Starting phenix.real_space_refine on Fri Jun 6 15:14:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4x_41903/06_2025/8u4x_41903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4x_41903/06_2025/8u4x_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u4x_41903/06_2025/8u4x_41903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4x_41903/06_2025/8u4x_41903.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4x_41903/06_2025/8u4x_41903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4x_41903/06_2025/8u4x_41903.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7873 Number of models: 1 Model: "" Number of chains: 3 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Classifications: {'peptide': 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} Restraints were copied for chains: B Time building chain proxies: 8.84, per 1000 atoms: 1.12 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 Links applied TRANS " LEU B 12 " - " VAL B 11 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.00 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: 2.50 Time building geometry restraints manager: 3.32 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: 1933 1.45 - 1.57: 4569 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8036 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 8031 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 10458 1.11 - 2.22: 312 2.22 - 3.33: 129 3.33 - 4.44: 14 4.44 - 5.55: 14 Bond angle restraints: 10927 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 10922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.64: 4019 14.64 - 29.29: 542 29.29 - 43.93: 217 43.93 - 58.58: 77 58.58 - 73.22: 37 Dihedral angle restraints: 4892 sinusoidal: 1999 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 4889 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 516 or resid 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: 5.540 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.290 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- 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 1428 Dihedral : 17.694 73.223 3009 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.012 0.001 TRP A 476 HIS 0.003 0.001 HIS A 287 PHE 0.008 0.001 PHE B 493 TYR 0.008 0.001 TYR A 172 ARG 0.007 0.000 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00064 ( 1) link_TRANS : angle 0.23514 ( 3) hydrogen bonds : bond 0.13468 ( 422) hydrogen bonds : angle 5.62178 ( 1182) SS BOND : bond 0.00080 ( 2) SS BOND : angle 0.14166 ( 4) covalent geometry : bond 0.00221 ( 8036) covalent geometry : angle 0.55852 (10927) 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 : 0.829 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: 0.7980 (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: 1.3545 time to fit residues: 360.0956 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 : 0.900 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.0370 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.139149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126521 restraints weight = 10456.416| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.88 r_work: 0.3603 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8041 Z= 0.167 Angle : 0.554 5.218 10934 Z= 0.284 Chirality : 0.044 0.136 1222 Planarity : 0.005 0.033 1428 Dihedral : 6.452 53.165 1132 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.74 % Allowed : 22.04 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 991 helix: 2.07 (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 TRP 0.015 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.025 0.002 PHE B 493 TYR 0.011 0.001 TYR B 172 ARG 0.005 0.001 ARG B 168 Details of bonding type rmsd link_TRANS : bond 0.00020 ( 1) link_TRANS : angle 0.05542 ( 3) hydrogen bonds : bond 0.03708 ( 422) hydrogen bonds : angle 4.71927 ( 1182) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.89121 ( 4) covalent geometry : bond 0.00395 ( 8036) covalent geometry : angle 0.55416 (10927) Misc. bond : bond 0.00018 ( 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 273 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 224 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7866 (tp30) cc_final: 0.7583 (mm-30) REVERT: A 336 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7789 (mm110) REVERT: A 504 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7595 (mt-10) REVERT: B 118 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7735 (mt-10) REVERT: B 163 MET cc_start: 0.8513 (ptm) cc_final: 0.8202 (ptp) REVERT: B 187 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7819 (t) REVERT: B 206 GLU cc_start: 0.7370 (tp30) cc_final: 0.7132 (tp30) REVERT: B 265 VAL cc_start: 0.8334 (m) cc_final: 0.8080 (p) REVERT: B 336 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7634 (mm110) REVERT: B 372 GLN cc_start: 0.7207 (mm110) cc_final: 0.6975 (mp10) outliers start: 49 outliers final: 21 residues processed: 259 average time/residue: 1.3502 time to fit residues: 367.3036 Evaluate side-chains 242 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 97 VAL 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 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 15 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 241 GLN B 332 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.138913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125926 restraints weight = 10536.267| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.89 r_work: 0.3590 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8041 Z= 0.194 Angle : 0.568 5.505 10934 Z= 0.288 Chirality : 0.044 0.133 1222 Planarity : 0.005 0.036 1428 Dihedral : 6.436 52.912 1123 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.16 % Allowed : 23.