Starting phenix.real_space_refine on Fri Aug 22 21:00:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4x_41903/08_2025/8u4x_41903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4x_41903/08_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_41903/08_2025/8u4x_41903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4x_41903/08_2025/8u4x_41903.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4x_41903/08_2025/8u4x_41903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4x_41903/08_2025/8u4x_41903.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.75, per 1000 atoms: 0.35 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: 0.70 Conformation dependent library (CDL) restraints added in 443.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.34 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: 1.23 Time building geometry restraints manager: 0.89 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 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.740 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 ( 8036) covalent geometry : angle 0.55852 (10927) 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) link_TRANS : bond 0.00064 ( 1) link_TRANS : angle 0.23514 ( 3) *********************** 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 : 0.293 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: 0.5765 time to fit residues: 153.2767 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 : 0.292 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.138982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.126308 restraints weight = 10584.711| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.89 r_work: 0.3597 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1344 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= 0.180 Angle : 0.560 5.303 10934 Z= 0.287 Chirality : 0.044 0.137 1222 Planarity : 0.005 0.033 1428 Dihedral : 6.453 53.071 1132 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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 aren not related in a simple way. whole: 0.76 (0.27), residues: 991 helix: 2.05 (0.26), residues: 374 sheet: -0.39 (0.36), residues: 202 loop : -0.40 (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 B 172 PHE 0.025 0.002 PHE B 493 TRP 0.014 0.001 TRP A 476 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8036) covalent geometry : angle 0.55997 (10927) SS BOND : bond 0.00142 ( 2) SS BOND : angle 0.92479 ( 4) hydrogen bonds : bond 0.03810 ( 422) hydrogen bonds : angle 4.73997 ( 1182) Misc. bond : bond 0.00010 ( 2) link_TRANS : bond 0.00025 ( 1) link_TRANS : angle 0.07181 ( 3) *********************** 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 : 0.309 Fit side-chains revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 504 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7606 (mt-10) REVERT: B 118 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 163 MET cc_start: 0.8530 (ptm) cc_final: 0.8202 (ptp) REVERT: B 187 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7853 (t) REVERT: B 206 GLU cc_start: 0.7363 (tp30) cc_final: 0.7137 (tp30) REVERT: B 265 VAL cc_start: 0.8342 (m) cc_final: 0.8091 (p) REVERT: B 336 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7647 (mm110) REVERT: B 372 GLN cc_start: 0.7246 (mm110) cc_final: 0.7034 (mp10) outliers start: 50 outliers final: 21 residues processed: 261 average time/residue: 0.5299 time to fit residues: 145.5645 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 170 LEU 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: 0.6980 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 54 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.139299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126203 restraints weight = 10465.410| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.98 r_work: 0.3595 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1497 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= 0.142 Angle : 0.533 4.984 10934 Z= 0.271 Chirality : 0.042 0.132 1222 Planarity : 0.004 0.035 1428 Dihedral : 6.348 52.724 1124 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.69 % Allowed : 23.45 % Favored : 71.86 % 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 aren not related in a simple way. whole: 0.78 (0.27), residues: 991 helix: 2.10 (0.26), residues: 374 sheet: -0.36 (0.36), residues: 199 loop : -0.45 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.009 0.001 TYR A 172 PHE 0.036 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 0.00335 ( 8036) covalent geometry : angle 0.53268 (10927) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.80979 ( 4) hydrogen bonds : bond 0.03504 ( 422) hydrogen bonds : angle 4.64344 ( 1182) Misc. bond : bond 0.00004 ( 2) link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.06667 ( 3) *********************** 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: 40 poor density : 225 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7896 (tp30) cc_final: 0.7637 (tp30) REVERT: A 207 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7293 (pt0) REVERT: A 288 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8221 (mtm180) REVERT: A 454 LYS cc_start: 0.8285 (ttmm) cc_final: 0.8074 (ttmm) REVERT: A 504 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7602 (mt-10) REVERT: B 163 MET cc_start: 0.8492 (ptm) cc_final: 0.8132 (ptp) REVERT: B 187 SER cc_start: 0.8229 (OUTLIER) cc_final: 0.7872 (t) REVERT: B 206 GLU cc_start: 0.7424 (tp30) cc_final: 0.7177 (tp30) REVERT: B 336 GLN cc_start: 0.7931 (mm-40) cc_final: 0.7599 (mm110) REVERT: B 372 GLN cc_start: 0.7279 (mm110) cc_final: 0.6966 (mp10) outliers start: 40 outliers final: 21 residues processed: 254 average time/residue: 0.5905 time to fit residues: 157.6278 Evaluate side-chains 242 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 330 THR 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 28 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.0050 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 