Starting phenix.real_space_refine on Tue Feb 3 23:30:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4x_41903/02_2026/8u4x_41903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4x_41903/02_2026/8u4x_41903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_2026/8u4x_41903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_2026/8u4x_41903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_2026/8u4x_41903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_2026/8u4x_41903.map" } resolution = 2.81 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= 0.020 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 46 5.16 5 C 4963 2.51 5 N 1373 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 7873 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3890 Classifications: {'peptide': 499} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3897 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 471} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.19 Number of scatterers: 7873 At special positions: 0 Unit cell: (100.521, 80.811, 102.492, 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 46 16.00 O 1491 8.00 N 1373 7.00 C 4963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 379 " distance=2.03 Simple disulfide: pdb=" SG CYS B 375 " - pdb=" SG CYS B 379 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 311.7 milliseconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1874 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 43.2% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 12 through 18 Processing helix chain 'A' and resid 49 through 52 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.983A pdb=" N ARG A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 133' Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 148 through 165 Processing helix chain 'A' and resid 205 through 215 removed outlier: 3.820A pdb=" N ARG A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 294 through 340 removed outlier: 4.301A pdb=" N GLN A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.595A pdb=" N LEU A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 396 removed outlier: 3.951A pdb=" N ALA A 394 " --> pdb=" O THR A 390 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 395 " --> pdb=" O TRP A 391 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 396 " --> pdb=" O MET A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.901A pdb=" N VAL A 408 " --> pdb=" O HIS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.604A pdb=" N GLU A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 414 " --> pdb=" O PRO A 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 488 through 516 Processing helix chain 'B' and resid 12 through 18 Processing helix chain 'B' and resid 49 through 52 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 71 through 83 Processing helix chain 'B' and resid 121 through 127 Processing helix chain 'B' and resid 128 through 133 removed outlier: 3.984A pdb=" N ARG B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 133 " --> pdb=" O TYR B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 133' Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 148 through 165 Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.821A pdb=" N ARG B 214 " --> pdb=" O GLU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 264 Processing helix chain 'B' and resid 294 through 340 removed outlier: 4.302A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N THR B 330 " --> pdb=" O THR B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.595A pdb=" N LEU B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 396 removed outlier: 3.951A pdb=" N ALA B 394 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY B 395 " --> pdb=" O TRP B 391 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 396 " --> pdb=" O MET B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.901A pdb=" N VAL B 408 " --> pdb=" O HIS B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 3.605A pdb=" N GLU B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA B 414 " --> pdb=" O PRO B 411 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 488 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.204A pdb=" N ILE A 43 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS A 37 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU A 33 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A 101 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.580A pdb=" N GLY A 180 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 185 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 169 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP A 280 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN A 275 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 281 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 269 " --> pdb=" O CYS A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 372 through 377 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 449 removed outlier: 3.956A pdb=" N GLN A 444 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27 removed outlier: 6.204A pdb=" N ILE B 43 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS B 37 