Starting phenix.real_space_refine on Wed Aug 5 13:12:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjw_39352/08_2026/8yjw_39352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjw_39352/08_2026/8yjw_39352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yjw_39352/08_2026/8yjw_39352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjw_39352/08_2026/8yjw_39352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjw_39352/08_2026/8yjw_39352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjw_39352/08_2026/8yjw_39352.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 164 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 63 5.16 5 C 6067 2.51 5 N 1667 2.21 5 O 2086 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9946 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "C" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "D" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2774 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1955 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain: "J" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 407 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 621 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "F" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 9946 At special positions: 0 Unit cell: (102.09, 101.26, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 63 15.00 O 2086 8.00 N 1667 7.00 C 6067 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 162 " 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=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 304.7 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 29.9% alpha, 24.9% beta 11 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 9 through 20 removed outlier: 3.937A pdb=" N LYS B 13 " --> pdb=" O GLY B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'C' and resid 8 through 23 removed outlier: 4.088A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 118 removed outlier: 3.740A pdb=" N ALA D 116 " --> pdb=" O GLN D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 134 through 149 removed outlier: 3.520A pdb=" N ASN D 138 " --> pdb=" O THR D 134 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 169 Processing helix chain 'D' and resid 181 through 186 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 231 removed outlier: 3.501A pdb=" N PHE D 223 " --> pdb=" O ASN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 253 removed outlier: 3.569A pdb=" N ALA D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.617A pdb=" N ILE D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.826A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 23 removed outlier: 4.269A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 Processing helix chain 'A' and resid 140 through 155 removed outlier: 4.369A pdb=" N HIS A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.558A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 4 " --> pdb=" O LEU B 90 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 112 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 71 removed outlier: 4.006A pdb=" N MET B 68 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU B 25 " --> pdb=" O MET B 40 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N MET B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS B 27 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLN B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS B 240 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR B 224 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 227 " --> pdb=" O VAL B 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 208 removed outlier: 5.207A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 67 through 71 removed outlier: 5.865A pdb=" N CYS C 27 " --> pdb=" O GLN C 38 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 49 " --> pdb=" O LYS C 248 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 123 Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 208 removed outlier: 5.381A pdb=" N ALA C 157 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 172 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU A 99 " --> pdb=" O MET A 116 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 59 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 18 through 21 removed outlier: 6.653A pdb=" N ALA D 175 " --> pdb=" O MET D 191 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS D 30 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA D 176 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA D 32 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71 removed outlier: 3.521A pdb=" N MET A 68 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 226 433 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2601 1.33 - 1.46: 2082 1.46 - 1.58: 5315 1.58 - 1.70: 123 1.70 - 1.82: 102 Bond restraints: 10223 Sorted by residual: bond pdb=" CA MET D 191 " pdb=" CB MET D 191 " ideal model delta sigma weight residual 1.526 1.456 0.070 1.53e-02 4.27e+03 2.09e+01 bond pdb=" C3' DA