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 991 helix: 1.96 (0.26), residues: 375 sheet: -0.46 (0.36), residues: 200 loop : -0.47 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.040 0.002 PHE B 493 TYR 0.010 0.001 TYR A 172 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd link_TRANS : bond 0.00042 ( 1) link_TRANS : angle 0.06791 ( 3) hydrogen bonds : bond 0.03791 ( 422) hydrogen bonds : angle 4.71966 ( 1182) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.98280 ( 4) covalent geometry : bond 0.00458 ( 8036) covalent geometry : angle 0.56777 (10927) Misc. bond : bond 0.00005 ( 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 265 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.829 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8056 (tp30) cc_final: 0.7790 (tp30) REVERT: A 207 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: A 288 ARG cc_start: 0.8595 (mtm-85) cc_final: 0.8232 (mtm180) REVERT: A 454 LYS cc_start: 0.8321 (ttmm) cc_final: 0.8108 (ttmm) REVERT: A 504 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 187 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7905 (t) REVERT: B 206 GLU cc_start: 0.7427 (tp30) cc_final: 0.7177 (tp30) REVERT: B 336 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7593 (mm110) outliers start: 44 outliers final: 25 residues processed: 252 average time/residue: 1.3516 time to fit residues: 357.4694 Evaluate side-chains 238 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 417 THR 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 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 57 optimal weight: 0.1980 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 71 optimal weight: 0.0670 chunk 84 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.4128 ------------------------------------------------------------------------------- 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 241 GLN A 306 GLN A 374 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN A 510 GLN B 60 GLN B 241 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.126892 restraints weight = 10459.321| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.88 r_work: 0.3599 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8041 Z= 0.138 Angle : 0.538 5.050 10934 Z= 0.274 Chirality : 0.042 0.131 1222 Planarity : 0.005 0.036 1428 Dihedral : 6.324 52.843 1122 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.16 % Allowed : 23.80 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 991 helix: 2.06 (0.26), residues: 375 sheet: -0.39 (0.36), residues: 199 loop : -0.48 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.043 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.006 0.000 ARG B 235 Details of bonding type rmsd link_TRANS : bond 0.00025 ( 1) link_TRANS : angle 0.10298 ( 3) hydrogen bonds : bond 0.03447 ( 422) hydrogen bonds : angle 4.64424 ( 1182) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.75714 ( 4) covalent geometry : bond 0.00323 ( 8036) covalent geometry : angle 0.53809 (10927) 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 : 0.819 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 207 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7246 (pt0) REVERT: A 231 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7655 (p) REVERT: A 372 GLN cc_start: 0.7311 (mp10) cc_final: 0.6959 (mp10) REVERT: B 76 GLU cc_start: 0.8076 (tp30) cc_final: 0.7804 (mm-30) REVERT: B 187 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7942 (t) REVERT: B 206 GLU cc_start: 0.7414 (tp30) cc_final: 0.7198 (tp30) REVERT: B 336 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7596 (mm110) REVERT: B 446 VAL cc_start: 0.7868 (t) cc_final: 0.7553 (m) outliers start: 44 outliers final: 25 residues processed: 257 average time/residue: 1.3444 time to fit residues: 362.7904 Evaluate side-chains 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 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 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 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 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 67 optimal weight: 0.0470 chunk 82 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 120 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.139791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126858 restraints weight = 10518.163| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.90 r_work: 0.3603 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8041 Z= 0.137 Angle : 0.549 5.117 10934 Z= 0.279 Chirality : 0.043 0.139 1222 Planarity : 0.005 0.036 1428 Dihedral : 6.274 52.712 1122 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.16 % Allowed : 24.