Starting phenix.real_space_refine on Wed Feb 12 12:40:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u4x_41903/02_2025/8u4x_41903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u4x_41903/02_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_41903/02_2025/8u4x_41903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_2025/8u4x_41903.map" model { file = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_2025/8u4x_41903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u4x_41903/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 7.70, per 1000 atoms: 0.98 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 375 " - pdb=" SG CYS A 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: 1.92 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: 0.86 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: 2.34 Time building geometry restraints manager: 2.25 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: 4018 14.64 - 29.29: 541 29.29 - 43.93: 216 43.93 - 58.58: 77 58.58 - 73.22: 37 Dihedral angle restraints: 4889 sinusoidal: 1996 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=" 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 dihedral pdb=" CG ARG A 173 " pdb=" CD ARG A 173 " pdb=" NE ARG A 173 " pdb=" CZ ARG A 173 " ideal model delta sinusoidal sigma weight residual 90.00 133.32 -43.32 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 4886 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: 2.03 - 2.61: 53 2.61 - 3.18: 6340 3.18 - 3.75: 12440 3.75 - 4.33: 16693 4.33 - 4.90: 27873 Nonbonded interactions: 63399 Sorted by model distance: nonbonded pdb=" SG CYS B 375 " pdb=" SG CYS B 379 " model vdw 2.032 3.760 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 ... (remaining 63394 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: 2.610 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.610 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- 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 0.032 8036 Z= 0.144 Angle : 0.559 5.548 10927 Z= 0.300 Chirality : 0.042 0.159 1222 Planarity : 0.004 0.032 1428 Dihedral : 17.694 73.223 3009 Min Nonbonded Distance : 2.032 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 *********************** 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 : 0.661 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: 1.3818 time to fit residues: 367.0638 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 : 0.947 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.139259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126615 restraints weight = 10465.477| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.88 r_work: 0.3605 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8036 Z= 0.261 Angle : 0.551 5.124 10927 Z= 0.283 Chirality : 0.044 0.137 1222 Planarity : 0.005 0.033 1428 Dihedral : 6.346 53.282 1132 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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 (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: 2.07 (0.26), residues: 374 sheet: -0.38 (0.36), residues: 202 loop : -0.40 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.026 0.002 PHE B 493 TYR 0.010 0.001 TYR B 172 ARG 0.005 0.001 ARG B 235 *********************** 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 274 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7839 (tp30) cc_final: 0.7587 (mm-30) REVERT: A 504 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 118 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7727 (mt-10) REVERT: B 187 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7858 (t) REVERT: B 206 GLU cc_start: 0.7363 (tp30) cc_final: 0.7135 (tp30) REVERT: B 265 VAL cc_start: 0.8331 (m) cc_final: 0.8079 (p) REVERT: B 336 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7651 (mm110) REVERT: B 372 GLN cc_start: 0.7214 (mm110) cc_final: 0.6948 (mp10) outliers start: 50 outliers final: 20 residues processed: 260 average time/residue: 1.3782 time to fit residues: 376.1746 Evaluate side-chains 241 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 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 268 SER 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 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: 0.9980 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 49 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 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 = 0.139597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.126697 restraints weight = 10555.934| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.90 r_work: 0.3598 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8036 Z= 0.220 Angle : 0.531 4.911 10927 Z= 0.270 Chirality : 0.042 0.132 1222 Planarity : 0.004 0.034 1428 Dihedral : 6.146 52.719 1123 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.81 % Allowed : 23.21 % Favored : 71.98 % 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: 2.10 (0.26), residues: 374 sheet: -0.41 (0.36), residues: 200 loop : -0.41 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 476 HIS 0.005 0.001 HIS B 30 PHE 0.032 0.002 PHE B 493 TYR 0.010 0.001 TYR A 172 ARG 0.004 0.000 ARG A 173 *********************** 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: 41 poor density : 224 time to evaluate : 0.791 Fit side-chains REVERT: A 185 GLU cc_start: 0.7924 (tp30) cc_final: 0.7666 (mm-30) REVERT: A 207 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7290 (pt0) REVERT: A 288 ARG cc_start: 0.8573 (mtm-85) cc_final: 0.8226 (mtm180) REVERT: A 454 LYS cc_start: 0.8287 (ttmm) cc_final: 0.8073 (ttmm) REVERT: B 