E 25 " pdb=" O3' DA E 25 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.30e-02 5.92e+03 1.70e+01 bond pdb=" C3' DA J 15 " pdb=" O3' DA J 15 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.27e+01 bond pdb=" C3' DA J 15 " pdb=" C2' DA J 15 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT J 10 " pdb=" C2' DT J 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 ... (remaining 10218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 13510 2.46 - 4.93: 441 4.93 - 7.39: 80 7.39 - 9.86: 18 9.86 - 12.32: 10 Bond angle restraints: 14059 Sorted by residual: angle pdb=" N THR A 219 " pdb=" CA THR A 219 " pdb=" C THR A 219 " ideal model delta sigma weight residual 109.81 121.33 -11.52 2.21e+00 2.05e-01 2.72e+01 angle pdb=" C ALA C 231 " pdb=" N ASP C 232 " pdb=" CA ASP C 232 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C3' DA E 25 " pdb=" O3' DA E 25 " pdb=" P DA E 26 " ideal model delta sigma weight residual 119.70 125.75 -6.05 1.20e+00 6.94e-01 2.54e+01 angle pdb=" C LYS D 314 " pdb=" N GLN D 315 " pdb=" CA GLN D 315 " ideal model delta sigma weight residual 122.82 129.56 -6.74 1.42e+00 4.96e-01 2.25e+01 angle pdb=" N MET C 244 " pdb=" CA MET C 244 " pdb=" C MET C 244 " ideal model delta sigma weight residual 114.56 108.73 5.83 1.27e+00 6.20e-01 2.11e+01 ... (remaining 14054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.34: 5783 35.34 - 70.67: 385 70.67 - 106.00: 10 106.00 - 141.34: 1 141.34 - 176.67: 1 Dihedral angle restraints: 6180 sinusoidal: 2931 harmonic: 3249 Sorted by residual: dihedral pdb=" CA GLU B 191 " pdb=" C GLU B 191 " pdb=" N GLU B 192 " pdb=" CA GLU B 192 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA HIS D 253 " pdb=" C HIS D 253 " pdb=" N LYS D 254 " pdb=" CA LYS D 254 " ideal model delta harmonic sigma weight residual -180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA MET C 139 " pdb=" C MET C 139 " pdb=" N PRO C 140 " pdb=" CA PRO C 140 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 6177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1322 0.070 - 0.140: 250 0.140 - 0.209: 33 0.209 - 0.279: 10 0.279 - 0.349: 3 Chirality restraints: 1618 Sorted by residual: chirality pdb=" CG LEU D 144 " pdb=" CB LEU D 144 " pdb=" CD1 LEU D 144 " pdb=" CD2 LEU D 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB THR A 216 " pdb=" CA THR A 216 " pdb=" OG1 THR A 216 " pdb=" CG2 THR A 216 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB VAL D 52 " pdb=" CA VAL D 52 " pdb=" CG1 VAL D 52 " pdb=" CG2 VAL D 52 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1615 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 219 " 0.050 5.00e-02 4.00e+02 7.48e-02 8.95e+00 pdb=" N PRO A 220 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 219 " 0.048 5.00e-02 4.00e+02 7.09e-02 8.05e+00 pdb=" N PRO B 220 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 220 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 220 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 264 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO D 265 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 265 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 265 " -0.033 5.00e-02 4.00e+02 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2413 2.81 - 3.33: 8050 3.33 - 3.86: 17616 3.86 - 4.38: 19708 4.38 - 4.90: 33071 Nonbonded interactions: 80858 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR D 40 " pdb=" OP2 DT H 3 " model vdw 2.310 3.040 nonbonded pdb=" O SER B 31 " pdb=" OH TYR B 60 " model vdw 2.347 3.040 nonbonded pdb=" O ILE C 255 " pdb=" OG1 THR D 336 " model vdw 2.369 3.040 nonbonded pdb=" OG SER D 157 " pdb=" O GLU D 287 " model vdw 2.378 3.040 ... (remaining 80853 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' selection = (chain 'C' and resid 1 through 254) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.006 0.070 10225 Z= 0.366 Angle : 1.086 12.323 14063 Z= 0.656 Chirality : 0.060 0.349 1618 Planarity : 0.008 0.084 1595 Dihedral : 20.201 176.673 4066 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.21), residues: 1108 helix: -2.81 (0.20), residues: 323 sheet: -1.31 (0.27), residues: 340 loop : -2.02 (0.24), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 64 TYR 0.024 0.003 TYR D 40 PHE 0.019 0.003 PHE D 42 TRP 0.008 0.002 TRP A 28 HIS 0.008 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.37 (10223) covalent geometry : angle 1.08595 / 0.66 (14059) SS BOND : bond 0.00202 / 0.10 ( 2) SS BOND : angle 1.55866 / 0.78 ( 4) hydrogen bonds : bond 0.20503 / 13.09 ( 455) hydrogen bonds : angle 9.67495 / 6.62 ( 1271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.385 Fit side-chains REVERT: B 10 SER cc_start: 0.8346 (m) cc_final: 0.7806 (m) REVERT: B 84 ASN cc_start: 0.7420 (m-40) cc_final: 0.6660 (t0) REVERT: A 55 GLU cc_start: 0.6808 (mp0) cc_final: 0.6585 (tp30) REVERT: A 64 ARG cc_start: 0.7419 (mtm-85) cc_final: 0.7113 (mtm110) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0951 time to fit residues: 22.5723 Evaluate side-chains 137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 125 GLN D 77 ASN A 179 ASN A 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.155774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.122728 restraints weight = 12786.