Starting phenix.real_space_refine on Sun May 11 10:12:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4x_41903/05_2025/8u4x_41903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4x_41903/05_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_41903/05_2025/8u4x_41903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4x_41903/05_2025/8u4x_41903.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4x_41903/05_2025/8u4x_41903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4x_41903/05_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-5687/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: 7.62, per 1000 atoms: 0.97 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: 2.03 Conformation dependent library (CDL) restraints added in 1.2 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: 0.97 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: 2.43 Time building geometry restraints manager: 2.38 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: 3.570 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.290 Find NCS groups from input model: 0.280 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- 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 : 0.923 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: 1.3032 time to fit residues: 346.9460 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 : 0.862 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126523 restraints weight = 10456.216| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.88 r_work: 0.3602 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 53.164 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 0.05563 ( 3) hydrogen bonds : bond 0.03708 ( 422) hydrogen bonds : angle 4.71928 ( 1182) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.89107 ( 4) covalent geometry : bond 0.00395 ( 8036) covalent geometry : angle 0.55417 (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 : 0.883 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: 0.7834 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 118 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7737 (mt-10) REVERT: B 163 MET cc_start: 0.8514 (ptm) cc_final: 0.8202 (ptp) REVERT: B 187 SER cc_start: 0.8189 (OUTLIER) cc_final: 0.7818 (t) REVERT: B 206 GLU cc_start: 0.7370 (tp30) cc_final: 0.7131 (tp30) REVERT: B 265 VAL cc_start: 0.8335 (m) cc_final: 0.8082 (p) REVERT: B 336 GLN cc_start: 0.7967 (mm-40) cc_final: 0.7634 (mm110) REVERT: B 372 GLN cc_start: 0.7212 (mm110) cc_final: 0.6982 (mp10) outliers start: 49 outliers final: 21 residues processed: 259 average time/residue: 1.2857 time to fit residues: 350.3738 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 : 0.802 ------------------------------------------------------------------------------- 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: 0.7980 chunk 49 optimal weight: 0.0270 chunk 42 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 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 = 0.3884 r_free = 0.3884 target = 0.139807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126434 restraints weight = 10542.364| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.99 r_work: 0.3592 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1559 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 : 0.541 5.135 10934 Z= 0.275 Chirality : 0.043 0.133 1222 Planarity : 0.005 0.035 1428 Dihedral : 6.343 52.876 1123 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 0.74 (0.27), residues: 991 helix: 2.09 (0.26), residues: 374 sheet: -0.43 (0.36), residues: 200 loop : -0.46 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.035 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.004 0.000 ARG A 173 Details of bonding type rmsd link_TRANS : bond 0.00018 ( 1) link_TRANS : angle 0.06631 ( 3) hydrogen bonds : bond 0.03574 ( 422) hydrogen bonds : angle 4.65252 ( 1182) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.85369 ( 4) covalent geometry : bond 0.00370 ( 8036) covalent geometry : angle 0.54112 (10927) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8037 (tp30) cc_final: 0.7777 (mm-30) REVERT: A 207 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: A 288 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8244 (mtm180) REVERT: A 336 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7736 (mm110) REVERT: A 454 LYS cc_start: 0.8266 (ttmm) cc_final: 0.8046 (ttmm) REVERT: B 163 MET cc_start: 0.8543 (ptm) cc_final: 0.8179 (ptp) REVERT: B 187 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7889 (t) REVERT: B 206 GLU cc_start: 0.7443 (tp30) cc_final: 0.7195 (tp30) REVERT: B 235 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7556 (mtp180) REVERT: B 336 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7584 (mm110) outliers start: 44 outliers final: 25 residues processed: 253 average time/residue: 1.3449 time to fit residues: 357.2725 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 : 0.817 ------------------------------------------------------------------------------- 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 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 235 ARG 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: 0.8980 chunk 55 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 73 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 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.125951 restraints weight = 10432.598| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.95 r_work: 0.3586 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1770 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= 0.179 Angle : 0.561 5.329 10934 Z= 0.285 Chirality : 0.043 0.139 1222 Planarity : 0.005 0.036 1428 Dihedral : 6.365 52.580 1122 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.74 % Allowed : 23.56 % 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: 0.69 (0.27), residues: 991 helix: 2.00 (0.26), residues: 375 sheet: -0.43 (0.36), residues: 200 loop : -0.46 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.043 0.002 PHE B 493 TYR 0.010 0.001 TYR A 172 ARG 0.003 0.000 ARG A 173 Details of bonding type rmsd link_TRANS : bond 0.00019 ( 1) link_TRANS : angle 0.09157 ( 3) hydrogen bonds : bond 0.03629 ( 422) hydrogen bonds : angle 4.66232 ( 1182) SS BOND : bond 0.00095 ( 2) SS BOND : angle 0.94386 ( 4) covalent geometry : bond 0.00424 ( 8036) covalent geometry : angle 0.56085 (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 276 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 227 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 207 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: A 231 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7691 (p) REVERT: A 336 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7759 (mm110) REVERT: B 187 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7901 (t) REVERT: B 206 GLU cc_start: 0.7438 (tp30) cc_final: 0.7218 (tp30) REVERT: B 235 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6574 (mtm180) outliers start: 49 outliers final: 26 residues processed: 261 average time/residue: 1.3534 time to fit residues: 370.8264 Evaluate side-chains 249 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 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 187 SER Chi-restraints excluded: chain B residue 235 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 0.4980 chunk 82 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 0.0040 chunk 22 optimal weight: 0.0070 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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 120 GLN B 241 GLN B 306 GLN B 336 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.140401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127148 restraints weight = 10473.646| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.97 r_work: 0.3605 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1740 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= 0.123 Angle : 0.530 5.053 10934 Z= 0.270 Chirality : 0.042 0.139 1222 Planarity : 0.005 0.036 1428 Dihedral : 6.253 52.849 1122 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.04 % Allowed : 24.50 % 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: 0.78 (0.27), residues: 991 helix: 2.09 (0.26), residues: 375 sheet: -0.37 (0.36), residues: 199 loop : -0.44 (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 0.004 0.000 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00041 ( 1) link_TRANS : angle 0.11322 ( 3) hydrogen bonds : bond 0.03392 ( 422) hydrogen bonds : angle 4.62137 ( 1182) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.71272 ( 4) covalent geometry : bond 0.00287 ( 8036) covalent geometry : angle 0.52957 (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 262 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8057 (tp30) cc_final: 0.7700 (mm-30) REVERT: A 207 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: A 231 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7635 (p) REVERT: A 336 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7705 (mm110) REVERT: B 76 GLU cc_start: 0.8045 (tp30) cc_final: 0.7749 (mm-30) REVERT: B 187 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7964 (t) REVERT: B 206 GLU cc_start: 0.7442 (tp30) cc_final: 0.7235 (tp30) REVERT: B 235 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.6502 (mtm180) REVERT: B 336 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7596 (mm110) REVERT: B 446 VAL cc_start: 0.7842 (t) cc_final: 0.7552 (m) REVERT: B 493 PHE cc_start: 0.7956 (t80) cc_final: 0.7725 (t80) outliers start: 43 outliers final: 22 residues processed: 248 average time/residue: 1.3880 time to fit residues: 361.7739 Evaluate side-chains 236 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 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 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.0000 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 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 = 0.3880 r_free = 0.3880 target = 0.139432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126531 restraints weight = 10456.679| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.89 r_work: 0.3602 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1876 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= 0.168 Angle : 0.576 6.292 10934 Z= 0.292 Chirality : 0.044 0.149 1222 Planarity : 0.005 0.037 1428 Dihedral : 6.318 52.464 1122 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.57 % Allowed : 25.44 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.27), residues: 991 helix: 2.03 (0.26), residues: 375 sheet: -0.42 (0.36), residues: 200 loop : -0.44 (0.32), residues: 416 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 0.034 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.005 0.000 ARG B 288 Details of bonding type rmsd link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.11928 ( 3) hydrogen bonds : bond 0.03570 ( 422) hydrogen bonds : angle 4.64238 ( 1182) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.85478 ( 4) covalent geometry : bond 0.00398 ( 8036) covalent geometry : angle 0.57554 (10927) Misc. bond : bond 0.00007 ( 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 255 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7736 (mt-10) REVERT: A 207 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: A 231 VAL cc_start: 0.7875 (OUTLIER) cc_final: 0.7651 (p) REVERT: A 336 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7742 (mm110) REVERT: B 118 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 187 SER cc_start: 0.8197 (p) cc_final: 0.7928 (t) REVERT: B 235 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6587 (mtm180) outliers start: 39 outliers final: 22 residues processed: 245 average time/residue: 1.3456 time to fit residues: 346.1451 Evaluate side-chains 