187 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7842 (t) REVERT: B 206 GLU cc_start: 0.7404 (tp30) cc_final: 0.7159 (tp30) REVERT: B 235 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7553 (mtp180) REVERT: B 336 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7575 (mm110) REVERT: B 372 GLN cc_start: 0.7231 (mm110) cc_final: 0.6911 (mp10) outliers start: 41 outliers final: 21 residues processed: 253 average time/residue: 1.4267 time to fit residues: 378.7356 Evaluate side-chains 243 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 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 235 ARG 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 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 67 optimal weight: 0.0070 chunk 38 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 71 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.3398 ------------------------------------------------------------------------------- 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 A 510 GLN B 60 GLN B 120 GLN B 241 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.140962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127971 restraints weight = 10401.386| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.89 r_work: 0.3619 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8036 Z= 0.189 Angle : 0.521 4.711 10927 Z= 0.266 Chirality : 0.042 0.135 1222 Planarity : 0.004 0.034 1428 Dihedral : 6.048 52.653 1121 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.81 % Allowed : 23.68 % 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: 0.83 (0.27), residues: 991 helix: 2.16 (0.26), residues: 374 sheet: -0.39 (0.37), residues: 197 loop : -0.40 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.039 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.003 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7743 (mt-10) REVERT: A 185 GLU cc_start: 0.7933 (tp30) cc_final: 0.7604 (tp30) REVERT: A 207 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: B 139 MET cc_start: 0.7950 (tmm) cc_final: 0.7717 (ttm) REVERT: B 187 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.7864 (t) REVERT: B 206 GLU cc_start: 0.7422 (tp30) cc_final: 0.7211 (tp30) REVERT: B 235 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7565 (mtp180) REVERT: B 336 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7606 (mm110) outliers start: 41 outliers final: 19 residues processed: 257 average time/residue: 1.4320 time to fit residues: 385.5541 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 474 GLU Chi-restraints excluded: chain B residue 476 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 444 GLN 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 = 0.3886 r_free = 0.3886 target = 0.139985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126616 restraints weight = 10457.340| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.98 r_work: 0.3590 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8036 Z= 0.245 Angle : 0.548 5.174 10927 Z= 0.278 Chirality : 0.043 0.142 1222 Planarity : 0.005 0.035 1428 Dihedral : 6.084 52.405 1121 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.45 % Allowed : 25.67 % 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 (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: 0.79 (0.27), residues: 991 helix: 2.06 (0.26), residues: 375 sheet: -0.41 (0.36), residues: 200 loop : -0.36 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.045 0.002 PHE B 493 TYR 0.009 0.001 TYR A 172 ARG 0.005 0.000 ARG A 509 *********************** 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 263 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 225 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.8073 (tp30) cc_final: 0.7780 (mm-30) REVERT: A 207 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: A 231 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7669 (p) REVERT: B 139 MET cc_start: 0.7976 (tmm) cc_final: 0.7721 (ttm) REVERT: B 187 SER cc_start: 0.8228 (OUTLIER) cc_final: 0.7896 (t) REVERT: B 206 GLU cc_start: 0.7465 (tp30) cc_final: 0.7259 (tp30) REVERT: B 235 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6583 (mtm180) REVERT: B 336 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7591 (mm110) outliers start: 38 outliers final: 24 residues processed: 248 average time/residue: 1.4196 time to fit residues: 369.4051 Evaluate side-chains 251 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 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 444 GLN Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 295 HIS B 306 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 = 0.3867 r_free = 0.3867 target = 0.138347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.125383 restraints weight = 10405.269| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.87 r_work: 0.3580 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8036 Z= 0.343 Angle : 0.602 5.759 10927 Z= 0.306 Chirality : 0.045 0.151 1222 Planarity : 0.005 0.046 1428 Dihedral : 6.261 52.154 1121 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.57 % Allowed : 26.14 % Favored : 69.28 % 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: 0.64 (0.27), residues: 991 helix: 1.92 (0.26), residues: 375 sheet: -0.45 (0.36), residues: 200 loop : -0.45 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.049 0.003 PHE B 493 TYR 0.010 0.001 TYR A 259 ARG 0.004 0.000 ARG A 173 *********************** 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 259 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 220 time to evaluate : 0.820 Fit side-chains