier: 6.773A pdb=" N GLN A 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN C 279 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLN C 276 " --> pdb=" O ILE Q 277 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN Q 279 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 278 " --> pdb=" O ASN Q 279 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 285 through 287 removed outlier: 8.761A pdb=" N SER E 285 " --> pdb=" O ASN I 286 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N SER A 285 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 287 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL Q 287 " --> pdb=" O ASN C 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 306 through 310 removed outlier: 6.662A pdb=" N GLN E 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR I 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL E 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 314 through 315 removed outlier: 6.094A pdb=" N ASP A 314 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP C 314 " --> pdb=" O LEU Q 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 318 through 322 removed outlier: 6.611A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 318 " --> pdb=" O THR Q 319 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LYS Q 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER C 320 " --> pdb=" O LYS Q 321 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 336 through 341 removed outlier: 6.410A pdb=" N VAL C 337 " --> pdb=" O GLU Q 338 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LYS Q 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 339 " --> pdb=" O LYS Q 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AA8, first strand: chain 'J' and resid 275 through 279 removed outlier: 6.714A pdb=" N VAL F 275 " --> pdb=" O GLN J 276 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE J 278 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE F 277 " --> pdb=" O ILE J 278 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLN B 276 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN D 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 278 " --> pdb=" O ASN D 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 285 through 287 removed outlier: 8.703A pdb=" N SER F 285 " --> pdb=" O ASN J 286 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N SER B 285 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL D 287 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL R 287 " --> pdb=" O ASN D 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 306 through 310 removed outlier: 6.698A pdb=" N GLN F 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N TYR J 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL F 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 314 through 315 removed outlier: 6.120A pdb=" N ASP B 314 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP D 314 " --> pdb=" O LEU R 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 318 through 322 removed outlier: 6.448A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 318 " --> pdb=" O THR R 319 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LYS R 321 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER D 320 " --> pdb=" O LYS R 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 336 through 341 removed outlier: 6.301A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 337 " --> pdb=" O GLU R 338 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS R 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL D 339 " --> pdb=" O LYS R 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 351 removed outlier: 6.140A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL D 350 " --> pdb=" O GLN R 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 376 through 377 removed outlier: 6.738A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 376 " --> pdb=" O THR R 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 351 removed outlier: 6.173A pdb=" N VAL C 350 " --> pdb=" O GLN Q 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AB9, first strand: chain 'F' and resid 350 through 351 Processing sheet with id=AC1, first strand: chain 'F' and resid 376 through 377 85 hydrogen bonds defined for protein. 