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 991 helix: 2.09 (0.26), residues: 375 sheet: -0.38 (0.36), residues: 199 loop : -0.49 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.045 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.004 0.000 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.12314 ( 3) hydrogen bonds : bond 0.03446 ( 422) hydrogen bonds : angle 4.62514 ( 1182) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.80838 ( 4) covalent geometry : bond 0.00324 ( 8036) covalent geometry : angle 0.54888 (10927) Misc. bond : bond 0.00004 ( 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 259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8037 (tp30) cc_final: 0.7745 (tp30) REVERT: A 207 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7243 (pt0) REVERT: A 231 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7661 (p) REVERT: A 372 GLN cc_start: 0.7382 (mp10) cc_final: 0.7033 (mp10) REVERT: A 504 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 118 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 187 SER cc_start: 0.8216 (p) cc_final: 0.7916 (t) REVERT: B 206 GLU cc_start: 0.7464 (tp30) cc_final: 0.7254 (tp30) REVERT: B 336 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7587 (mm110) REVERT: B 493 PHE cc_start: 0.7960 (t80) cc_final: 0.7735 (t80) outliers start: 44 outliers final: 25 residues processed: 246 average time/residue: 1.3466 time to fit residues: 347.9873 Evaluate side-chains 241 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 328 ILE 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 417 THR 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 116 GLU Chi-restraints excluded: chain B residue 177 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 444 GLN A 468 GLN B 60 GLN B 444 GLN 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 = 0.3866 r_free = 0.3866 target = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.125203 restraints weight = 10466.732| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.97 r_work: 0.3577 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8041 Z= 0.194 Angle : 0.583 5.923 10934 Z= 0.296 Chirality : 0.044 0.148 1222 Planarity : 0.005 0.050 1428 Dihedral : 6.388 52.342 1122 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.51 % Allowed : 23.92 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 991 helix: 1.99 (0.26), residues: 375 sheet: -0.44 (0.36), residues: 200 loop : -0.51 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.036 0.002 PHE B 493 TYR 0.009 0.001 TYR A 259 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.11703 ( 3) hydrogen bonds : bond 0.03714 ( 422) hydrogen bonds : angle 4.70355 ( 1182) SS BOND : bond 0.00107 ( 2) SS BOND : angle 0.95272 ( 4) covalent geometry : bond 0.00460 ( 8036) covalent geometry : angle 0.58262 (10927) Misc. bond : bond 0.00008 ( 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 269 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 207 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7268 (pt0) REVERT: A 231 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7688 (p) REVERT: A 288 ARG cc_start: 0.8604 (mtm-85) cc_final: 0.8194 (mtm180) REVERT: A 480 MET cc_start: 0.8066 (mmm) cc_final: 0.7732 (mmm) REVERT: A 504 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 187 SER cc_start: 0.8269 (p) cc_final: 0.7963 (t) REVERT: B 336 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7597 (mm110) outliers start: 47 outliers final: 30 residues processed: 256 average time/residue: 1.4035 time to fit residues: 376.9578 Evaluate side-chains 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 328 ILE 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 417 THR 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 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 319 GLU 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 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 67 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 0.0170 chunk 47 optimal weight: 0.0670 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.0670 chunk 93 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 overall best weight: 0.2294 ------------------------------------------------------------------------------- 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 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 = 0.3896 r_free = 0.3896 target = 0.140805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127814 restraints weight = 10554.952| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.92 r_work: 0.3621 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8041 Z= 0.116 Angle : 0.542 5.649 10934 Z= 0.278 Chirality : 0.042 0.169 1222 Planarity : 0.005 0.051 1428 Dihedral : 6.219 52.681 1122 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.22 % Allowed : 25.67 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 991 helix: 2.08 (0.26), residues: 375 sheet: -0.38 (0.36), residues: 197 loop : -0.45 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 PHE 0.043 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.000 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.13473 ( 3) hydrogen bonds : bond 0.03348 ( 422) hydrogen bonds : angle 4.62326 ( 1182) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.66293 ( 4) covalent geometry : bond 0.00270 ( 8036) covalent geometry : angle 0.54241 (10927) Misc. bond : bond 0.00005 ( 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 255 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7807 (m) cc_final: 0.7499 (t) REVERT: A 118 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 139 MET cc_start: 0.7836 (tmm) cc_final: 