REVERT: A 118 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 185 GLU cc_start: 0.8115 (tp30) cc_final: 0.7771 (mm-30) REVERT: A 207 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: A 231 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7725 (p) REVERT: A 288 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.8180 (mtm180) REVERT: A 336 GLN cc_start: 0.7991 (mm110) cc_final: 0.7678 (mm110) REVERT: B 187 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7947 (t) REVERT: B 206 GLU cc_start: 0.7467 (tp30) cc_final: 0.7259 (tp30) REVERT: B 235 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6523 (mtm180) outliers start: 39 outliers final: 23 residues processed: 246 average time/residue: 1.4375 time to fit residues: 371.1049 Evaluate side-chains 243 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 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 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 235 ARG 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 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: 0.8980 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 chunk 47 optimal weight: 0.0670 chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 306 GLN B 336 GLN B 444 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.139714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.126351 restraints weight = 10513.868| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.97 r_work: 0.3594 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8036 Z= 0.220 Angle : 0.572 7.707 10927 Z= 0.289 Chirality : 0.043 0.151 1222 Planarity : 0.005 0.051 1428 Dihedral : 6.164 52.275 1121 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.99 % Allowed : 26.85 % 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: 0.69 (0.27), residues: 991 helix: 1.98 (0.26), residues: 375 sheet: -0.43 (0.36), residues: 197 loop : -0.44 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 476 HIS 0.005 0.001 HIS B 30 PHE 0.045 0.002 PHE B 493 TYR 0.009 0.001 TYR A 259 ARG 0.009 0.000 ARG A 509 *********************** 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 253 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.785 Fit side-chains REVERT: A 207 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7232 (pt0) REVERT: A 231 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7672 (p) REVERT: A 288 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8204 (mtm180) REVERT: A 336 GLN cc_start: 0.8005 (mm110) cc_final: 0.7666 (mm110) REVERT: A 372 GLN cc_start: 0.7339 (mp10) cc_final: 0.7031 (mp10) REVERT: B 187 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7957 (t) REVERT: B 206 GLU cc_start: 0.7479 (tp30) cc_final: 0.7272 (tp30) REVERT: B 235 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.6495 (mtm180) REVERT: B 336 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7597 (mm-40) REVERT: B 446 VAL cc_start: 0.7822 (t) cc_final: 0.7509 (m) outliers start: 34 outliers final: 20 residues processed: 243 average time/residue: 1.4711 time to fit residues: 374.8443 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 : 0.794 ------------------------------------------------------------------------------- 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 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 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 87 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN A 468 GLN B 60 GLN B 468 GLN B 510 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.138767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.125538 restraints weight = 10555.480| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.97 r_work: 0.3583 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8036 Z= 0.270 Angle : 0.586 7.165 10927 Z= 0.295 Chirality : 0.044 0.158 1222 Planarity : 0.005 0.054 1428 Dihedral : 6.194 51.978 1121 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.22 % Allowed : 26.73 % 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 (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: 0.63 (0.27), residues: 991 helix: 1.90 (0.26), residues: 375 sheet: -0.42 (0.36), residues: 200 loop : -0.46 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.041 0.002 PHE B 493 TYR 0.010 0.001 TYR A 259 ARG 0.008 0.001 ARG A 509 *********************** 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 252 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.948 Fit side-chains REVERT: A 50 VAL cc_start: 0.7826 (m) cc_final: 0.7513 (t) REVERT: A 207 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: A 231 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7686 (p) REVERT: A 288 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8178 (mtm180) REVERT: A 336 GLN cc_start: 0.8008 (mm110) cc_final: 0.7671 (mm110) REVERT: A 443 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7801 (mmtm) REVERT: A 480 MET cc_start: 0.8057 (mmm) cc_final: 0.7718 (mmm) REVERT: B 187 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.8031 (t) REVERT: B 235 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.6544 (mtm180) REVERT: B 288 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8216 (mtt90) REVERT: B 336 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7519 (mm110) REVERT: B 446 VAL cc_start: 0.7802 (t) cc_final: 0.7533 (m) outliers start: 36 outliers final: 24 residues processed: 242 average time/residue: 1.4423 time to fit residues: 365.9820 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 : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 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 417 