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU B 33 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU B 101 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 198 through 199 removed outlier: 3.580A pdb=" N GLY B 180 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE B 171 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU B 185 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 169 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP B 280 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN B 275 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 281 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 269 " --> pdb=" O CYS B 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 377 Processing sheet with id=AA8, first strand: chain 'B' and resid 444 through 449 removed outlier: 3.957A pdb=" N GLN B 444 " --> pdb=" O MET B 480 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1182 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: 1.05 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1456 1.33 - 1.45: 1934 1.45 - 1.57: 4569 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8037 Sorted by residual: bond pdb=" C PRO B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.83e+00 bond pdb=" C PRO A 410 " pdb=" N PRO A 411 " ideal model delta sigma weight residual 1.334 1.345 -0.011 8.40e-03 1.42e+04 1.81e+00 bond pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.57e-01 bond pdb=" CD GLU A 98 " pdb=" OE1 GLU A 98 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.46e-01 ... (remaining 8032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 10461 1.11 - 2.22: 312 2.22 - 3.33: 129 3.33 - 4.44: 14 4.44 - 5.55: 14 Bond angle restraints: 10930 Sorted by residual: angle pdb=" CA GLU A 98 " pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " ideal model delta sigma weight residual 114.10 119.65 -5.55 2.00e+00 2.50e-01 7.70e+00 angle pdb=" CA GLU B 98 " pdb=" CB GLU B 98 " pdb=" CG GLU B 98 " ideal model delta sigma weight residual 114.10 119.64 -5.54 2.00e+00 2.50e-01 7.68e+00 angle pdb=" CA GLN B 372 " pdb=" CB GLN B 372 " pdb=" CG GLN B 372 " ideal model delta sigma weight residual 114.10 119.23 -5.13 2.00e+00 2.50e-01 6.59e+00 angle pdb=" CA GLN A 372 " pdb=" CB GLN A 372 " pdb=" CG GLN A 372 " ideal model delta sigma weight residual 114.10 119.18 -5.08 2.00e+00 2.50e-01 6.45e+00 angle pdb=" C PRO B 410 " pdb=" N PRO B 411 " pdb=" CA PRO B 411 " ideal model delta sigma weight residual 120.83 118.40 2.43 1.02e+00 9.61e-01 5.67e+00 ... (remaining 10925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 4018 14.64 - 29.29: 542 29.29 - 43.93: 216 43.93 - 58.58: 77 58.58 - 73.22: 37 Dihedral angle restraints: 4890 sinusoidal: 1997 harmonic: 2893 Sorted by residual: dihedral pdb=" CB CYS A 375 " pdb=" SG CYS A 375 " pdb=" SG CYS A 379 " pdb=" CB CYS A 379 " ideal model delta sinusoidal sigma weight residual -86.00 -58.35 -27.65 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CB CYS B 375 " pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " pdb=" CB CYS B 379 " ideal model delta sinusoidal sigma weight residual -86.00 -58.38 -27.62 1 1.00e+01 1.00e-02 1.09e+01 dihedral pdb=" CG ARG B 173 " pdb=" CD ARG B 173 " pdb=" NE ARG B 173 " pdb=" CZ ARG B 173 " ideal model delta sinusoidal sigma weight residual 90.00 133.34 -43.34 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 4887 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 822 0.032 - 0.064: 249 0.064 - 0.095: 83 0.095 - 0.127: 57 0.127 - 0.159: 11 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CB THR A 390 " pdb=" CA THR A 390 " pdb=" OG1 THR A 390 " pdb=" CG2 THR A 390 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" CB THR B 390 " pdb=" CA THR B 390 " pdb=" OG1 THR B 390 " pdb=" CG2 THR B 390 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA VAL A 97 " pdb=" N VAL A 97 " pdb=" C VAL A 97 " pdb=" CB VAL A 97 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 1219 not shown) Planarity restraints: 1429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 409 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO A 410 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 410 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 410 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 409 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 410 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 410 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 410 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 454 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C LYS A 454 " 0.021 2.00e-02 2.50e+03 pdb=" O LYS A 454 " -0.008 2.00e-02 2.50e+03 pdb=" N PRO A 455 " -0.007 2.00e-02 2.50e+03 ... (remaining 1426 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1629 2.79 - 3.32: 7219 3.32 - 3.84: 13233 3.84 - 4.37: 15171 4.37 - 4.90: 26144 Nonbonded interactions: 63396 Sorted by model distance: nonbonded pdb=" O GLN B 416 " pdb=" OG SER B 420 " model vdw 2.259 3.040 nonbonded pdb=" O GLN A 416 " pdb=" OG SER A 420 " model vdw 2.259 3.040 nonbonded pdb=" OE1 GLU B 118 " pdb=" OH TYR B 292 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU A 118 " pdb=" OH TYR A 292 " model vdw 2.264 3.040 nonbonded pdb=" OE1 GLU B 116 " pdb=" OG SER B 247 " model vdw 2.268 3.040 ... (remaining 63391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 12 through 900) } 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: 4.900 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.940 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: 0.010 Load rotamer database and sin/cos tables:5.