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123865 restraints weight = 9829.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125001 restraints weight = 9296.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125212 restraints weight = 7393.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126742 restraints weight = 6887.925| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10225 Z= 0.195 Angle : 0.678 9.860 14063 Z= 0.366 Chirality : 0.048 0.253 1618 Planarity : 0.005 0.046 1595 Dihedral : 21.325 171.748 1923 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.83 % Allowed : 8.77 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.23), residues: 1108 helix: -1.12 (0.25), residues: 329 sheet: -1.38 (0.29), residues: 310 loop : -1.79 (0.24), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 73 TYR 0.012 0.002 TYR D 40 PHE 0.017 0.002 PHE C 144 TRP 0.004 0.001 TRP A 28 HIS 0.011 0.002 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (10223) covalent geometry : angle 0.67847 / 0.37 (14059) SS BOND : bond 0.00174 / 0.09 ( 2) SS BOND : angle 0.48423 / 0.24 ( 4) hydrogen bonds : bond 0.05437 / 3.51 ( 455) hydrogen bonds : angle 7.16572 / 4.91 ( 1271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.347 Fit side-chains REVERT: B 10 SER cc_start: 0.8443 (m) cc_final: 0.7993 (m) REVERT: B 84 ASN cc_start: 0.7733 (m-40) cc_final: 0.7067 (t0) REVERT: D 325 VAL cc_start: 0.7207 (t) cc_final: 0.6995 (t) REVERT: A 170 SER cc_start: 0.8510 (m) cc_final: 0.8070 (t) outliers start: 8 outliers final: 5 residues processed: 158 average time/residue: 0.0917 time to fit residues: 20.8735 Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN A 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120660 restraints weight = 12729.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121433 restraints weight = 10051.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122762 restraints weight = 9566.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123008 restraints weight = 7984.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124269 restraints weight = 7495.323| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10225 Z= 0.177 Angle : 0.625 10.245 14063 Z= 0.335 Chirality : 0.046 0.293 1618 Planarity : 0.004 0.040 1595 Dihedral : 21.568 170.748 1923 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.55 % Allowed : 12.49 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.24), residues: 1108 helix: -0.17 (0.28), residues: 324 sheet: -1.42 (0.27), residues: 319 loop : -1.66 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.011 0.002 TYR C 211 PHE 0.028 0.002 PHE B 207 TRP 0.029 0.002 TRP D 274 HIS 0.007 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (10223) covalent geometry : angle 0.62468 / 0.34 (14059) SS BOND : bond 0.00127 / 0.07 ( 2) SS BOND : angle 0.62571 / 0.32 ( 4) hydrogen bonds : bond 0.04270 / 2.73 ( 455) hydrogen bonds : angle 6.49798 / 4.46 ( 1271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.332 Fit side-chains REVERT: B 10 SER cc_start: 0.8473 (m) cc_final: 0.8028 (m) REVERT: B 84 ASN cc_start: 0.7754 (m-40) cc_final: 0.6998 (t0) REVERT: D 77 ASN cc_start: 0.7940 (m-40) cc_final: 0.7707 (m-40) REVERT: D 108 GLU cc_start: 0.7292 (tp30) cc_final: 0.7013 (tm-30) REVERT: A 141 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7670 (t) REVERT: A 170 SER cc_start: 0.8554 (m) cc_final: 0.8133 (t) REVERT: A 235 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7827 (pt) outliers start: 15 outliers final: 9 residues processed: 159 average time/residue: 0.0875 time to fit residues: 20.4490 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 61 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 HIS ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.153822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119217 restraints weight = 12803.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121210 restraints weight = 8866.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122050 restraints weight = 8273.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.122673 restraints weight = 6170.