THR Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 96 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.138504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.125130 restraints weight = 10678.340| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.00 r_work: 0.3571 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8036 Z= 0.314 Angle : 0.623 7.355 10927 Z= 0.314 Chirality : 0.045 0.163 1222 Planarity : 0.005 0.058 1428 Dihedral : 6.290 52.056 1121 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 28.02 % Favored : 68.23 % 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: 0.52 (0.27), residues: 991 helix: 1.82 (0.26), residues: 375 sheet: -0.50 (0.36), residues: 198 loop : -0.53 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 476 HIS 0.007 0.001 HIS B 30 PHE 0.014 0.002 PHE A 34 TYR 0.012 0.001 TYR A 259 ARG 0.008 0.001 ARG A 509 *********************** 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 249 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.851 Fit side-chains REVERT: A 185 GLU cc_start: 0.8158 (tp30) cc_final: 0.7879 (tp30) REVERT: A 207 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: A 231 VAL cc_start: 0.7962 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 443 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7750 (mmtt) REVERT: A 480 MET cc_start: 0.8050 (mmm) cc_final: 0.7708 (mmm) REVERT: B 76 GLU cc_start: 0.8069 (tp30) cc_final: 0.7822 (mm-30) REVERT: B 187 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7977 (t) REVERT: B 235 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6524 (mtm180) REVERT: B 288 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8101 (mtt90) REVERT: B 336 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7603 (mm110) REVERT: B 446 VAL cc_start: 0.7824 (t) cc_final: 0.7550 (m) outliers start: 32 outliers final: 24 residues processed: 240 average time/residue: 1.4370 time to fit residues: 361.7185 Evaluate side-chains 244 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 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 417 THR Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 80 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 444 GLN A 468 GLN B 60 GLN B 306 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 = 0.3861 r_free = 0.3861 target = 0.138026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125117 restraints weight = 10490.212| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.88 r_work: 0.3574 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8036 Z= 0.344 Angle : 0.656 7.827 10927 Z= 0.331 Chirality : 0.046 0.180 1222 Planarity : 0.005 0.060 1428 Dihedral : 6.387 52.364 1121 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.75 % Allowed : 28.02 % Favored : 68.23 % 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: 0.46 (0.27), residues: 991 helix: 1.78 (0.26), residues: 375 sheet: -0.51 (0.36), residues: 198 loop : -0.58 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 476 HIS 0.008 0.001 HIS B 30 PHE 0.018 0.002 PHE B 493 TYR 0.011 0.001 TYR A 259 ARG 0.008 0.001 ARG A 509 ********************** 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 242 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.819 Fit side-chains REVERT: A 185 GLU cc_start: 0.8143 (tp30) cc_final: 0.7819 (mm-30) REVERT: A 207 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7274 (pt0) REVERT: A 231 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7745 (p) REVERT: A 480 MET cc_start: 0.8030 (mmm) cc_final: 0.7694 (mmm) REVERT: B 76 GLU cc_start: 0.8049 (tp30) cc_final: 0.7768 (mm-30) REVERT: B 187 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.8022 (t) REVERT: B 235 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6500 (mtm180) REVERT: B 288 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8088 (mtt180) REVERT: B 336 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7618 (mm110) REVERT: B 446 VAL cc_start: 0.7859 (t) cc_final: 0.7590 (m) outliers start: 32 outliers final: 24 residues processed: 235 average time/residue: 1.4031 time to fit residues: 346.1665 Evaluate side-chains 237 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 341 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 375 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 235 ARG 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 417 THR Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 486 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 47 optimal weight: 0.0010 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 73 optimal weight: 0.5980 chunk 86 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN A 468 GLN A 496 ASN B 468 GLN B 510 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.139286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126282 restraints weight = 10551.639| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.91 r_work: 0.3595 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8036 Z= 0.234 Angle : 0.622 8.103 10927 Z= 0.314 Chirality : 0.044 0.209 1222 Planarity : 0.005 0.057 1428 Dihedral : 6.279 52.178 1121 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.81 % Allowed : 28.84 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.27), residues: 991 helix: 1.85 (0.26), residues: 375 sheet: -0.50 (0.36), residues: 192 loop : -0.54 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 476 HIS 0.006 0.001 HIS B 30 PHE 0.011 0.002 PHE A 102 TYR 0.012 0.001 TYR A 259 ARG 0.008 0.000 ARG A 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7613.28 seconds wall clock time: 134 minutes 25.89 seconds (8065.89 seconds total)