Starting phenix.real_space_refine on Wed Feb 4 00:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p6e_13227/02_2026/7p6e_13227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p6e_13227/02_2026/7p6e_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_2026/7p6e_13227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2026/7p6e_13227.map" model { file = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2026/7p6e_13227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p6e_13227/02_2026/7p6e_13227.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: B, C, D, E, F, I, J, Q, R Time building chain proxies: 0.87, per 1000 atoms: 0.11 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: 0.50 Conformation dependent library (CDL) restraints added in 203.1 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: 0.27 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: 1.07 Time building geometry restraints manager: 0.67 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 2.410 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 7.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.360 ------------------------------------------------------------------------------- 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= 0.385 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.001 0.000 ARG I 349 TYR 0.010 0.006 TYR I 310 PHE 0.015 0.006 PHE J 378 HIS 0.009 0.004 HIS J 299 Details of bonding type rmsd covalent geometry : bond 0.00883 ( 8190) covalent geometry : angle 0.95730 (10940) hydrogen bonds : bond 0.18452 ( 85) hydrogen bonds : angle 6.67371 ( 252) *********************** 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 : 0.347 Fit side-chains REVERT: A 281 LYS cc_start: 0.8489 (tmtt) cc_final: 0.8174 (ttmt) REVERT: A 295 ASP cc_start: 0.8839 (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: 0.7189 (tmtt) REVERT: E 281 LYS cc_start: 0.8845 (tmtt) cc_final: 0.8430 (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: 0.0869 time to fit residues: 34.2502 Evaluate side-chains 124 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.259407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5371 r_free = 0.5371 target = 0.211220 restraints weight = 15738.287| |-----------------------------------------------------------------------------| r_work (start): 0.4535 rms_B_bonded: 1.98 r_work: 0.4432 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4320 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8190 Z= 0.199 Angle : 0.647 7.955 10940 Z= 0.322 Chirality : 0.051 0.140 1250 Planarity : 0.005 0.035 1390 Dihedral : 5.062 13.078 1060 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.79 % Allowed : 10.00 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 349 TYR 0.027 0.003 TYR I 310 PHE 0.013 0.003 PHE A 346 HIS 0.007 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 8190) covalent geometry : angle 0.64716 (10940) hydrogen bonds : bond 0.02375 ( 85) hydrogen bonds : angle 5.14551 ( 252) *********************** 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 194 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 0.348 Fit side-chains REVERT: A 281 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8303 (ttpt) REVERT: B 281 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8351 (ttmt) REVERT: B 283 ASP cc_start: 0.8020 (t0) cc_final: 0.7705 (t0) REVERT: B 338 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7347 (tm-30) REVERT: C 314 ASP cc_start: 0.8091 (t0) cc_final: 0.7889 (t0) REVERT: C 321 LYS cc_start: 0.7342 (mtpt) cc_final: 0.7086 (tmtt) REVERT: C 362 HIS cc_start: 0.7863 (t-170) cc_final: 0.7371 (t-90) REVERT: D 338 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7358 (tm-30) REVERT: D 349 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7574 (mtt-85) REVERT: D 362 HIS cc_start: 0.7879 (t-170) cc_final: 0.7389 (t-90) REVERT: E 281 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8599 (tptp) REVERT: E 282 LEU cc_start: 0.8006 (tt) cc_final: 0.7788 (tt) REVERT: E 349 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7673 (mtm-85) REVERT: E 372 GLU cc_start: 0.8099 (mt-10) cc_final: 0.6851 (mp0) REVERT: F 281 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8576 (tptp) REVERT: F 349 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7599 (mtm-85) REVERT: F 372 GLU cc_start: 0.8101 (mt-10) cc_final: 0.6945 (mp0) REVERT: I 281 LYS cc_start: 0.8958 (tmtt) cc_final: 0.8608 (tptp) REVERT: I 348 ASP cc_start: 0.8718 (t0) cc_final: 0.8134 (p0) REVERT: I 362 HIS cc_start: 0.7491 (t-90) cc_final: 0.7058 (t-90) REVERT: I 372 GLU cc_start: 0.7948 (mt-10) cc_final: 0.6881 (mp0) REVERT: J 281 LYS cc_start: 0.8966 (tmtt) cc_final: 0.8602 (tptp) REVERT: J 314 ASP cc_start: 0.8325 (t0) cc_final: 0.8112 (t0) REVERT: J 348 ASP cc_start: 0.8776 (t0) cc_final: 0.8149 (p0) REVERT: J 372 GLU cc_start: 0.7716 (mt-10) cc_final: 0.6727 (mp0) REVERT: Q 356 SER cc_start: 0.8614 (m) cc_final: 0.8189 (p) outliers start: 17 outliers final: 14 residues processed: 189 average time/residue: 0.0798 time to fit residues: 21.0521 Evaluate side-chains 142 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 37 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 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 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.256183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5348 r_free = 0.5348 target = 0.206660 restraints weight = 15612.932| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 1.96 r_work: 0.4378 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4268 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8190 Z= 0.224 Angle : 0.648 7.656 10940 Z= 0.322 Chirality : 0.051 0.144 1250 Planarity : 0.004 0.036 1390 Dihedral : 4.994 12.984 1060 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.47 % Allowed : 13.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.15), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 349 TYR 0.018 0.003 TYR I 310 PHE 0.013 0.003 PHE J 378 HIS 0.005 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8190) covalent geometry : angle 0.64802 (10940) hydrogen bonds : bond 0.02191 ( 85) hydrogen bonds : angle 4.79512 ( 252) *********************** 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 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8381 (ttmt) REVERT: A 338 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 281 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8379 (ttmt) REVERT: B 283 ASP cc_start: 0.8161 (t0) cc_final: 0.7732 (t0) REVERT: B 338 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 283 ASP cc_start: 0.8173 (t0) cc_final: 0.7706 (t0) REVERT: D 283 ASP cc_start: 0.7993 (t0) cc_final: 0.7722 (t0) REVERT: D 338 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7600 (tm-30) REVERT: D 349 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7666 (mtt-85) REVERT: E 349 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7705 (mtm-85) REVERT: E 372 GLU cc_start: 0.8156 (mt-10) cc_final: 0.6905 (mp0) REVERT: F 281 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8625 (tptp) REVERT: F 338 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7629 (tm-30) REVERT: F 349 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7693 (mtm-85) REVERT: F 372 GLU cc_start: 0.8143 (mt-10) cc_final: 0.6888 (mp0) REVERT: I 281 LYS cc_start: 0.9046 (tmtt) cc_final: 0.8732 (tptp) REVERT: I 310 TYR cc_start: 0.9129 (t80) cc_final: 0.8655 (t80) REVERT: I 348 ASP cc_start: 0.8787 (t0) cc_final: 0.8117 (p0) REVERT: I 362 HIS cc_start: 0.7435 (t-90) cc_final: 0.7156 (t-90) REVERT: I 379 ARG cc_start: 0.8060 (ttt-90) cc_final: 0.6826 (tmm160) REVERT: J 281 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8667 (tptp) REVERT: J 310 TYR cc_start: 0.9140 (t80) cc_final: 0.8673 (t80) REVERT: J 314 ASP cc_start: 0.8327 (t0) cc_final: 0.8076 (t0) REVERT: J 338 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7992 (tm-30) REVERT: J 348 ASP cc_start: 0.8670 (t0) cc_final: 0.8093 (p0) REVERT: J 379 ARG cc_start: 0.8056 (ttt-90) cc_final: 0.6784 (tmm160) REVERT: Q 349 ARG cc_start: 0.4962 (mmp-170) cc_final: 0.4742 (mmm160) REVERT: R 349 ARG cc_start: 0.4910 (mmp-170) cc_final: 0.4685 (mmm160) outliers start: 33 outliers final: 