252 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: 1.88 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: 1.22 - 1.33: 2575 1.33 - 1.45: 675 1.45 - 1.56: 4920 1.56 - 1.68: 0 1.68 - 1.79: 20 Bond restraints: 8190 Sorted by residual: bond pdb=" CA ASN J 359 " pdb=" CB ASN J 359 " ideal model delta sigma weight residual 1.526 1.487 0.039 1.76e-02 3.23e+03 4.89e+00 bond pdb=" CA ASN D 359 " pdb=" CB ASN D 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.78e+00 bond pdb=" CA ASN E 359 " pdb=" CB ASN E 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.65e+00 bond pdb=" CA ASN A 359 " pdb=" CB ASN A 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.65e+00 bond pdb=" CA ASN Q 359 " pdb=" CB ASN Q 359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.76e-02 3.23e+03 4.64e+00 ... (remaining 8185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 9729 1.39 - 2.77: 975 2.77 - 4.16: 156 4.16 - 5.55: 60 5.55 - 6.93: 20 Bond angle restraints: 10940 Sorted by residual: angle pdb=" N ASP B 295 " pdb=" CA ASP B 295 " pdb=" C ASP B 295 " ideal model delta sigma weight residual 108.13 115.06 -6.93 1.72e+00 3.38e-01 1.63e+01 angle pdb=" N ASP E 295 " pdb=" CA ASP E 295 " pdb=" C ASP E 295 " ideal model delta sigma weight residual 108.13 115.04 -6.91 1.72e+00 3.38e-01 1.62e+01 angle pdb=" N ASP I 295 " pdb=" CA ASP I 295 " pdb=" C ASP I 295 " ideal model delta sigma weight residual 108.13 115.02 -6.89 1.72e+00 3.38e-01 1.60e+01 angle pdb=" N ASP R 295 " pdb=" CA ASP R 295 " pdb=" C ASP R 295 " ideal model delta sigma weight residual 108.13 115.02 -6.89 1.72e+00 3.38e-01 1.60e+01 angle pdb=" N ASP A 295 " pdb=" CA ASP A 295 " pdb=" C ASP A 295 " ideal model delta sigma weight residual 108.13 115.02 -6.89 1.72e+00 3.38e-01 1.60e+01 ... (remaining 10935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.54: 4200 7.54 - 15.09: 720 15.09 - 22.63: 100 22.63 - 30.17: 40 30.17 - 37.71: 40 Dihedral angle restraints: 5100 sinusoidal: 2160 harmonic: 2940 Sorted by residual: dihedral pdb=" CA PRO R 301 " pdb=" C PRO R 301 " pdb=" N GLY R 302 " pdb=" CA GLY R 302 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PRO C 301 " pdb=" C PRO C 301 " pdb=" N GLY C 302 " pdb=" CA GLY C 302 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA PRO A 301 " pdb=" C PRO A 301 " pdb=" N GLY A 302 " pdb=" CA GLY A 302 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 990 0.073 - 0.146: 240 0.146 - 0.220: 10 0.220 - 0.293: 0 0.293 - 0.366: 10 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB ILE R 360 " pdb=" CA ILE R 360 " pdb=" CG1 ILE R 360 " pdb=" CG2 ILE R 360 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB ILE J 360 " pdb=" CA ILE J 360 " pdb=" CG1 ILE J 360 " pdb=" CG2 ILE J 360 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE I 360 " pdb=" CA ILE I 360 " pdb=" CG1 ILE I 360 " pdb=" CG2 ILE I 360 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 1247 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 300 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO E 301 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL Q 300 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO Q 301 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO Q 301 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO Q 301 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 300 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO R 301 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " -0.032 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2457 2.87 - 3.37: 6930 3.37 - 3.88: 13405 3.88 - 4.39: 13511 4.39 - 4.90: 28040 Nonbonded interactions: 64343 Sorted by model distance: nonbonded pdb=" OD2 ASP D 295 " pdb=" NZ LYS D 311 " model vdw 2.358 3.120 nonbonded pdb=" OD2 ASP J 295 " pdb=" NZ LYS J 311 " model vdw 2.358 3.120 nonbonded pdb=" OD2 ASP E 295 " pdb=" NZ LYS E 311 " model vdw 2.359 3.120 nonbonded pdb=" OD2 ASP A 295 " pdb=" NZ LYS A 311 " model vdw 2.359 3.120 nonbonded pdb=" OD2 ASP Q 295 " pdb=" NZ LYS Q 311 " model vdw 2.359 3.120 ... (remaining 64338 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'Q' selection = chain 'R' } 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: 1.960 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 18.210 Find NCS groups from input model: 0.160 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.009 0.066 8190 Z= 0.582 Angle : 0.957 6.934 10940 Z= 0.533 Chirality : 0.065 0.366 1250 Planarity : 0.008 0.057 1390 Dihedral : 8.257 37.712 3200 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.18), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.14), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS J 299 PHE 0.015 0.006 PHE J 378 TYR 0.010 0.006 TYR I 310 ARG 0.001 0.000 ARG I 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.978 Fit side-chains REVERT: A 281 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8174 (ttmt) REVERT: A 295 ASP cc_start: 0.8838 (p0) cc_final: 0.8510 (p0) REVERT: B 281 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8352 (ttmt) REVERT: C 321 