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.002 0.066 8041 Z= 0.152 Angle : 0.558 5.548 10934 Z= 0.300 Chirality : 0.042 0.159 1222 Planarity : 0.004 0.032 1429 Dihedral : 17.691 73.223 3010 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.11 % Allowed : 27.43 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.85 (0.28), residues: 991 helix: 1.98 (0.27), residues: 370 sheet: -0.28 (0.37), residues: 194 loop : -0.21 (0.33), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 509 TYR 0.008 0.001 TYR A 172 PHE 0.008 0.001 PHE B 493 TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 287 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8037) covalent geometry : angle 0.55846 (10930) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.14166 ( 4) hydrogen bonds : bond 0.13468 ( 422) hydrogen bonds : angle 5.62178 ( 1182) Misc. bond : bond 0.06598 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.191 Fit side-chains REVERT: A 132 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7513 (mtt180) REVERT: A 265 VAL cc_start: 0.8133 (m) cc_final: 0.7904 (p) REVERT: B 40 GLU cc_start: 0.6098 (tt0) cc_final: 0.5838 (tt0) REVERT: B 50 VAL cc_start: 0.7879 (m) cc_final: 0.7583 (t) REVERT: B 118 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 138 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.7157 (mtp180) REVERT: B 206 GLU cc_start: 0.7324 (tp30) cc_final: 0.7042 (tp30) REVERT: B 231 VAL cc_start: 0.7883 (p) cc_final: 0.7621 (m) REVERT: B 265 VAL cc_start: 0.7979 (m) cc_final: 0.7731 (p) REVERT: B 454 LYS cc_start: 0.8227 (ttmm) cc_final: 0.8024 (ttpp) outliers start: 18 outliers final: 10 residues processed: 253 average time/residue: 0.5298 time to fit residues: 140.8270 Evaluate side-chains 234 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 456 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 374 HIS A 444 GLN A 468 GLN B 306 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.138952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126249 restraints weight = 10583.496| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.89 r_work: 0.3598 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8041 Z= 0.179 Angle : 0.560 5.349 10934 Z= 0.287 Chirality : 0.044 0.137 1222 Planarity : 0.005 0.033 1429 Dihedral : 6.464 52.981 1133 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.86 % Allowed : 22.04 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.76 (0.27), residues: 991 helix: 2.06 (0.26), residues: 374 sheet: -0.39 (0.36), residues: 202 loop : -0.41 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.010 0.001 TYR A 172 PHE 0.027 0.002 PHE B 493 TRP 0.015 0.001 TRP A 476 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8037) covalent geometry : angle 0.56014 (10930) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.90402 ( 4) hydrogen bonds : bond 0.03824 ( 422) hydrogen bonds : angle 4.73887 ( 1182) Misc. bond : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7887 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 504 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7615 (mt-10) REVERT: B 118 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 163 MET cc_start: 0.8530 (ptm) cc_final: 0.8198 (ptp) REVERT: B 187 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7842 (t) REVERT: B 206 GLU cc_start: 0.7362 (tp30) cc_final: 0.7122 (tp30) REVERT: B 265 VAL cc_start: 0.8347 (m) cc_final: 0.8100 (p) REVERT: B 336 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7652 (mm110) REVERT: B 372 GLN cc_start: 0.7249 (mm110) cc_final: 0.7034 (mp10) outliers start: 50 outliers final: 22 residues processed: 261 average time/residue: 0.5612 time to fit residues: 153.9101 Evaluate side-chains 246 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.0170 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN A 374 HIS A 468 GLN B 60 GLN B 241 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.139295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126465 restraints weight = 10464.978| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.90 r_work: 0.3601 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8041 Z= 0.146 Angle : 0.536 5.040 10934 Z= 0.273 Chirality : 0.042 0.132 1222 Planarity : 0.005 0.035 1429 Dihedral : 6.329 52.623 1125 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.04 % Allowed : 23.45 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.76 (0.27), residues: 991 helix: 2.10 (0.26), residues: 374 sheet: -0.42 (0.36), residues: 200 loop : -0.44 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.010 0.001 TYR A 172 PHE 0.035 0.002 PHE B 493 TRP 0.016 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8037) covalent geometry : angle 0.53579 (10930) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.81954 ( 