23 residues processed: 168 average time/residue: 0.0815 time to fit residues: 18.9029 Evaluate side-chains 152 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.315 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 4 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 299 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 = 0.4907 r_free = 0.4907 target = 0.212278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5138 r_free = 0.5138 target = 0.184229 restraints weight = 14710.720| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 2.10 r_work: 0.4408 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4299 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 8190 Z= 0.134 Angle : 0.588 7.681 10940 Z= 0.281 Chirality : 0.050 0.138 1250 Planarity : 0.003 0.033 1390 Dihedral : 4.590 13.024 1060 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.53 % Allowed : 14.74 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 349 TYR 0.012 0.002 TYR I 310 PHE 0.018 0.003 PHE J 378 HIS 0.003 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8190) covalent geometry : angle 0.58808 (10940) hydrogen bonds : bond 0.01521 ( 85) hydrogen bonds : angle 4.65665 ( 252) *********************** 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 183 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.349 Fit side-chains REVERT: A 281 LYS cc_start: 0.8812 (tmtt) cc_final: 0.8343 (ttmt) REVERT: A 283 ASP cc_start: 0.8200 (t0) cc_final: 0.7995 (t0) REVERT: A 338 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 281 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8367 (ttmt) REVERT: B 283 ASP cc_start: 0.8165 (t0) cc_final: 0.7797 (t0) REVERT: C 283 ASP cc_start: 0.8138 (t0) cc_final: 0.7820 (t0) REVERT: C 307 GLN cc_start: 0.9120 (tt0) cc_final: 0.8892 (tt0) REVERT: C 314 ASP cc_start: 0.8073 (t0) cc_final: 0.7842 (t0) REVERT: C 338 GLU cc_start: 0.8084 (tt0) cc_final: 0.7229 (tm-30) REVERT: D 283 ASP cc_start: 0.7924 (t0) cc_final: 0.7703 (t0) REVERT: D 307 GLN cc_start: 0.9094 (tt0) cc_final: 0.8893 (tt0) REVERT: D 338 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 349 ARG cc_start: 0.7874 (mtt-85) cc_final: 0.7651 (mtt-85) REVERT: E 338 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7506 (tm-30) REVERT: E 349 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7717 (mtm-85) REVERT: E 372 GLU cc_start: 0.8100 (mt-10) cc_final: 0.6814 (mp0) REVERT: E 378 PHE cc_start: 0.8273 (m-10) cc_final: 0.8008 (m-10) REVERT: F 281 LYS cc_start: 0.8823 (tmtt) cc_final: 0.8386 (tptp) REVERT: F 295 ASP cc_start: 0.8935 (p0) cc_final: 0.8494 (p0) REVERT: F 338 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7423 (tm-30) REVERT: F 349 ARG cc_start: 0.8318 (mtp85) cc_final: 0.7804 (mtm-85) REVERT: F 372 GLU cc_start: 0.8075 (mt-10) cc_final: 0.6784 (mp0) REVERT: I 281 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8658 (tptp) REVERT: I 348 ASP cc_start: 0.8554 (t0) cc_final: 0.8164 (p0) REVERT: I 362 HIS cc_start: 0.7361 (t-90) cc_final: 0.7060 (t-90) REVERT: I 372 GLU cc_start: 0.7848 (mt-10) cc_final: 0.6726 (mp0) REVERT: I 378 PHE cc_start: 0.8487 (m-10) cc_final: 0.8192 (m-10) REVERT: I 379 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.6750 (tmm160) REVERT: J 281 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8633 (tptp) REVERT: J 314 ASP cc_start: 0.8328 (t0) cc_final: 0.8024 (t0) REVERT: J 338 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7785 (tm-30) REVERT: J 348 ASP cc_start: 0.8616 (t0) cc_final: 0.8155 (p0) REVERT: J 372 GLU cc_start: 0.7824 (mt-10) cc_final: 0.6722 (mp0) REVERT: J 379 ARG cc_start: 0.8075 (ttt-90) cc_final: 0.6728 (tmm160) REVERT: Q 349 ARG cc_start: 0.4746 (mmp-170) cc_final: 0.4487 (mmm160) REVERT: R 349 ARG cc_start: 0.4866 (mmp-170) cc_final: 0.4563 (mmm160) outliers start: 24 outliers final: 17 residues processed: 177 average time/residue: 0.0747 time to fit residues: 18.3329 Evaluate side-chains 156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 295 ASP 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 F residue 289 SER Chi-restraints excluded: chain I residue 289 SER 