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7223 (tmtt) REVERT: D 321 LYS cc_start: 0.7467 (mtpt) cc_final: 0.7188 (tmtt) REVERT: E 281 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8429 (ttmt) REVERT: E 372 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7146 (mp0) REVERT: F 281 LYS cc_start: 0.8767 (tmtt) cc_final: 0.8370 (ttmt) REVERT: F 372 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7167 (mp0) REVERT: I 281 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8559 (tptp) REVERT: I 321 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7410 (pptt) REVERT: I 348 ASP cc_start: 0.8625 (t0) cc_final: 0.7856 (p0) REVERT: I 372 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7246 (mp0) REVERT: J 281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8663 (ttpt) REVERT: J 321 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7357 (pptt) REVERT: J 348 ASP cc_start: 0.8631 (t0) cc_final: 0.7846 (p0) REVERT: J 372 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6843 (mp0) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.2027 time to fit residues: 78.7214 Evaluate side-chains 127 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 HIS ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN ** E 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 374 HIS ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 336 GLN J 374 HIS Q 286 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.125258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.103286 restraints weight = 14369.797| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 3.76 r_work: 0.4111 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8190 Z= 0.343 Angle : 0.666 8.049 10940 Z= 0.335 Chirality : 0.051 0.143 1250 Planarity : 0.005 0.041 1390 Dihedral : 5.136 13.079 1060 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.79 % Allowed : 9.79 % Favored : 88.42 % 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: -4.57 (0.19), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 362 PHE 0.013 0.003 PHE A 346 TYR 0.026 0.003 TYR I 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8710 (tmtt) cc_final: 0.8265 (ttmt) REVERT: B 281 LYS cc_start: 0.8722 (tmtt) cc_final: 0.8287 (ttmt) REVERT: B 283 ASP cc_start: 0.8002 (t0) cc_final: 0.7582 (t0) REVERT: B 338 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7140 (tm-30) REVERT: C 321 LYS cc_start: 0.7117 (mtpt) cc_final: 0.6896 (tmtt) REVERT: C 362 HIS cc_start: 0.7697 (t-170) cc_final: 0.7161 (t-90) REVERT: D 338 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7392 (tm-30) REVERT: D 349 ARG cc_start: 0.7702 (mtt-85) cc_final: 0.7460 (mtt-85) REVERT: D 362 HIS cc_start: 0.7712 (t-170) cc_final: 0.7219 (t-90) REVERT: E 281 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8530 (tptp) REVERT: E 282 LEU cc_start: 0.7879 (tt) cc_final: 0.7679 (tt) REVERT: E 349 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7553 (mtm-85) REVERT: E 362 HIS cc_start: 0.7677 (t-90) cc_final: 0.7465 (t70) REVERT: E 372 GLU cc_start: 0.7855 (mt-10) cc_final: 0.6613 (mp0) REVERT: F 281 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8497 (tptp) REVERT: F 349 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7435 (mtm-85) REVERT: F 362 HIS cc_start: 0.7684 (t-90) cc_final: 0.7288 (t-90) REVERT: F 372 GLU cc_start: 0.7891 (mt-10) cc_final: 0.6733 (mp0) REVERT: I 281 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8621 (tptp) REVERT: I 314 ASP cc_start: 0.8311 (t0) cc_final: 0.8085 (t0) REVERT: I 348 ASP cc_start: 0.8708 (t0) cc_final: 0.8089 (p0) REVERT: I 362 HIS cc_start: 0.7500 (t70) cc_final: 0.7012 (t70) REVERT: J 281 LYS cc_start: 0.9021 (tmtt) cc_final: 0.8644 (tptp) REVERT: J 314 ASP cc_start: 0.8296 (t0) cc_final: 0.8074 (t0) REVERT: J 348 ASP cc_start: 0.8744 (t0) cc_final: 0.8100 (p0) REVERT: J 362 HIS cc_start: 0.7493 (t70) cc_final: 0.7140 (t70) REVERT: J 372 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6521 (mp0) REVERT: Q 356 SER cc_start: 0.8513 (m) cc_final: 0.8027 (p) outliers start: 17 outliers final: 14 residues processed: 186 average time/residue: 0.1916 time to fit residues: 49.2234 Evaluate side-chains 136 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS E 351 GLN F 351 GLN ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.207890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.180159 restraints weight = 14631.200| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 2.16 r_work: 0.4385 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4268 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8190 Z= 0.284 Angle : 0.628 8.343 10940 Z= 0.307 Chirality : 0.051 0.145 1250 Planarity : 