0.7627 (tmm) REVERT: A 207 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7204 (pt0) REVERT: A 231 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7610 (p) REVERT: A 288 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8171 (mtm180) REVERT: A 372 GLN cc_start: 0.7448 (mp10) cc_final: 0.7213 (mp10) REVERT: A 443 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7656 (mmtm) REVERT: B 40 GLU cc_start: 0.6098 (pm20) cc_final: 0.5876 (pm20) REVERT: B 185 GLU cc_start: 0.8002 (tp30) cc_final: 0.7731 (tp30) REVERT: B 187 SER cc_start: 0.8238 (p) cc_final: 0.7979 (t) REVERT: B 288 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8182 (mtt90) REVERT: B 336 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7556 (mm110) REVERT: B 446 VAL cc_start: 0.7788 (t) cc_final: 0.7502 (m) outliers start: 36 outliers final: 22 residues processed: 243 average time/residue: 1.5042 time to fit residues: 383.1279 Evaluate side-chains 235 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 328 ILE 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 474 GLU Chi-restraints excluded: chain A residue 476 TRP 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 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 444 GLN 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 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 0.4980 chunk 8 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 60 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 = 0.3882 r_free = 0.3882 target = 0.139659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126395 restraints weight = 10556.813| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.00 r_work: 0.3599 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8041 Z= 0.150 Angle : 0.562 5.134 10934 Z= 0.286 Chirality : 0.043 0.156 1222 Planarity : 0.005 0.054 1428 Dihedral : 6.242 52.138 1122 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.34 % Allowed : 26.26 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.27), residues: 991 helix: 2.03 (0.26), residues: 375 sheet: -0.31 (0.36), residues: 201 loop : -0.43 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.045 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.009 0.001 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00007 ( 1) link_TRANS : angle 0.12869 ( 3) hydrogen bonds : bond 0.03519 ( 422) hydrogen bonds : angle 4.63945 ( 1182) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.84778 ( 4) covalent geometry : bond 0.00355 ( 8036) covalent geometry : angle 0.56164 (10927) 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 250 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7834 (m) cc_final: 0.7519 (t) REVERT: A 118 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7733 (mt-10) REVERT: A 185 GLU cc_start: 0.8082 (tp30) cc_final: 0.7732 (mm-30) REVERT: A 207 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (pt0) REVERT: A 231 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7641 (p) REVERT: A 288 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8193 (mtm180) REVERT: A 372 GLN cc_start: 0.7465 (mp10) cc_final: 0.7191 (mp10) REVERT: A 480 MET cc_start: 0.8078 (mmm) cc_final: 0.7738 (mmm) REVERT: A 504 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 185 GLU cc_start: 0.8062 (tp30) cc_final: 0.7727 (tp30) REVERT: B 187 SER cc_start: 0.8249 (p) cc_final: 0.8000 (t) REVERT: B 288 ARG cc_start: 0.8396 (mtm-85) cc_final: 0.8160 (mtt90) REVERT: B 336 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7546 (mm110) REVERT: B 446 VAL cc_start: 0.7767 (t) cc_final: 0.7493 (m) outliers start: 37 outliers final: 24 residues processed: 238 average time/residue: 1.6788 time to fit residues: 418.1758 Evaluate side-chains 237 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 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 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 268 SER Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 319 GLU 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 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 96 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 295 HIS B 302 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 = 0.3873 r_free = 0.3873 target = 0.139001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125993 restraints weight = 10662.566| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.92 r_work: 0.3588 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8041 Z= 0.192 Angle : 0.603 6.906 10934 Z= 0.305 Chirality : 0.045 0.163 1222 Planarity : 0.005 0.057 1428 Dihedral : 6.377 52.222 1122 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.99 % Allowed : 27.