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 300 VAL 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 78 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 88 optimal weight: 0.0670 chunk 24 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 overall best weight: 4.7924 ------------------------------------------------------------------------------- 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** ** D 299 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 = 0.4925 r_free = 0.4925 target = 0.254390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5320 r_free = 0.5320 target = 0.203603 restraints weight = 15824.421| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 1.96 r_work: 0.4260 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4161 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8190 Z= 0.248 Angle : 0.648 7.886 10940 Z= 0.325 Chirality : 0.052 0.143 1250 Planarity : 0.003 0.031 1390 Dihedral : 4.879 13.614 1060 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.47 % Allowed : 15.89 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 349 TYR 0.023 0.004 TYR Q 310 PHE 0.018 0.003 PHE A 346 HIS 0.005 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00571 ( 8190) covalent geometry : angle 0.64779 (10940) hydrogen bonds : bond 0.01863 ( 85) hydrogen bonds : angle 4.67897 ( 252) *********************** 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 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8340 (ttmt) REVERT: A 283 ASP cc_start: 0.8210 (t0) cc_final: 0.7901 (t0) REVERT: A 338 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 281 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8362 (ttmt) REVERT: B 283 ASP cc_start: 0.8168 (t0) cc_final: 0.7778 (t0) REVERT: C 314 ASP cc_start: 0.8051 (t0) cc_final: 0.7850 (t0) REVERT: D 338 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 349 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7518 (mtt-85) REVERT: E 281 LYS cc_start: 0.8622 (tptp) cc_final: 0.8229 (tptp) REVERT: E 338 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7367 (tm-30) REVERT: E 349 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7792 (mtm-85) REVERT: E 372 GLU cc_start: 0.8036 (mt-10) cc_final: 0.6804 (mp0) REVERT: F 281 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8463 (tptp) REVERT: F 338 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7386 (tm-30) REVERT: F 349 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7833 (mtm-85) REVERT: I 281 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8712 (tptp) REVERT: I 348 ASP cc_start: 0.8682 (t0) cc_final: 0.8058 (p0) REVERT: I 362 HIS cc_start: 0.7429 (t-90) cc_final: 0.7144 (t-90) REVERT: I 379 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.6724 (tmm160) REVERT: J 281 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8701 (tptp) REVERT: J 338 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7892 (tm-30) REVERT: J 348 ASP cc_start: 0.8787 (t0) cc_final: 0.8061 (p0) REVERT: J 379 ARG cc_start: 0.8218 (ttt-90) cc_final: 0.6793 (tmm160) REVERT: Q 307 GLN cc_start: 0.8894 (tt0) cc_final: 0.8688 (tt0) REVERT: R 307 GLN cc_start: 0.8891 (tt0) cc_final: 0.8684 (tt0) outliers start: 33 outliers final: 27 residues processed: 163 average time/residue: 0.0697 time to fit residues: 16.1002 Evaluate side-chains 155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 ASP Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 363 VAL 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 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 300 VAL 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 5 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 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 = 0.4646 r_free = 0.4646 target = 0.133425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.112613 restraints weight = 15010.625| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 3.53 r_work: 0.4226 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8190 Z= 0.276 Angle : 0.669 6.565 10940 Z= 0.344 Chirality : 0.052 0.143 1250 Planarity : 0.004 0.039 1390 Dihedral : 5.048 