0.004 0.037 1390 Dihedral : 4.870 13.081 1060 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.37 % Allowed : 13.16 % Favored : 83.47 % 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: -4.29 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.014 0.003 PHE J 378 TYR 0.018 0.002 TYR I 310 ARG 0.002 0.000 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8382 (ttmt) REVERT: A 338 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 281 LYS cc_start: 0.8840 (tmtt) cc_final: 0.8409 (ttpt) REVERT: B 283 ASP cc_start: 0.8108 (t0) cc_final: 0.7719 (t0) REVERT: B 338 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 283 ASP cc_start: 0.8156 (t0) cc_final: 0.7668 (t0) REVERT: D 338 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7509 (tm-30) REVERT: D 349 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7675 (mtt-85) REVERT: E 338 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7731 (tm-30) REVERT: E 349 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7808 (mtm-85) REVERT: E 372 GLU cc_start: 0.8176 (mt-10) cc_final: 0.6943 (mp0) REVERT: F 281 LYS cc_start: 0.8838 (tmtt) cc_final: 0.8635 (tptp) REVERT: F 338 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7698 (tm-30) REVERT: F 349 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7782 (mtm-85) REVERT: F 372 GLU cc_start: 0.8160 (mt-10) cc_final: 0.6879 (mp0) REVERT: I 281 LYS cc_start: 0.9026 (tmtt) cc_final: 0.8722 (tptp) REVERT: I 314 ASP cc_start: 0.8376 (t0) cc_final: 0.8134 (t0) REVERT: I 348 ASP cc_start: 0.8637 (t0) cc_final: 0.8160 (p0) REVERT: I 362 HIS cc_start: 0.7566 (t70) cc_final: 0.7244 (t-90) REVERT: I 379 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.6806 (tmm160) REVERT: J 281 LYS cc_start: 0.8983 (tmtt) cc_final: 0.8661 (tptp) REVERT: J 348 ASP cc_start: 0.8657 (t0) cc_final: 0.8181 (p0) REVERT: J 362 HIS cc_start: 0.7555 (t70) cc_final: 0.7276 (t-90) REVERT: J 372 GLU cc_start: 0.7920 (mt-10) cc_final: 0.6823 (mp0) REVERT: J 379 ARG cc_start: 0.8018 (ttt-90) cc_final: 0.6762 (tmm160) REVERT: R 349 ARG cc_start: 0.4734 (mmp-170) cc_final: 0.4515 (mmm160) outliers start: 32 outliers final: 22 residues processed: 176 average time/residue: 0.1940 time to fit residues: 46.7783 Evaluate side-chains 150 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 295 ASP Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.255663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5341 r_free = 0.5341 target = 0.205755 restraints weight = 15723.281| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.95 r_work: 0.4304 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4203 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8190 Z= 0.320 Angle : 0.638 7.247 10940 Z= 0.314 Chirality : 0.051 0.142 1250 Planarity : 0.003 0.032 1390 Dihedral : 4.829 13.237 1060 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.16 % Allowed : 14.32 % Favored : 82.53 % 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: -4.23 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 374 PHE 0.019 0.003 PHE A 346 TYR 0.010 0.002 TYR C 310 ARG 0.002 0.000 ARG R 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8352 (ttmt) REVERT: A 283 ASP cc_start: 0.8271 (t0) cc_final: 0.7966 (t0) REVERT: A 338 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7566 (tm-30) REVERT: B 281 LYS cc_start: 0.8851 (tmtt) cc_final: 0.8412 (ttmt) REVERT: B 283 ASP cc_start: 0.8185 (t0) cc_final: 0.7779 (t0) REVERT: B 338 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7301 (tm-30) REVERT: C 307 GLN cc_start: 0.9128 (tt0) cc_final: 0.8919 (tt0) REVERT: D 283 ASP cc_start: 0.7953 (t0) cc_final: 0.7711 (t0) REVERT: D 338 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7524 (tm-30) REVERT: D 349 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7647 (mtt-85) REVERT: E 338 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7417 (tm-30) REVERT: E 349 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7763 (mtm-85) REVERT: E 372 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6807 (mp0) REVERT: F 281 LYS cc_start: 0.8879 (tmtt) cc_final: 0.8437 (tptp) REVERT: F 295 ASP cc_start: 0.8920 (p0) cc_final: 0.8507 (p0) REVERT: F 338 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7326 (tm-30) REVERT: F 349 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7743 (mtm-85) REVERT: F 372 GLU cc_start: 0.8034 (mt-10) cc_final: 0.6788 (mp0) REVERT: I 281 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8709 (tptp) REVERT: I 338 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8023 (tm-30) REVERT: I 348 ASP cc_start: 0.8630 (t0) cc_final: 0.8113 (p0) REVERT: I 362 HIS cc_start: 0.7390 (t70) cc_final: 