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 991 helix: 1.92 (0.26), residues: 375 sheet: -0.44 (0.36), residues: 200 loop : -0.49 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.017 0.002 PHE B 493 TYR 0.010 0.001 TYR A 259 ARG 0.009 0.001 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00036 ( 1) link_TRANS : angle 0.14068 ( 3) hydrogen bonds : bond 0.03753 ( 422) hydrogen bonds : angle 4.72787 ( 1182) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.94652 ( 4) covalent geometry : bond 0.00455 ( 8036) covalent geometry : angle 0.60247 (10927) Misc. bond : bond 0.00008 ( 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 251 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 207 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7255 (pt0) REVERT: A 231 VAL cc_start: 0.7923 (OUTLIER) cc_final: 0.7708 (p) REVERT: A 288 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8167 (mtm180) REVERT: A 336 GLN cc_start: 0.8039 (mm110) cc_final: 0.7709 (mm110) REVERT: A 504 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 118 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7586 (mt-10) REVERT: B 185 GLU cc_start: 0.8084 (tp30) cc_final: 0.7795 (tp30) REVERT: B 187 SER cc_start: 0.8215 (p) cc_final: 0.7973 (t) REVERT: B 288 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.8043 (mtt90) REVERT: B 336 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7560 (mm110) REVERT: B 446 VAL cc_start: 0.7829 (t) cc_final: 0.7565 (m) outliers start: 34 outliers final: 26 residues processed: 242 average time/residue: 1.3038 time to fit residues: 331.9181 Evaluate side-chains 241 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 328 ILE 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 417 THR 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 278 LYS Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 319 GLU 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 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 68 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 93 optimal weight: 0.0670 chunk 81 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.139220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.126309 restraints weight = 10530.366| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.91 r_work: 0.3599 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8041 Z= 0.164 Angle : 0.598 7.314 10934 Z= 0.304 Chirality : 0.045 0.233 1222 Planarity : 0.005 0.058 1428 Dihedral : 6.390 52.377 1122 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.87 % Allowed : 27.43 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 991 helix: 1.91 (0.26), residues: 375 sheet: -0.34 (0.37), residues: 188 loop : -0.48 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.024 0.002 PHE B 493 TYR 0.011 0.001 TYR A 259 ARG 0.009 0.001 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00004 ( 1) link_TRANS : angle 0.13110 ( 3) hydrogen bonds : bond 0.03650 ( 422) hydrogen bonds : angle 4.72331 ( 1182) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.86709 ( 4) covalent geometry : bond 0.00387 ( 8036) covalent geometry : angle 0.59780 (10927) 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 245 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 139 MET cc_start: 0.7745 (tmm) cc_final: 0.7403 (tmt) REVERT: A 207 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7221 (pt0) REVERT: A 231 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7673 (p) REVERT: A 288 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8142 (mtm180) REVERT: A 336 GLN cc_start: 0.8038 (mm110) cc_final: 0.7695 (mm110) REVERT: A 480 MET cc_start: 0.8049 (mmm) cc_final: 0.7708 (mmm) REVERT: A 504 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7445 (mt-10) REVERT: B 118 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7686 (mt-10) REVERT: B 185 GLU cc_start: 0.8075 (tp30) cc_final: 0.7728 (tp30) REVERT: B 187 SER cc_start: 0.8240 (p) cc_final: 0.7996 (t) REVERT: B 288 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8080 (mtt90) REVERT: B 336 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7557 (mm110) REVERT: B 446 VAL cc_start: 0.7821 (t) cc_final: 0.7571 (m) outliers start: 33 outliers final: 25 residues processed: 237 average time/residue: 1.3149 time to fit residues: 327.9103 Evaluate side-chains 236 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 328 ILE 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 417 THR 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 308 LEU Chi-restraints excluded: chain B residue 319 GLU 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 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 47 optimal weight: 0.0020 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 GLN A 302 GLN A 374 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN B 144 HIS B 444 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 = 0.139464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126496 restraints weight = 10579.467| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.91 r_work: 0.3592 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.179 8041 Z= 0.256 Angle : 0.985 59.126 10934 Z= 0.560 Chirality : 0.047 0.455 1222 Planarity : 0.005 0.058 1428 Dihedral : 6.387 52.414 1122 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.22 % Allowed : 27.55 % Favored : 68.23 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 991 helix: 1.90 (0.26), residues: 375 sheet: -0.46 (0.36), residues: 198 loop : -0.48 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.021 0.002 PHE B 493 TYR 0.014 0.001 TYR B 400 ARG 0.007 0.001 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00019 ( 1) link_TRANS : angle 0.13221 ( 3) hydrogen bonds : bond 0.03686 ( 422) hydrogen bonds : angle 4.72258 ( 1182) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.85178 ( 4) covalent geometry : bond 0.00560 ( 8036) covalent geometry : angle 0.98561 (10927) Misc. bond : bond 0.00009 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8220.10 seconds wall clock time: 140 minutes 37.59 seconds (8437.59 seconds total)