14.431 1060 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.26 % Allowed : 18.21 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.001 ARG R 349 TYR 0.013 0.003 TYR A 310 PHE 0.019 0.003 PHE A 346 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00630 ( 8190) covalent geometry : angle 0.66944 (10940) hydrogen bonds : bond 0.01950 ( 85) hydrogen bonds : angle 4.75158 ( 252) *********************** 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 174 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8789 (tmtt) cc_final: 0.8257 (ttmt) REVERT: A 338 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 281 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8303 (ttmt) REVERT: B 283 ASP cc_start: 0.8211 (t0) cc_final: 0.7973 (t0) REVERT: C 314 ASP cc_start: 0.8140 (t0) cc_final: 0.7929 (t0) REVERT: C 349 ARG cc_start: 0.7845 (mtt-85) cc_final: 0.7511 (mtt-85) REVERT: D 338 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7282 (tm-30) REVERT: D 349 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7473 (mtt-85) REVERT: E 338 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7172 (tm-30) REVERT: E 349 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7771 (mtm-85) REVERT: E 372 GLU cc_start: 0.7901 (mt-10) cc_final: 0.6439 (mp0) REVERT: F 281 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8646 (tptp) REVERT: F 338 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 349 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7781 (mtm-85) REVERT: I 281 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8740 (tptp) REVERT: I 348 ASP cc_start: 0.8818 (t0) cc_final: 0.7974 (p0) REVERT: I 362 HIS cc_start: 0.7329 (t-90) cc_final: 0.7053 (t-90) REVERT: I 379 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.6778 (tmm160) REVERT: J 310 TYR cc_start: 0.9051 (t80) cc_final: 0.8504 (t80) REVERT: J 314 ASP cc_start: 0.8271 (t0) cc_final: 0.7986 (t0) REVERT: J 338 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8018 (tm-30) REVERT: J 348 ASP cc_start: 0.8874 (t0) cc_final: 0.7959 (p0) REVERT: J 379 ARG cc_start: 0.8036 (ttt-90) cc_final: 0.6746 (tmm160) REVERT: Q 307 GLN cc_start: 0.8848 (tt0) cc_final: 0.8586 (tt0) REVERT: R 307 GLN cc_start: 0.8827 (tt0) cc_final: 0.8560 (tt0) outliers start: 31 outliers final: 30 residues processed: 167 average time/residue: 0.0772 time to fit residues: 17.7340 Evaluate side-chains 163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain C residue 300 VAL 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 300 VAL 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 38 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 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 = 0.4935 r_free = 0.4935 target = 0.256235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5350 r_free = 0.5350 target = 0.206165 restraints weight = 15764.739| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 1.97 r_work: 0.4399 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4293 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 8190 Z= 0.164 Angle : 0.615 8.941 10940 Z= 0.303 Chirality : 0.051 0.138 1250 Planarity : 0.003 0.022 1390 Dihedral : 4.680 14.053 1060 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.84 % Allowed : 18.95 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.001 ARG F 379 TYR 0.023 0.003 TYR R 310 PHE 0.023 0.003 PHE J 378 HIS 0.003 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8190) covalent geometry : angle 0.61459 (10940) hydrogen bonds : bond 0.01624 ( 85) hydrogen bonds : angle 4.67628 ( 252) *********************** 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 172 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8890 (tmtt) cc_final: 0.8410 (ttmt) REVERT: B 281 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8333 (ttmt) REVERT: B 283 ASP cc_start: 0.8248 (t0) cc_final: 0.8007 (t0) REVERT: C 349 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7524 (mtp85) REVERT: D 338 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7319 (tm-30) REVERT: E 338 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7467 (tm-30) REVERT: E 349 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7807 (mtm-85) REVERT: E 372 GLU cc_start: 0.8041 (mt-10) cc_final: 0.6847 (mp0) REVERT: F 281 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8758 (tptp) REVERT: F 338 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7360 (tm-30) REVERT: F 349 ARG cc_start: 0.8397 (mtp85) cc_final: 0.7884 (mtm-85) REVERT: F 372 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6728 (mp0) REVERT: I 281 LYS cc_start: 0.9002 (tmtt) cc_final: 0.8722 (tptp) REVERT: I 348 ASP cc_start: 0.8634 (t0) cc_final: 0.8109 (p0) REVERT: I 362 HIS cc_start: 0.7400 (t-90) cc_final: 0.7122 (t-90) REVERT: I 379 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.6748 (tmm160) REVERT: J 338 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8007 (tm-30) REVERT: J 348 ASP cc_start: 0.8690 (t0) cc_final: 0.8052 (p0) REVERT: J 379 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.6607 (tmm160) outliers start: 27 outliers final: 24 residues processed: 166 average time/residue: 0.0850 time to fit residues: 19.3263 Evaluate side-chains 160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 295 ASP Chi-restraints excluded: chain C residue 300 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.135002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.114320 restraints weight = 14903.883| |-----------------------------------------------------------------------------| r_work (start): 0.4366 rms_B_bonded: 3.57 r_work: 0.4256 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3681 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= 0.216 Angle : 0.659 8.282 10940 Z= 0.328 Chirality : 0.051 0.138 1250 Planarity : 0.003 0.028 1390 Dihedral : 4.772 14.206 1060 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.47 % Allowed : 18.74 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG R 349 TYR 0.018 0.003 TYR E 310 PHE 0.023 0.003 PHE J 378 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 8190) covalent geometry : angle 0.65890 (10940) hydrogen bonds : bond 0.01718 ( 85) hydrogen bonds : angle 4.72892 ( 252) *********************** 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 169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8332 (ttmt) REVERT: A 283 ASP cc_start: 0.8104 (t0) cc_final: 0.7877 (t0) REVERT: B 281 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8278 (ttmt) REVERT: B 283 ASP cc_start: 0.8312 (t0) cc_final: 0.8004 (t0) REVERT: C 349 ARG cc_start: 0.7875 (mtt-85) cc_final: 0.7448 (mtp85) REVERT: D 307 GLN cc_start: 0.9077 (tt0) cc_final: 0.8853 (tt0) REVERT: D 338 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7190 (tm-30) REVERT: E 338 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7246 (tm-30) REVERT: E 349 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7779 (mtm-85) REVERT: E 372 GLU cc_start: 0.7915 (mt-10) cc_final: 0.6656 (mp0) REVERT: F 338 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7141 (tm-30) REVERT: F 349 ARG cc_start: 0.8363 (mtp85) cc_final: 0.7812 (mtm-85) REVERT: F 372 GLU cc_start: 0.7823 (mt-10) cc_final: 0.6587 (mp0) REVERT: I 281 LYS cc_start: 0.9056 (tmtt) cc_final: 0.8771 (tptp) REVERT: I 348 ASP cc_start: 0.8642 (t0) cc_final: 0.7983 (p0) REVERT: I 362 HIS cc_start: 0.7371 (t-90) cc_final: 0.7093 (t-90) REVERT: I 379 ARG cc_start: 0.8113 (ttt-90) cc_final: 0.6639 (tmm160) REVERT: J 338 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7960 (tm-30) REVERT: J 348 ASP cc_start: 0.8722 (t0) cc_final: 0.7949 (p0) REVERT: J 379 ARG cc_start: 0.8129 (ttt-90) cc_final: 0.6576 (tmm160) REVERT: R 349 ARG cc_start: 0.5209 (mmp-170) cc_final: 0.4857 (mmm160) outliers start: 33 outliers final: 28 residues processed: 161 average time/residue: 0.0741 time to fit residues: 16.5775 Evaluate side-chains 160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain C residue 300 VAL 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 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 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 291 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 50 optimal weight: 0.0170 chunk 46 