0.7087 (t-90) REVERT: I 379 ARG cc_start: 0.8137 (ttt-90) cc_final: 0.6745 (tmm160) REVERT: J 281 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8669 (tptp) REVERT: J 314 ASP cc_start: 0.8316 (t0) cc_final: 0.8046 (t0) REVERT: J 338 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7933 (tm-30) REVERT: J 348 ASP cc_start: 0.8637 (t0) cc_final: 0.8067 (p0) REVERT: J 362 HIS cc_start: 0.7377 (t70) cc_final: 0.7024 (t-170) REVERT: J 379 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.6711 (tmm160) outliers start: 30 outliers final: 24 residues processed: 167 average time/residue: 0.1961 time to fit residues: 45.1894 Evaluate side-chains 151 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.133778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.112850 restraints weight = 14900.171| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 3.52 r_work: 0.4232 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 8190 Z= 0.416 Angle : 0.669 6.604 10940 Z= 0.341 Chirality : 0.052 0.145 1250 Planarity : 0.003 0.033 1390 Dihedral : 5.057 14.226 1060 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.05 % Allowed : 16.63 % Favored : 80.32 % 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: -4.23 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 374 PHE 0.017 0.003 PHE A 346 TYR 0.013 0.003 TYR E 310 ARG 0.003 0.001 ARG R 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8243 (ttmt) REVERT: A 283 ASP cc_start: 0.8336 (t0) cc_final: 0.8133 (t0) REVERT: B 281 LYS cc_start: 0.8799 (tmtt) cc_final: 0.8331 (ttmt) REVERT: B 283 ASP cc_start: 0.8195 (t0) cc_final: 0.7907 (t0) REVERT: B 338 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7130 (tm-30) REVERT: C 307 GLN cc_start: 0.9120 (tt0) cc_final: 0.8910 (tt0) REVERT: D 338 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7326 (tm-30) REVERT: D 349 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7456 (mtt-85) REVERT: E 338 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7336 (tm-30) REVERT: E 349 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7572 (mtm-85) REVERT: F 281 LYS cc_start: 0.8940 (tmtt) cc_final: 0.8435 (tptp) REVERT: F 283 ASP cc_start: 0.8440 (t0) cc_final: 0.8212 (t0) REVERT: F 338 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7236 (tm-30) REVERT: F 349 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7663 (mtm-85) REVERT: I 281 LYS cc_start: 0.9043 (tmtt) cc_final: 0.8777 (tptp) REVERT: I 310 TYR cc_start: 0.9081 (t80) cc_final: 0.8535 (t80) REVERT: I 314 ASP cc_start: 0.8289 (t0) cc_final: 0.8030 (t0) REVERT: I 338 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7966 (tm-30) REVERT: I 348 ASP cc_start: 0.8835 (t0) cc_final: 0.7974 (p0) REVERT: I 362 HIS cc_start: 0.7374 (t70) cc_final: 0.7072 (t-90) REVERT: I 379 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.6756 (tmm160) REVERT: J 281 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8700 (tptp) REVERT: J 314 ASP cc_start: 0.8292 (t0) cc_final: 0.7974 (t0) REVERT: J 338 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7924 (tm-30) REVERT: J 348 ASP cc_start: 0.8840 (t0) cc_final: 0.7971 (p0) REVERT: J 362 HIS cc_start: 0.7399 (t70) cc_final: 0.7055 (t-170) REVERT: J 378 PHE cc_start: 0.8751 (m-10) cc_final: 0.8537 (m-10) REVERT: J 379 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.6808 (tmm160) outliers start: 29 outliers final: 27 residues processed: 160 average time/residue: 0.1931 time to fit residues: 42.7052 Evaluate side-chains 157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 360 ILE Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 360 ILE Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 0.0070 chunk 89 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.136173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.115169 restraints weight = 14740.418| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 3.54 r_work: 0.4261 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8190 Z= 0.297 Angle : 0.617 7.881 10940 Z= 0.309 Chirality : 0.051 0.140 1250 Planarity : 0.003 0.027 1390 Dihedral : 4.789 14.105 1060 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.95 % Allowed : 18.00 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 299 PHE 0.016 0.003 PHE A 346 TYR 0.024 0.004 TYR Q 310 ARG 0.002 0.000 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8840 (tmtt) cc_final: 0.8298 (ttmt) REVERT: B 281 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8302 (ttmt) REVERT: B 283 ASP cc_start: 0.8196 (t0) cc_final: 0.7803 (t0) REVERT: C 349 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7368 (mtp85) REVERT: D 338 