444 GLN A 468 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.140422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127105 restraints weight = 10682.375| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.00 r_work: 0.3597 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8041 Z= 0.136 Angle : 0.531 4.869 10934 Z= 0.270 Chirality : 0.042 0.136 1222 Planarity : 0.004 0.035 1428 Dihedral : 6.263 52.914 1122 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.51 % Allowed : 23.09 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.27), residues: 991 helix: 2.17 (0.26), residues: 374 sheet: -0.36 (0.36), residues: 197 loop : -0.44 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.009 0.001 TYR A 172 PHE 0.041 0.002 PHE B 493 TRP 0.017 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8036) covalent geometry : angle 0.53063 (10927) SS BOND : bond 0.00062 ( 2) SS BOND : angle 0.81333 ( 4) hydrogen bonds : bond 0.03383 ( 422) hydrogen bonds : angle 4.58296 ( 1182) Misc. bond : bond 0.00004 ( 2) link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.09858 ( 3) *********************** 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 269 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 185 GLU cc_start: 0.7993 (tp30) cc_final: 0.7650 (tp30) REVERT: A 207 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: B 139 MET cc_start: 0.7971 (tmm) cc_final: 0.7725 (ttm) REVERT: B 187 SER cc_start: 0.8260 (OUTLIER) cc_final: 0.7896 (t) REVERT: B 206 GLU cc_start: 0.7452 (tp30) cc_final: 0.7233 (tp30) REVERT: B 336 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7612 (mm110) outliers start: 47 outliers final: 22 residues processed: 254 average time/residue: 0.5978 time to fit residues: 159.1725 Evaluate side-chains 239 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.139745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.126700 restraints weight = 10579.661| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.91 r_work: 0.3593 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1764 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= 0.157 Angle : 0.548 5.211 10934 Z= 0.278 Chirality : 0.043 0.144 1222 Planarity : 0.005 0.036 1428 Dihedral : 6.292 52.715 1122 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.69 % Allowed : 24.85 % 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 aren not related in a simple way. whole: 0.81 (0.27), residues: 991 helix: 2.06 (0.26), residues: 375 sheet: -0.32 (0.36), residues: 202 loop : -0.38 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.009 0.001 TYR A 172 PHE 0.046 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 0.00372 ( 8036) covalent geometry : angle 0.54839 (10927) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.83159 ( 4) hydrogen bonds : bond 0.03496 ( 422) hydrogen bonds : angle 4.61385 ( 1182) Misc. bond : bond 0.00005 ( 2) link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.09976 ( 3) *********************** 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 265 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8021 (tp30) cc_final: 0.7657 (tp30) REVERT: A 207 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: A 231 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 504 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7463 (mt-10) REVERT: B 187 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7953 (t) REVERT: B 206 GLU cc_start: 0.7448 (tp30) cc_final: 0.7247 (tp30) REVERT: B 336 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7600 (mm110) REVERT: B 493 PHE cc_start: 0.7985 (t80) cc_final: 0.7749 (t80) outliers start: 40 outliers final: 26 residues processed: 253 average time/residue: 0.6278 time to fit residues: 166.9516 Evaluate side-chains 249 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 98 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 44 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 144 HIS 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 = 0.3887 r_free = 0.3887 target = 0.140044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.127196 restraints weight = 10571.476| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.89 r_work: 0.3610 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1813 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= 0.146 Angle : 0.557 6.248 10934 Z= 0.284 Chirality : 0.043 0.147 1222 Planarity : 0.005 0.047 1428 Dihedral : 6.296 52.640 1122 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.69 % Allowed : 25.44 % Favored : 69.87 % 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 aren not related in a simple way. whole: 0.77 (0.27), residues: 991 helix: 2.04 (0.26), residues: 375 sheet: -0.39 (0.36), residues: 198 loop : -0.37 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.010 0.001 TYR A 259 PHE 0.034 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 0.00345 ( 8036) covalent geometry : angle 0.55737 (10927) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.78804 ( 4) hydrogen bonds : bond 0.03462 ( 422) hydrogen bonds : angle 4.61052 ( 1182) Misc. bond : bond 0.00005 ( 2) link_TRANS : bond 0.00016 ( 1) link_TRANS : angle 0.11071 ( 3) *********************** 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 262 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 185 GLU cc_start: 0.8015 (tp30) cc_final: 0.7635 (tp30) REVERT: A 207 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: A 231 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7664 (p) REVERT: A 288 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8154 (mtm180) REVERT: A 336 GLN cc_start: 0.8009 (mm110) cc_final: 0.7678 (mm110) REVERT: A 504 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 118 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7716 (mt-10) REVERT: B 139 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: B 187 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7888 (t) REVERT: B 206 GLU cc_start: 0.7453 (tp30) cc_final: 0.7243 (tp30) REVERT: B 336 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7576 (mm110) outliers start: 40 outliers final: 23 residues processed: 251 average time/residue: 0.6616 time to fit residues: 174.1133 Evaluate side-chains 247 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 139 MET 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 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: 0.6980 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.139369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126470 restraints weight = 10582.229| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.90 r_work: 0.3596 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1944 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= 0.163 Angle : 0.568 5.610 10934 Z= 0.289 Chirality : 0.043 0.150 1222 Planarity : 0.005 0.044 1428 Dihedral : 6.295 52.505 1122 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.57 % Allowed : 25.56 % Favored : 69.87 % 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 aren not related in a simple way. whole: 0.72 (0.27), residues: 991 helix: 1.98 (0.26), residues: 375 sheet: -0.40 (0.36), residues: 198 loop : -0.41 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.010 0.001 TYR A 172 PHE 0.045 0.002 PHE B 493 TRP 0.020 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8036) covalent geometry : angle 0.56821 (10927) SS BOND : bond 0.00087 ( 2) SS BOND : angle 0.90189 ( 4) hydrogen bonds : bond 0.03586 ( 422) hydrogen bonds : angle 4.64666 ( 1182) Misc. bond : bond 0.00006 ( 2) link_TRANS : bond 0.00007 ( 1) link_TRANS : angle 0.12957 ( 3) *********************** 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 262 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 185 GLU cc_start: 0.8051 (tp30) cc_final: 0.7662 (tp30) REVERT: A 207 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: A 231 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7676 (p) REVERT: A 288 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.8199 (mtm180) REVERT: A 336 GLN cc_start: 0.8014 (mm110) cc_final: 0.7682 (mm110) REVERT: A 443 LYS cc_start: 0.7956 (mmtm) cc_final: 0.7706 (mmtm) REVERT: A 504 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7428 (mt-10) REVERT: B 187 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7963 (t) REVERT: B 206 GLU cc_start: 0.7474 (tp30) cc_final: 0.7263 (tp30) REVERT: B 288 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8168 (mtt180) REVERT: B 336 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7540 (mm110) outliers start: 39 outliers final: 26 residues processed: 250 average time/residue: 0.6795 time to fit residues: 178.1563 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 : 0.301 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 56 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 42 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 468 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.141240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127941 restraints weight = 10675.254| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.01 r_work: 0.3610 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1857 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 : 0.549 6.658 10934 Z= 0.280 Chirality : 0.042 0.153 1222 Planarity : 0.005 0.053 1428 Dihedral : 6.199 52.414 1122 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.99 % Allowed : 26.96 % Favored : 69.05 % 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 aren not related in a simple way. whole: 0.80 (0.27), residues: 991 helix: 2.03 (0.26), residues: 375 sheet: -0.28 (0.37), residues: 196 loop : -0.39 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.010 0.001 TYR A 259 PHE 0.042 0.002 PHE B 493 TRP 0.019 0.001 TRP A 476 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8036) covalent geometry : angle 0.54947 (10927) SS BOND : bond 0.00024 ( 2) SS BOND : angle 0.63087 ( 4) hydrogen bonds : bond 0.03320 ( 422) hydrogen bonds : angle 4.58635 ( 1182) Misc. bond : bond 0.00004 ( 2) link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.13792 ( 3) *********************** 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 247 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 213 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7826 (m) cc_final: 0.7521 (t) REVERT: A 185 GLU cc_start: 0.8033 (tp30) cc_final: 0.7627 (tp30) REVERT: A 207 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: A 231 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7618 (p) REVERT: A 288 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8176 (mtm180) REVERT: A 504 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 105 LEU cc_start: 0.8495 (mm) cc_final: 0.8266 (mp) REVERT: B 187 SER cc_start: 0.8224 (p) cc_final: 0.7937 (t) REVERT: B 288 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8153 (mtt90) REVERT: B 336 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7529 (mm110) REVERT: B 446 VAL cc_start: 0.7822 (t) cc_final: 0.7515 (m) outliers start: 34 outliers final: 23 residues processed: 238 average time/residue: 0.6879 time to fit residues: 171.6504 Evaluate side-chains 235 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 308 LEU Chi-restraints excluded: chain A residue 330 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 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 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: 0.7980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** B 60 GLN B 332 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 = 0.3882 r_free = 0.3882 target = 0.139732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126786 restraints weight = 10478.574| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.89 r_work: 0.3599 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2021 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= 0.173 Angle : 0.602 8.800 10934 Z= 0.304 Chirality : 0.044 0.158 1222 Planarity : 0.005 0.058 1428 Dihedral : 6.328 52.855 1122 