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 6.8026 ------------------------------------------------------------------------------- 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** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 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** ** J 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 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 = 0.4621 r_free = 0.4621 target = 0.130586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.109859 restraints weight = 15275.462| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 3.53 r_work: 0.4180 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 8190 Z= 0.341 Angle : 0.744 7.939 10940 Z= 0.385 Chirality : 0.053 0.141 1250 Planarity : 0.004 0.045 1390 Dihedral : 5.248 15.176 1060 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.79 % Allowed : 18.95 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.20), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 349 TYR 0.027 0.005 TYR R 310 PHE 0.019 0.004 PHE C 378 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 8190) covalent geometry : angle 0.74409 (10940) hydrogen bonds : bond 0.02056 ( 85) hydrogen bonds : angle 4.75984 ( 252) *********************** 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: 36 poor density : 132 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8199 (ttmt) REVERT: A 283 ASP cc_start: 0.8187 (t0) cc_final: 0.7894 (t0) REVERT: A 379 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.7217 (tpt90) REVERT: B 281 LYS cc_start: 0.8738 (tmtt) cc_final: 0.8208 (ttmt) REVERT: B 283 ASP cc_start: 0.8245 (t0) cc_final: 0.7959 (t0) REVERT: B 379 ARG cc_start: 0.7524 (ttt-90) cc_final: 0.7247 (tpt90) REVERT: C 349 ARG cc_start: 0.7852 (mtt-85) cc_final: 0.7520 (mtt-85) REVERT: D 307 GLN cc_start: 0.9148 (tt0) cc_final: 0.8872 (tt0) REVERT: D 338 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7222 (tm-30) REVERT: D 379 ARG cc_start: 0.7734 (ttt-90) cc_final: 0.7278 (tpt-90) REVERT: E 338 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7032 (tm-30) REVERT: E 349 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7775 (mtm-85) REVERT: E 372 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7411 (mt-10) REVERT: F 338 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7058 (tm-30) REVERT: F 349 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7731 (mtm-85) REVERT: F 372 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7379 (mt-10) REVERT: I 281 LYS cc_start: 0.9095 (tmtt) cc_final: 0.8803 (tptp) REVERT: I 310 TYR cc_start: 0.9052 (t80) cc_final: 0.8539 (t80) REVERT: I 348 ASP cc_start: 0.8861 (t0) cc_final: 0.7859 (p0) REVERT: I 378 PHE cc_start: 0.8583 (m-10) cc_final: 0.8377 (m-10) REVERT: I 379 ARG cc_start: 0.8272 (ttt-90) cc_final: 0.6710 (tmm160) REVERT: J 338 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7945 (tm-30) REVERT: J 348 ASP cc_start: 0.8912 (t0) cc_final: 0.7878 (p0) REVERT: J 379 ARG cc_start: 0.8042 (ttt-90) cc_final: 0.6781 (tmm160) REVERT: Q 307 GLN cc_start: 0.8837 (tt0) cc_final: 0.8586 (tt0) REVERT: Q 321 LYS cc_start: 0.7440 (mtpt) cc_final: 0.7240 (tppt) REVERT: R 349 ARG cc_start: 0.5181 (mmp-170) cc_final: 0.4884 (mmm160) outliers start: 36 outliers final: 31 residues processed: 160 average time/residue: 0.0807 time to fit residues: 17.5753 Evaluate side-chains 158 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 295 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS 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 308 ILE 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 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 287 VAL 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 4 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 90 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 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 = 0.4924 r_free = 0.4924 target = 0.254305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5338 r_free = 0.5338 target = 0.203336 restraints weight = 15710.840| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 1.96 r_work: 