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7174 (tm-30) REVERT: D 349 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7480 (mtt-85) REVERT: E 338 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7297 (tm-30) REVERT: E 349 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7709 (mtm-85) REVERT: E 372 GLU cc_start: 0.7904 (mt-10) cc_final: 0.6647 (mp0) REVERT: F 281 LYS cc_start: 0.8850 (tmtt) cc_final: 0.8378 (tptp) REVERT: F 338 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7246 (tm-30) REVERT: F 349 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7737 (mtm-85) REVERT: F 372 GLU cc_start: 0.7828 (mt-10) cc_final: 0.6601 (mp0) REVERT: I 281 LYS cc_start: 0.9024 (tmtt) cc_final: 0.8741 (tptp) REVERT: I 283 ASP cc_start: 0.8949 (t0) cc_final: 0.8478 (t0) REVERT: I 314 ASP cc_start: 0.8278 (t0) cc_final: 0.7985 (t0) REVERT: I 338 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7942 (tm-30) REVERT: I 348 ASP cc_start: 0.8782 (t0) cc_final: 0.8073 (p0) REVERT: I 362 HIS cc_start: 0.7406 (t70) cc_final: 0.7072 (t-90) REVERT: I 379 ARG cc_start: 0.8119 (ttt-90) cc_final: 0.6728 (tmm160) REVERT: J 281 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8677 (tptp) REVERT: J 338 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7874 (tm-30) REVERT: J 348 ASP cc_start: 0.8807 (t0) cc_final: 0.8072 (p0) REVERT: J 362 HIS cc_start: 0.7368 (t70) cc_final: 0.7033 (t-170) REVERT: J 379 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.6740 (tmm160) outliers start: 28 outliers final: 25 residues processed: 172 average time/residue: 0.2152 time to fit residues: 49.7115 Evaluate side-chains 164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 24 optimal weight: 0.4980 chunk 79 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.209792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5097 r_free = 0.5097 target = 0.179203 restraints weight = 14654.268| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 2.07 r_work: 0.4371 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4260 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8190 Z= 0.281 Angle : 0.618 8.670 10940 Z= 0.308 Chirality : 0.051 0.141 1250 Planarity : 0.003 0.025 1390 Dihedral : 4.709 13.864 1060 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.05 % Allowed : 18.21 % Favored : 78.74 % 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: -4.14 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 299 PHE 0.015 0.003 PHE F 346 TYR 0.016 0.003 TYR E 310 ARG 0.002 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8944 (tmtt) cc_final: 0.8456 (ttmt) REVERT: A 283 ASP cc_start: 0.8159 (t0) cc_final: 0.7958 (t0) REVERT: B 281 LYS cc_start: 0.8877 (tmtt) cc_final: 0.8427 (ttmt) REVERT: C 349 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7621 (mtp85) REVERT: D 338 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7372 (tm-30) REVERT: D 349 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7747 (mtt-85) REVERT: E 338 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7563 (tm-30) REVERT: E 349 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7895 (mtm-85) REVERT: E 372 GLU cc_start: 0.8113 (mt-10) cc_final: 0.6902 (mp0) REVERT: F 281 LYS cc_start: 0.8937 (tmtt) cc_final: 0.8546 (tptt) REVERT: F 338 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7425 (tm-30) REVERT: F 349 ARG cc_start: 0.8424 (mtp85) cc_final: 0.7937 (mtm-85) REVERT: F 372 GLU cc_start: 0.8056 (mt-10) cc_final: 0.6871 (mp0) REVERT: I 281 LYS cc_start: 0.9043 (tmtt) cc_final: 0.8800 (tptp) REVERT: I 314 ASP cc_start: 0.8442 (t0) cc_final: 0.8173 (t0) REVERT: I 338 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8026 (tm-30) REVERT: I 348 ASP cc_start: 0.8688 (t0) cc_final: 0.8142 (p0) REVERT: I 362 HIS cc_start: 0.7549 (t70) cc_final: 0.7220 (t-90) REVERT: I 379 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.6780 (tmm160) REVERT: J 281 LYS cc_start: 0.9040 (tmtt) cc_final: 0.8754 (tptp) REVERT: J 314 ASP cc_start: 0.8414 (t0) cc_final: 0.8179 (t0) REVERT: J 338 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8026 (tm-30) REVERT: J 348 ASP cc_start: 0.8703 (t0) cc_final: 0.8150 (p0) REVERT: J 362 HIS cc_start: 0.7516 (t70) cc_final: 0.7188 (t-170) REVERT: J 379 ARG cc_start: 0.8239 (ttt-90) cc_final: 0.6684 (tmm160) outliers start: 29 outliers final: 25 residues processed: 165 average time/residue: 0.2071 time to fit residues: 46.1647 Evaluate side-chains 162 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 95 optimal weight: 0.0040 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.208608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5089 r_free = 0.5089 target = 0.177860 restraints