240 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 341 SER 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 235 ARG 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 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: 0.0170 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 0.0040 chunk 47 optimal weight: 0.0060 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 93 optimal weight: 0.0670 chunk 29 optimal weight: 0.5980 overall best weight: 0.1384 ------------------------------------------------------------------------------- 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 A 496 ASN B 60 GLN B 144 HIS 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 = 0.3914 r_free = 0.3914 target = 0.142181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129273 restraints weight = 10588.477| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.92 r_work: 0.3643 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8041 Z= 0.102 Angle : 0.517 5.192 10934 Z= 0.265 Chirality : 0.042 0.135 1222 Planarity : 0.005 0.053 1428 Dihedral : 6.086 53.100 1122 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.10 % Allowed : 26.49 % 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: 0.85 (0.28), residues: 991 helix: 2.12 (0.26), residues: 375 sheet: -0.33 (0.37), residues: 196 loop : -0.38 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 476 HIS 0.003 0.001 HIS A 295 PHE 0.039 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.009 0.000 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00074 ( 1) link_TRANS : angle 0.14017 ( 3) hydrogen bonds : bond 0.03150 ( 422) hydrogen bonds : angle 4.53190 ( 1182) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.52964 ( 4) covalent geometry : bond 0.00236 ( 8036) covalent geometry : angle 0.51657 (10927) Misc. bond : bond 0.00003 ( 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 249 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7789 (m) cc_final: 0.7486 (t) REVERT: A 139 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: A 207 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: B 118 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7726 (mt-10) REVERT: B 132 ARG cc_start: 0.8244 (mtp180) cc_final: 0.7964 (mtp180) REVERT: B 185 GLU cc_start: 0.7931 (tp30) cc_final: 0.7628 (tp30) REVERT: B 187 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7960 (t) REVERT: B 336 GLN cc_start: 0.7774 (mm110) cc_final: 0.7472 (mm110) REVERT: B 446 VAL cc_start: 0.7754 (t) cc_final: 0.7483 (m) outliers start: 35 outliers final: 21 residues processed: 238 average time/residue: 1.3999 time to fit residues: 349.9697 Evaluate side-chains 237 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 289 THR 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 444 GLN 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 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 306 GLN A 336 GLN B 60 GLN B 332 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 = 0.3886 r_free = 0.3886 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.127108 restraints weight = 10575.861| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.91 r_work: 0.3609 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1953 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= 0.162 Angle : 0.575 6.259 10934 Z= 0.293 Chirality : 0.044 0.158 1222 Planarity : 0.005 0.050 1428 Dihedral : 6.227 52.401 1122 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.57 % Allowed : 26.03 % 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 (0.28), residues: 991 helix: 2.03 (0.26), residues: 375 sheet: -0.36 (0.36), residues: 202 loop : -0.41 (0.33), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 476 HIS 0.007 0.001 HIS B 30 PHE 0.014 0.002 PHE A 34 TYR 0.009 0.001 TYR A 172 ARG 0.009 0.000 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.12735 ( 3) hydrogen bonds : bond 0.03540 ( 422) hydrogen bonds : angle 4.62305 ( 1182) SS BOND : bond 0.00075 ( 2) SS BOND : angle 0.81080 ( 4) covalent geometry : bond 0.00385 ( 8036) covalent geometry : angle 0.57496 (10927) Misc. bond : bond 0.00005 ( 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 255 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 VAL cc_start: 0.7845 (m) cc_final: 0.7543 (t) REVERT: A 118 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 185 GLU cc_start: 0.8016 (tp30) cc_final: 0.7667 (mm-30) REVERT: A 207 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7247 (pt0) REVERT: A 231 VAL cc_start: 0.7815 (OUTLIER) cc_final: 0.7605 (p) REVERT: A 288 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8207 (mtm180) REVERT: B 185 GLU cc_start: 0.8041 (tp30) cc_final: 0.7812 (tp30) REVERT: B 187 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7949 (t) REVERT: B 336 GLN cc_start: 0.7817 (mm110) cc_final: 0.7516 (mm110) REVERT: B 446 VAL cc_start: 0.7786 (t) cc_final: 0.7548 (m) outliers start: 39 outliers final: 25 residues processed: 244 average time/residue: 1.3514 time to fit residues: 346.2023 Evaluate side-chains 239 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 49 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 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 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 60 GLN B 295 HIS B 302 GLN B 332 GLN B 444 GLN B 468 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.139100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.126207 restraints weight = 10689.986| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.92 r_work: 0.3590 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2090 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= 0.197 Angle : 0.613 7.260 10934 Z= 0.312 Chirality : 0.045 0.185 1222 Planarity : 0.005 0.052 1428 Dihedral : 6.361 52.281 1122 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.87 % Allowed : 26.96 % Favored : 69.17 % 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: 