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.99 % Allowed : 27.20 % Favored : 68.82 % 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 aren not related in a simple way. whole: 0.69 (0.27), residues: 991 helix: 1.94 (0.26), residues: 375 sheet: -0.38 (0.36), residues: 198 loop : -0.43 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 235 TYR 0.011 0.001 TYR A 259 PHE 0.039 0.002 PHE B 493 TRP 0.020 0.001 TRP A 476 HIS 0.007 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8036) covalent geometry : angle 0.60233 (10927) SS BOND : bond 0.00088 ( 2) SS BOND : angle 0.88600 ( 4) hydrogen bonds : bond 0.03657 ( 422) hydrogen bonds : angle 4.67610 ( 1182) Misc. bond : bond 0.00004 ( 2) link_TRANS : bond 0.00011 ( 1) link_TRANS : angle 0.13809 ( 3) *********************** 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: 34 poor density : 219 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7770 (mt-10) REVERT: A 185 GLU cc_start: 0.8044 (tp30) cc_final: 0.7672 (tp30) REVERT: A 207 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: A 231 VAL cc_start: 0.7893 (OUTLIER) cc_final: 0.7663 (p) REVERT: A 288 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8115 (mtm180) REVERT: A 443 LYS cc_start: 0.7934 (mmtm) cc_final: 0.7681 (mmtm) REVERT: A 504 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 105 LEU cc_start: 0.8498 (mm) cc_final: 0.8256 (mp) REVERT: B 118 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 185 GLU cc_start: 0.8014 (tp30) cc_final: 0.7812 (tp30) REVERT: B 187 SER cc_start: 0.8201 (OUTLIER) cc_final: 0.7963 (t) REVERT: B 288 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8101 (mtt90) REVERT: B 336 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7502 (mm110) REVERT: B 446 VAL cc_start: 0.7800 (t) cc_final: 0.7539 (m) outliers start: 34 outliers final: 25 residues processed: 243 average time/residue: 0.6727 time to fit residues: 171.7335 Evaluate side-chains 243 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.6980 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 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 336 GLN A 374 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 60 GLN B 302 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 = 0.3874 r_free = 0.3874 target = 0.139103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125857 restraints weight = 10536.330| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.98 r_work: 0.3584 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2150 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= 0.183 Angle : 0.618 7.525 10934 Z= 0.312 Chirality : 0.045 0.167 1222 Planarity : 0.005 0.060 1428 Dihedral : 6.397 52.490 1122 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.28 % Allowed : 28.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.27), residues: 991 helix: 1.82 (0.26), residues: 375 sheet: -0.42 (0.36), residues: 198 loop : -0.47 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.012 0.001 TYR A 259 PHE 0.013 0.002 PHE A 34 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 ( 8036) covalent geometry : angle 0.61798 (10927) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.92596 ( 4) hydrogen bonds : bond 0.03709 ( 422) hydrogen bonds : angle 4.74202 ( 1182) Misc. bond : bond 0.00004 ( 2) link_TRANS : bond 0.00024 ( 1) link_TRANS : angle 0.13603 ( 3) ********************** 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 240 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 155 VAL cc_start: 0.8693 (p) cc_final: 0.8447 (m) REVERT: A 185 GLU cc_start: 0.8121 (tp30) cc_final: 0.7598 (tt0) REVERT: A 207 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: A 231 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7694 (p) REVERT: A 288 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8196 (mtm180) REVERT: A 443 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7716 (mmtm) REVERT: A 504 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7454 (mt-10) REVERT: B 76 GLU cc_start: 0.8086 (tp30) cc_final: 0.7779 (mm-30) REVERT: B 187 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.8010 (t) REVERT: B 288 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8136 (mtt90) REVERT: B 336 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7532 (mm110) REVERT: B 446 VAL cc_start: 0.7861 (t) cc_final: 0.7601 (m) outliers start: 28 outliers final: 22 residues processed: 231 average time/residue: 0.7156 time to fit residues: 173.4102 Evaluate side-chains 235 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 289 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 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 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 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.138955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126086 restraints weight = 10543.035| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.89 r_work: 0.3591 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2254 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= 0.188 Angle : 0.635 9.600 10934 Z= 0.322 Chirality : 0.045 0.161 1222 Planarity : 0.005 0.060 1428 Dihedral : 6.470 52.481 1122 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.28 % Allowed : 27.90 % Favored : 68.82 % 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 aren not related in a simple way. whole: 0.61 (0.27), residues: 991 helix: 1.89 (0.26), residues: 375 sheet: -0.41 (0.36), residues: 198 loop : -0.49 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 235 TYR 0.012 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 0.00447 ( 8036) covalent geometry : angle 0.63528 (10927) SS BOND : bond 0.00097 ( 2) SS BOND : angle 0.94598 ( 4) hydrogen bonds : bond 0.03763 ( 422) hydrogen bonds : angle 4.73218 ( 1182) Misc. bond : bond 0.00005 ( 2) link_TRANS : bond 0.00029 ( 1) link_TRANS : angle 0.13173 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3704.39 seconds wall clock time: 63 minutes 42.14 seconds (3822.14 seconds total)