0.4297 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3876 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= 0.199 Angle : 0.667 8.476 10940 Z= 0.331 Chirality : 0.052 0.139 1250 Planarity : 0.003 0.024 1390 Dihedral : 4.881 16.157 1060 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.16 % Allowed : 19.79 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 349 TYR 0.022 0.004 TYR B 310 PHE 0.025 0.003 PHE J 378 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8190) covalent geometry : angle 0.66720 (10940) hydrogen bonds : bond 0.01712 ( 85) hydrogen bonds : angle 4.64590 ( 252) ********************** 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: 30 poor density : 141 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 LYS cc_start: 0.8881 (tmtt) cc_final: 0.8657 (tptp) REVERT: A 379 ARG cc_start: 0.7590 (ttt-90) cc_final: 0.7356 (tpt90) REVERT: B 281 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8297 (ttmt) REVERT: B 379 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7315 (tpt90) REVERT: C 349 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7516 (mtp85) REVERT: D 338 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 379 ARG cc_start: 0.7762 (ttt-90) cc_final: 0.7444 (tpt-90) REVERT: E 338 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7317 (tm-30) REVERT: E 349 ARG cc_start: 0.8437 (mtp85) cc_final: 0.7901 (mtm-85) REVERT: E 372 GLU cc_start: 0.7922 (mt-10) cc_final: 0.6709 (mp0) REVERT: F 338 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7234 (tm-30) REVERT: F 349 ARG cc_start: 0.8397 (mtp85) cc_final: 0.7891 (mtm-85) REVERT: F 372 GLU cc_start: 0.7887 (mt-10) cc_final: 0.6664 (mp0) REVERT: I 281 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8802 (tptp) REVERT: I 348 ASP cc_start: 0.8811 (t0) cc_final: 0.8002 (p0) REVERT: I 379 ARG cc_start: 0.8225 (ttt-90) cc_final: 0.6740 (tmm160) REVERT: J 338 GLU cc_start: 0.8417 (tm-30) cc_final: 0.7984 (tm-30) REVERT: J 348 ASP cc_start: 0.8821 (t0) cc_final: 0.7992 (p0) REVERT: J 379 ARG cc_start: 0.8116 (ttt-90) cc_final: 0.6764 (tmm160) REVERT: Q 307 GLN cc_start: 0.8836 (tt0) cc_final: 0.8621 (tt0) REVERT: R 349 ARG cc_start: 0.5393 (mmp-170) cc_final: 0.4928 (mmm160) REVERT: R 379 ARG cc_start: 0.7919 (ttt-90) cc_final: 0.7150 (tpm170) outliers start: 30 outliers final: 29 residues processed: 165 average time/residue: 0.0926 time to fit residues: 20.3769 Evaluate side-chains 164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 300 VAL Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 291 CYS 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 287 VAL Chi-restraints excluded: chain Q residue 291 CYS Chi-restraints excluded: chain Q residue 300 VAL Chi-restraints excluded: chain Q residue 324 SER Chi-restraints excluded: chain R residue 287 VAL 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 58 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 299 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 = 0.4929 r_free = 0.4929 target = 0.254636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.203932 restraints weight = 15655.718| |-----------------------------------------------------------------------------| r_work (start): 0.4482 rms_B_bonded: 1.97 r_work: 0.4378 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4268 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8190 Z= 0.193 Angle : 0.663 8.850 10940 Z= 0.327 Chirality : 0.052 0.138 1250 Planarity : 0.003 0.026 1390 Dihedral : 4.764 15.034 1060 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.16 % Allowed : 19.47 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.21), residues: 1010 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.16), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 349 TYR 0.024 0.005 TYR A 310 PHE 0.026 0.003 PHE J 378 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 8190) covalent geometry : angle 0.66334 (10940) hydrogen bonds : bond 0.01630 ( 85) hydrogen bonds : angle 4.53667 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1681.90 seconds wall clock time: 30 minutes 3.92 seconds (1803.92 seconds total)