1.94 (0.26), residues: 375 sheet: -0.41 (0.36), residues: 200 loop : -0.48 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 476 HIS 0.007 0.001 HIS B 30 PHE 0.024 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 0.00029 ( 1) link_TRANS : angle 0.13138 ( 3) hydrogen bonds : bond 0.03719 ( 422) hydrogen bonds : angle 4.67938 ( 1182) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.85509 ( 4) covalent geometry : bond 0.00467 ( 8036) covalent geometry : angle 0.61260 (10927) Misc. bond : bond 0.00006 ( 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 248 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7732 (mt-10) REVERT: A 207 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: A 231 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7690 (p) REVERT: A 288 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8239 (mtm180) REVERT: A 480 MET cc_start: 0.8065 (mmm) cc_final: 0.7747 (mmm) REVERT: B 40 GLU cc_start: 0.6086 (pm20) cc_final: 0.5841 (pm20) REVERT: B 118 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7761 (mt-10) REVERT: B 185 GLU cc_start: 0.8073 (tp30) cc_final: 0.7683 (tp30) REVERT: B 187 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7970 (t) REVERT: B 288 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8179 (mtt90) REVERT: B 336 GLN cc_start: 0.7800 (mm110) cc_final: 0.7512 (mm110) REVERT: B 386 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7785 (mmt90) REVERT: B 446 VAL cc_start: 0.7808 (t) cc_final: 0.7537 (m) outliers start: 33 outliers final: 24 residues processed: 238 average time/residue: 1.3656 time to fit residues: 341.1281 Evaluate side-chains 242 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 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 375 CYS Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 444 GLN Chi-restraints excluded: chain B residue 474 GLU 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: 0.5980 chunk 96 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 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 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 468 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.138981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126157 restraints weight = 10534.245| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.89 r_work: 0.3589 rms_B_bonded: 2.33 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: 0.7642 moved from start: 0.2177 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= 0.195 Angle : 0.622 7.052 10934 Z= 0.316 Chirality : 0.045 0.176 1222 Planarity : 0.005 0.062 1428 Dihedral : 6.418 52.216 1122 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.75 % Allowed : 27.67 % Favored : 68.58 % 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: 0.59 (0.27), residues: 991 helix: 1.87 (0.26), residues: 375 sheet: -0.40 (0.36), residues: 200 loop : -0.51 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 476 HIS 0.007 0.001 HIS B 30 PHE 0.015 0.002 PHE A 34 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.001 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00035 ( 1) link_TRANS : angle 0.13682 ( 3) hydrogen bonds : bond 0.03758 ( 422) hydrogen bonds : angle 4.72300 ( 1182) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.86459 ( 4) covalent geometry : bond 0.00464 ( 8036) covalent geometry : angle 0.62155 (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 247 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7718 (mt-10) REVERT: A 207 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7259 (pt0) REVERT: A 231 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7697 (p) REVERT: A 288 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8200 (mtm180) REVERT: A 443 LYS cc_start: 0.7966 (mmtm) cc_final: 0.7703 (mmtm) REVERT: B 185 GLU cc_start: 0.8105 (tp30) cc_final: 0.7841 (tp30) REVERT: B 187 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.8010 (t) REVERT: B 288 ARG cc_start: 0.8391 (mtm-85) cc_final: 0.8180 (mtt90) REVERT: B 336 GLN cc_start: 0.7819 (mm110) cc_final: 0.7530 (mm110) REVERT: B 446 VAL cc_start: 0.7826 (t) cc_final: 0.7547 (m) outliers start: 32 outliers final: 25 residues processed: 236 average time/residue: 1.3195 time to fit residues: 327.1909 Evaluate side-chains 238 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 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 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 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 0.0670 chunk 73 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN B 444 GLN B 468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126641 restraints weight = 10591.829| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.99 r_work: 0.3592 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2174 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= 0.162 Angle : 0.607 8.722 10934 Z= 0.307 Chirality : 0.044 0.171 1222 Planarity : 0.005 0.061 1428 Dihedral : 6.361 52.388 1122 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.75 % Allowed : 27.43 % 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 (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: 0.61 (0.27), residues: 991 helix: 1.88 (0.26), residues: 375 sheet: -0.40 (0.36), residues: 200 loop : -0.49 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 476 HIS 0.007 0.001 HIS B 30 PHE 0.013 0.002 PHE A 34 TYR 0.009 0.001 TYR A 172 ARG 0.008 0.001 ARG A 509 Details of bonding type rmsd link_TRANS : bond 0.00000 ( 1) link_TRANS : angle 0.13141 ( 3) hydrogen bonds : bond 0.03649 ( 422) hydrogen bonds : angle 4.68432 ( 1182) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.71133 ( 4) covalent geometry : bond 0.00386 ( 8036) covalent geometry : angle 0.60654 (10927) Misc. bond : bond 0.00006 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7707.63 seconds wall clock time: 132 minutes 50.53 seconds (7970.53 seconds total)