weight = 14780.702| |-----------------------------------------------------------------------------| r_work (start): 0.4465 rms_B_bonded: 2.08 r_work: 0.4353 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.4238 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8190 Z= 0.313 Angle : 0.632 8.032 10940 Z= 0.317 Chirality : 0.051 0.141 1250 Planarity : 0.003 0.026 1390 Dihedral : 4.720 14.024 1060 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.26 % Allowed : 18.11 % Favored : 78.63 % 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: -4.15 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Q 299 PHE 0.015 0.003 PHE F 346 TYR 0.026 0.004 TYR Q 310 ARG 0.002 0.000 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8977 (tmtt) cc_final: 0.8475 (ttmt) REVERT: B 281 LYS cc_start: 0.8901 (tmtt) cc_final: 0.8466 (ttmt) REVERT: C 349 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7661 (mtp85) REVERT: D 338 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7297 (tm-30) REVERT: D 349 ARG cc_start: 0.8095 (mtt-85) cc_final: 0.7772 (mtt-85) REVERT: E 338 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7502 (tm-30) REVERT: E 349 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7888 (mtm-85) REVERT: E 372 GLU cc_start: 0.8074 (mt-10) cc_final: 0.6895 (mp0) REVERT: F 281 LYS cc_start: 0.8971 (tmtt) cc_final: 0.8577 (tptp) REVERT: F 338 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7529 (tm-30) REVERT: F 349 ARG cc_start: 0.8406 (mtp85) cc_final: 0.7935 (mtm-85) REVERT: F 372 GLU cc_start: 0.8034 (mt-10) cc_final: 0.6842 (mp0) REVERT: I 281 LYS cc_start: 0.9063 (tmtt) cc_final: 0.8820 (tptp) REVERT: I 338 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8050 (tm-30) REVERT: I 348 ASP cc_start: 0.8719 (t0) cc_final: 0.8082 (p0) REVERT: I 362 HIS cc_start: 0.7552 (t70) cc_final: 0.7224 (t-90) REVERT: I 379 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.6789 (tmm160) REVERT: J 281 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8779 (tptp) REVERT: J 314 ASP cc_start: 0.8432 (t0) cc_final: 0.8183 (t0) REVERT: J 338 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8034 (tm-30) REVERT: J 348 ASP cc_start: 0.8723 (t0) cc_final: 0.8093 (p0) REVERT: J 362 HIS cc_start: 0.7522 (t70) cc_final: 0.7194 (t-170) REVERT: J 379 ARG cc_start: 0.8264 (ttt-90) cc_final: 0.6701 (tmm160) outliers start: 31 outliers final: 28 residues processed: 159 average time/residue: 0.2057 time to fit residues: 44.2117 Evaluate side-chains 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4855 r_free = 0.4855 target = 0.210564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5107 r_free = 0.5107 target = 0.179771 restraints weight = 14855.541| |-----------------------------------------------------------------------------| r_work (start): 0.4489 rms_B_bonded: 2.09 r_work: 0.4374 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8190 Z= 0.272 Angle : 0.626 8.531 10940 Z= 0.310 Chirality : 0.051 0.139 1250 Planarity : 0.003 0.022 1390 Dihedral : 4.644 14.010 1060 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.95 % Allowed : 19.16 % Favored : 77.89 % 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: -4.13 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 299 PHE 0.016 0.003 PHE F 346 TYR 0.017 0.003 TYR A 310 ARG 0.002 0.000 ARG Q 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8737 (tptp) REVERT: A 379 ARG cc_start: 0.7597 (ttt-90) cc_final: 0.7389 (tpt90) REVERT: B 281 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8439 (ttmt) REVERT: C 349 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7671 (mtp85) REVERT: D 338 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7381 (tm-30) REVERT: D 349 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7773 (mtt-85) REVERT: E 338 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7526 (tm-30) REVERT: E 349 ARG cc_start: 0.8341 (mtp85) cc_final: 0.7893 (mtm-85) REVERT: E 372 GLU cc_start: 0.8071 (mt-10) cc_final: 0.6892 (mp0) REVERT: F 281 LYS cc_start: 0.8890 (tmtt) cc_final: 0.8511 (tptp) REVERT: F 338 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7451 (tm-30) REVERT: F 349 ARG cc_start: 0.8357 (mtp85) cc_final: 0.7902 (mtm-85) REVERT: F 372 GLU cc_start: 0.8047 (mt-10) cc_final: 0.6858 (mp0) REVERT: I 281 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8810 (tptp) REVERT: I 338 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8003 (tm-30) REVERT: I 348 ASP cc_start: 0.8668 (t0) cc_final: 0.8140 (p0) REVERT: I 362 HIS cc_start: 0.7564 (t70) cc_final: 0.7248 (t-90) REVERT: I 379 ARG cc_start: 0.8280 (ttt-90) cc_final: 0.6797 (tmm160) REVERT: J 281 LYS cc_start: 