4) hydrogen bonds : bond 0.03527 ( 422) hydrogen bonds : angle 4.65404 ( 1182) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7953 (tp30) cc_final: 0.7698 (mm-30) REVERT: A 207 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: A 288 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8223 (mtm180) REVERT: A 454 LYS cc_start: 0.8295 (ttmm) cc_final: 0.8084 (ttmm) REVERT: B 163 MET cc_start: 0.8501 (ptm) cc_final: 0.8144 (ptp) REVERT: B 187 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7854 (t) REVERT: B 206 GLU cc_start: 0.7391 (tp30) cc_final: 0.7149 (tp30) REVERT: B 261 LYS cc_start: 0.8279 (mttt) cc_final: 0.8069 (mttm) REVERT: B 336 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7594 (mm110) REVERT: B 372 GLN cc_start: 0.7283 (mm110) cc_final: 0.6979 (mp10) outliers start: 43 outliers final: 26 residues processed: 255 average time/residue: 0.5421 time to fit residues: 145.2466 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.0770 chunk 34 optimal weight: 0.0000 chunk 28 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 73 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN A 306 GLN A 374 HIS A 444 GLN A 468 GLN A 510 GLN B 60 GLN B 120 GLN B 241 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.140803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.127873 restraints weight = 10666.342| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.90 r_work: 0.3613 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8041 Z= 0.121 Angle : 0.522 4.737 10934 Z= 0.266 Chirality : 0.042 0.135 1222 Planarity : 0.004 0.034 1429 Dihedral : 6.215 52.635 1123 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.16 % Allowed : 23.68 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.85 (0.27), residues: 991 helix: 2.20 (0.26), residues: 374 sheet: -0.38 (0.36), residues: 197 loop : -0.43 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.009 0.001 TYR A 172 PHE 0.041 0.002 PHE B 493 TRP 0.016 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8037) covalent geometry : angle 0.52149 (10930) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.74431 ( 4) hydrogen bonds : bond 0.03314 ( 422) hydrogen bonds : angle 4.57314 ( 1182) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 185 GLU cc_start: 0.7982 (tp30) cc_final: 0.7624 (mm-30) REVERT: A 207 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: B 139 MET cc_start: 0.7965 (tmm) cc_final: 0.7730 (ttm) REVERT: B 163 MET cc_start: 0.8490 (ptm) cc_final: 0.8119 (ptp) REVERT: B 187 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7876 (t) REVERT: B 206 GLU cc_start: 0.7412 (tp30) cc_final: 0.7204 (tp30) REVERT: B 336 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7607 (mm110) outliers start: 44 outliers final: 22 residues processed: 255 average time/residue: 0.5495 time to fit residues: 147.2870 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 72 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 374 HIS A 444 GLN A 468 GLN B 60 GLN B 241 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126507 restraints weight = 10617.426| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.99 r_work: 0.3592 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8041 Z= 0.152 Angle : 0.542 5.141 10934 Z= 0.276 Chirality : 0.043 0.142 1222 Planarity : 0.005 0.035 1429 Dihedral : 6.234 52.437 1123 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.81 % Allowed : 24.50 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.81 (0.27), residues: 991 helix: 2.08 (0.26), residues: 375 sheet: -0.33 (0.36), residues: 202 loop : -0.39 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 509 TYR 0.009 0.001 TYR A 172 PHE 0.044 0.002 PHE B 493 TRP 0.018 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8037) covalent geometry : angle 0.54190 (10930) SS BOND : bond 0.00070 ( 2) SS BOND : angle 0.83883 ( 4) hydrogen bonds : bond 0.03479 ( 422) hydrogen bonds : angle 4.59207 ( 1182) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8080 (tp30) cc_final: 0.7755 (mm-30) REVERT: A 207 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7281 (pt0) REVERT: A 231 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7654 (p) REVERT: A 288 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8244 (mtm180) REVERT: B 139 MET cc_start: 0.7977 (tmm) cc_final: 0.7722 (ttm) REVERT: B 187 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7963 (t) REVERT: B 206 GLU cc_start: 0.7459 (tp30) cc_final: 0.7258 (tp30) REVERT: B 336 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7597 (mm110) REVERT: B 493 PHE cc_start: 0.7978 (t80) cc_final: 0.7746 (t80) outliers start: 41 outliers final: 25 residues processed: 251 average time/residue: 0.5978 time to fit residues: 157.7760 Evaluate side-chains 251 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 444 GLN A 468 GLN B 60 GLN B 295 HIS B 468 GLN B 510 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126071 restraints weight = 10549.036| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.99 r_work: 0.3588 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8041 Z= 0.165 Angle : 0.564 6.207 10934 Z= 0.288 Chirality : 0.043 0.149 1222 Planarity : 0.005 0.047 1429 Dihedral : 6.297 