0.9084 (tmtt) cc_final: 0.8768 (tptp) REVERT: J 314 ASP cc_start: 0.8431 (t0) cc_final: 0.8173 (t0) REVERT: J 338 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8014 (tm-30) REVERT: J 348 ASP cc_start: 0.8672 (t0) cc_final: 0.8150 (p0) REVERT: J 362 HIS cc_start: 0.7528 (t70) cc_final: 0.7197 (t-170) REVERT: J 379 ARG cc_start: 0.8269 (ttt-90) cc_final: 0.6705 (tmm160) outliers start: 28 outliers final: 23 residues processed: 162 average time/residue: 0.2123 time to fit residues: 46.4143 Evaluate side-chains 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 360 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 97 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 99 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.211425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.180629 restraints weight = 14682.225| |-----------------------------------------------------------------------------| r_work (start): 0.4509 rms_B_bonded: 2.09 r_work: 0.4396 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4284 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8190 Z= 0.248 Angle : 0.623 8.860 10940 Z= 0.305 Chirality : 0.051 0.137 1250 Planarity : 0.003 0.022 1390 Dihedral : 4.542 13.523 1060 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.42 % Allowed : 19.47 % Favored : 78.11 % 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: -4.10 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS Q 299 PHE 0.015 0.003 PHE F 346 TYR 0.021 0.004 TYR R 310 ARG 0.001 0.000 ARG Q 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8737 (tptp) REVERT: A 379 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.7390 (tpt90) REVERT: B 281 LYS cc_start: 0.8884 (tmtt) cc_final: 0.8422 (ttmt) REVERT: C 349 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7689 (mtp85) REVERT: D 338 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7358 (tm-30) REVERT: D 349 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7776 (mtt-85) REVERT: E 310 TYR cc_start: 0.9199 (t80) cc_final: 0.8858 (t80) REVERT: E 338 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7505 (tm-30) REVERT: E 349 ARG cc_start: 0.8352 (mtp85) cc_final: 0.7887 (mtm-85) REVERT: E 372 GLU cc_start: 0.8060 (mt-10) cc_final: 0.6884 (mp0) REVERT: F 281 LYS cc_start: 0.8866 (tmtt) cc_final: 0.8492 (tptp) REVERT: F 310 TYR cc_start: 0.9189 (t80) cc_final: 0.8923 (t80) REVERT: F 338 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7440 (tm-30) REVERT: F 349 ARG cc_start: 0.8353 (mtp85) cc_final: 0.7899 (mtm-85) REVERT: F 372 GLU cc_start: 0.8039 (mt-10) cc_final: 0.6847 (mp0) REVERT: I 281 LYS cc_start: 0.9055 (tmtt) cc_final: 0.8803 (tptp) REVERT: I 338 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8032 (tm-30) REVERT: I 348 ASP cc_start: 0.8630 (t0) cc_final: 0.8126 (p0) REVERT: I 362 HIS cc_start: 0.7571 (t70) cc_final: 0.7230 (t-90) REVERT: I 379 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.6745 (tmm160) REVERT: J 281 LYS cc_start: 0.9085 (tmtt) cc_final: 0.8758 (tptp) REVERT: J 338 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7991 (tm-30) REVERT: J 348 ASP cc_start: 0.8636 (t0) cc_final: 0.8148 (p0) REVERT: J 362 HIS cc_start: 0.7527 (t70) cc_final: 0.7200 (t-90) REVERT: J 379 ARG cc_start: 0.8250 (ttt-90) cc_final: 0.6683 (tmm160) outliers start: 23 outliers final: 23 residues processed: 165 average time/residue: 0.2075 time to fit residues: 46.0732 Evaluate side-chains 167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 276 GLN Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain Q residue 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Chi-restraints excluded: chain R residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.0170 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4857 r_free = 0.4857 target = 0.210421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5111 r_free = 0.5111 target = 0.179484 restraints weight = 14820.949| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 2.12 r_work: 0.4385 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.4269 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8190 Z= 0.266 Angle : 0.633 9.141 10940 Z= 0.311 Chirality : 0.051 0.136 1250 Planarity : 0.003 0.023 1390 Dihedral : 4.549 14.114 1060 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.74 % Allowed : 19.37 % Favored : 77.89 % 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: -4.11 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Q 299 PHE 0.017 0.003 PHE E 346 TYR 0.023 0.004 TYR A 310 ARG 0.002 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3723.08 seconds wall clock time: 67 minutes 37.08 seconds (4057.08 seconds total)