52.315 1123 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.92 % Allowed : 25.09 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.77 (0.27), residues: 991 helix: 2.07 (0.26), residues: 375 sheet: -0.40 (0.36), residues: 200 loop : -0.41 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 173 TYR 0.009 0.001 TYR A 172 PHE 0.035 0.002 PHE B 493 TRP 0.019 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8037) covalent geometry : angle 0.56433 (10930) SS BOND : bond 0.00071 ( 2) SS BOND : angle 0.85891 ( 4) hydrogen bonds : bond 0.03547 ( 422) hydrogen bonds : angle 4.62243 ( 1182) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 226 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7752 (mt-10) REVERT: A 207 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: A 231 VAL cc_start: 0.7889 (OUTLIER) cc_final: 0.7659 (p) REVERT: A 288 ARG cc_start: 0.8582 (mtm-85) cc_final: 0.8206 (mtm180) REVERT: A 336 GLN cc_start: 0.8015 (mm110) cc_final: 0.7685 (mm110) REVERT: B 187 SER cc_start: 0.8199 (OUTLIER) cc_final: 0.7906 (t) REVERT: B 336 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7569 (mm110) REVERT: B 446 VAL cc_start: 0.7852 (t) cc_final: 0.7528 (m) outliers start: 42 outliers final: 26 residues processed: 255 average time/residue: 0.5943 time to fit residues: 159.3819 Evaluate side-chains 247 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.138703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.125400 restraints weight = 10569.060| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.98 r_work: 0.3575 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8041 Z= 0.185 Angle : 0.583 5.553 10934 Z= 0.296 Chirality : 0.044 0.157 1222 Planarity : 0.005 0.051 1429 Dihedral : 6.350 52.030 1123 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.57 % Allowed : 25.91 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.63 (0.27), residues: 991 helix: 1.94 (0.26), residues: 375 sheet: -0.47 (0.36), residues: 198 loop : -0.47 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 509 TYR 0.009 0.001 TYR A 172 PHE 0.046 0.002 PHE B 493 TRP 0.021 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8037) covalent geometry : angle 0.58255 (10930) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.93923 ( 4) hydrogen bonds : bond 0.03716 ( 422) hydrogen bonds : angle 4.68024 ( 1182) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 207 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: A 231 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7686 (p) REVERT: A 288 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8197 (mtm180) REVERT: A 336 GLN cc_start: 0.8013 (mm110) cc_final: 0.7684 (mm110) REVERT: A 443 LYS cc_start: 0.7973 (mmtm) cc_final: 0.7766 (mmtm) REVERT: A 480 MET cc_start: 0.8015 (mmm) cc_final: 0.7809 (mmm) REVERT: B 76 GLU cc_start: 0.8118 (tp30) cc_final: 0.7794 (mm-30) REVERT: B 175 GLU cc_start: 0.7994 (mp0) cc_final: 0.7779 (mm-30) REVERT: B 187 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7973 (t) REVERT: B 288 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8255 (mtt90) REVERT: B 336 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7574 (mm110) REVERT: B 446 VAL cc_start: 0.7891 (t) cc_final: 0.7565 (m) REVERT: B 493 PHE cc_start: 0.7923 (t80) cc_final: 0.7683 (t80) outliers start: 39 outliers final: 26 residues processed: 246 average time/residue: 0.6170 time to fit residues: 159.4787 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 86 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 chunk 50 optimal weight: 0.0870 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 60 GLN B 144 HIS B 306 GLN B 468 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126545 restraints weight = 10645.610| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.92 r_work: 0.3591 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8041 Z= 0.151 Angle : 0.590 7.049 10934 Z= 0.301 Chirality : 0.043 0.152 1222 Planarity : 0.005 0.055 1429 Dihedral : 6.338 52.096 1123 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.45 % Allowed : 27.20 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.67 (0.27), residues: 991 helix: 1.99 (0.26), residues: 375 sheet: -0.41 (0.36), residues: 197 loop : -0.49 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 509 TYR 0.009 0.001 TYR A 172 PHE 0.039 0.002 PHE B 493 TRP 0.021 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8037) covalent geometry : angle 0.58977 (10930) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.77495 ( 4) hydrogen bonds : bond 0.03543 ( 422) hydrogen bonds : angle 4.65675 ( 1182) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7723 (mt-10) REVERT: A 207 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: A 231 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7666 (p) REVERT: A 336 GLN cc_start: 0.8024 (mm110) cc_final: 0.7687 (mm110) REVERT: A 372 GLN cc_start: 0.7405 (mp10) cc_final: 0.7111 (mp10) REVERT: B 187 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7998 (t) REVERT: B 288 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.8104 (mtt90) REVERT: B 336 GLN cc_start: 0.7877 (mm-40) cc_final: 0.7569 (mm110) REVERT: B 446 VAL cc_start: 0.7871 (t) cc_final: 0.7553 (m) outliers start: 38 outliers final: 26 residues processed: 242 average time/residue: 0.6313 time to fit residues: 160.6757 Evaluate side-chains 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.138793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125924 restraints weight = 10506.654| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.89 r_work: 0.3584 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8041 Z= 0.183 Angle : 0.608 6.778 10934 Z= 0.310 Chirality : 0.044 0.156 1222 Planarity : 0.005 0.058 1429 Dihedral : 6.390 52.416 1123 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.22 % Allowed : 26.85 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.57 (0.27), residues: 991 helix: 1.89 (0.26), residues: 375 sheet: -0.49 (0.36), residues: 198 loop : -0.52 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.010 0.001 TYR A 259 PHE 0.044 0.002 PHE B 493 TRP 0.022 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8037) covalent geometry : angle 0.60792 (10930) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.90287 ( 4) hydrogen bonds : bond 0.03735 ( 422) hydrogen bonds : angle 4.69749 ( 1182) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7859 (m) cc_final: 0.7564 (t) REVERT: A 118 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7693 (mt-10) REVERT: A 207 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: A 231 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7705 (p) REVERT: A 288 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8133 (mtm180) REVERT: A 480 MET cc_start: 0.7998 (mmm) cc_final: 0.7672 (mmm) REVERT: B 187 SER cc_start: 0.8188 (p) cc_final: 0.7963 (t) REVERT: B 288 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8084 (mtt180) REVERT: B 336 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7563 (mm110) REVERT: B 446 VAL cc_start: 0.7883 (t) cc_final: 0.7623 (m) outliers start: 36 outliers final: 29 residues processed: 243 average time/residue: 0.5901 time to fit residues: 150.6872 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.0370 chunk 77 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 374 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 60 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.139350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126385 restraints weight = 10550.178| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.91 r_work: 0.3595 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8041 Z= 0.165 Angle : 0.612 6.715 10934 Z= 0.311 Chirality : 0.044 0.200 1222 Planarity : 0.005 0.061 1429 Dihedral : 6.387 52.133 1123 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.52 % Allowed : 28.02 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.55 (0.27), residues: 991 helix: 1.85 (0.26), residues: 375 sheet: -0.47 (0.36), residues: 198 loop : -0.52 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.012 0.001 TYR A 259 PHE 0.012 0.002 PHE A 34 TRP 0.022 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8037) covalent geometry : angle 0.61158 (10930) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.86052 ( 4) hydrogen bonds : bond 0.03644 ( 422) hydrogen bonds : angle 4.70730 ( 1182) Misc. bond : bond 0.00007 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7862 (m) cc_final: 0.7559 (t) REVERT: A 118 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 207 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7225 (pt0) REVERT: A 231 VAL cc_start: 0.7944 (OUTLIER) cc_final: 0.7706 (p) REVERT: A 288 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8163 (mtm180) REVERT: A 336 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7696 (mm-40) REVERT: B 187 SER cc_start: 0.8231 (p) cc_final: 0.7989 (t) REVERT: B 288 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8100 (mtt180) REVERT: B 336 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7554 (mm110) REVERT: B 446 VAL cc_start: 0.7886 (t) cc_final: 0.7631 (m) outliers start: 30 outliers final: 27 residues processed: 239 average time/residue: 0.6251 time to fit residues: 157.0071 Evaluate side-chains 243 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126179 restraints weight = 10551.213| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.90 r_work: 0.3592 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8041 Z= 0.181 Angle : 0.620 6.825 10934 Z= 0.315 Chirality : 0.045 0.210 1222 Planarity : 0.005 0.061 1429 Dihedral : 6.421 52.231 1123 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.75 % Allowed : 27.90 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.50 (0.27), residues: 991 helix: 1.80 (0.26), residues: 375 sheet: -0.47 (0.36), residues: 198 loop : -0.56 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 509 TYR 0.011 0.001 TYR A 259 PHE 0.016 0.002 PHE B 493 TRP 0.023 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 8037) covalent geometry : angle 0.61951 (10930) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.91598 ( 4) hydrogen bonds : bond 0.03742 ( 422) hydrogen bonds : angle 4.72067 ( 1182) Misc. bond : bond 0.00006 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3416.90 seconds wall clock time: 58 minutes 42.81 seconds (3522.81 seconds total)