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123929 restraints weight = 5646.828| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10225 Z= 0.169 Angle : 0.597 9.753 14063 Z= 0.321 Chirality : 0.045 0.292 1618 Planarity : 0.004 0.040 1595 Dihedral : 21.438 168.771 1923 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.65 % Allowed : 14.14 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1108 helix: 0.29 (0.28), residues: 324 sheet: -1.36 (0.28), residues: 315 loop : -1.54 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.011 0.002 TYR C 211 PHE 0.016 0.002 PHE B 207 TRP 0.021 0.002 TRP D 274 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (10223) covalent geometry : angle 0.59695 / 0.32 (14059) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 0.39048 / 0.20 ( 4) hydrogen bonds : bond 0.03869 / 2.47 ( 455) hydrogen bonds : angle 6.26107 / 4.29 ( 1271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.382 Fit side-chains REVERT: B 10 SER cc_start: 0.8449 (m) cc_final: 0.8060 (m) REVERT: B 84 ASN cc_start: 0.7785 (m-40) cc_final: 0.7021 (t0) REVERT: C 207 PHE cc_start: 0.8923 (m-80) cc_final: 0.8604 (m-80) REVERT: D 69 TYR cc_start: 0.7200 (m-10) cc_final: 0.6991 (m-10) REVERT: D 73 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6725 (ttm110) REVERT: D 77 ASN cc_start: 0.7918 (m-40) cc_final: 0.7697 (m-40) REVERT: D 108 GLU cc_start: 0.7229 (tp30) cc_final: 0.6988 (tm-30) REVERT: D 329 SER cc_start: 0.7345 (m) cc_final: 0.6525 (p) REVERT: A 170 SER cc_start: 0.8570 (m) cc_final: 0.8120 (t) REVERT: A 235 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7896 (pt) outliers start: 16 outliers final: 10 residues processed: 151 average time/residue: 0.0880 time to fit residues: 19.4927 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.0470 chunk 37 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.120168 restraints weight = 12568.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122843 restraints weight = 10162.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124179 restraints weight = 6905.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.124476 restraints weight = 5871.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124891 restraints weight = 5621.105| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10225 Z= 0.141 Angle : 0.568 9.628 14063 Z= 0.305 Chirality : 0.044 0.300 1618 Planarity : 0.003 0.045 1595 Dihedral : 21.368 167.726 1923 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.86 % Allowed : 15.58 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.24), residues: 1108 helix: 0.59 (0.29), residues: 324 sheet: -1.26 (0.27), residues: 331 loop : -1.41 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.011 0.001 TYR C 211 PHE 0.014 0.001 PHE D 126 TRP 0.020 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (10223) covalent geometry : angle 0.56757 / 0.31 (14059) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 0.27850 / 0.15 ( 4) hydrogen bonds : bond 0.03553 / 2.29 ( 455) hydrogen bonds : angle 6.06286 / 4.16 ( 1271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.218 Fit side-chains REVERT: B 10 SER cc_start: 0.8454 (m) cc_final: 0.8082 (m) REVERT: B 84 ASN cc_start: 0.7804 (m-40) cc_final: 0.7039 (t0) REVERT: C 41 ASP cc_start: 0.8331 (t0) cc_final: 0.8129 (t0) REVERT: C 207 PHE cc_start: 0.8939 (m-80) cc_final: 0.8615 (m-80) REVERT: D 69 TYR cc_start: 0.7224 (m-10) cc_final: 0.6597 (m-80) REVERT: D 77 ASN cc_start: 0.7912 (m-40) cc_final: 0.7646 (m-40) REVERT: D 108 GLU cc_start: 0.7165 (tp30) cc_final: 0.6960 (tm-30) REVERT: D 268 TYR cc_start: 0.6096 (m-10) cc_final: 0.5828 (m-10) REVERT: D 329 SER cc_start: 0.7365 (m) cc_final: 0.7051 (p) REVERT: A 16 LEU cc_start: 0.8590 (mm) cc_final: 0.8315 (mm) REVERT: A 141 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7739 (t) REVERT: A 170 SER cc_start: 0.8621 (m) cc_final: 0.8157 (t) REVERT: A 174 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 235 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7900 (pt) outliers start: 18 outliers final: 13 residues processed: 154 average time/residue: 0.0786 time to fit residues: 17.7637 Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.0770 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 89 optimal weight: 0.0770 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120436 restraints weight = 12613.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122205 restraints weight = 8848.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123561 restraints weight = 7735.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.124074 restraints weight = 5971.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124296 restraints weight = 6139.019| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10225 Z= 0.136 Angle : 0.567 9.079 14063 Z= 0.305 Chirality : 0.044 0.299 1618 Planarity : 0.003 0.044 1595 Dihedral : 21.283 168.194 1923 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.37 % Allowed : 16.10 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1108 helix: 0.70 (0.29), residues: 324 sheet: -1.16 (0.28), residues: 315 loop : -1.41 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.011 0.001 TYR C 211 PHE 0.014 0.001 PHE D 126 TRP 0.021 0.001 TRP D 274 HIS 0.002 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (10223) covalent geometry : angle 0.56719 / 0.31 (14059) SS BOND : bond 0.00204 / 0.10 ( 2) SS BOND : angle 0.34624 / 0.18 ( 4) hydrogen bonds : bond 0.03486 / 2.23 ( 455) hydrogen bonds : angle 5.93620 / 4.07 ( 1271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.284 Fit side-chains REVERT: B 10 SER cc_start: 0.8489 (m) cc_final: 0.8143 (m) REVERT: B 84 ASN cc_start: 0.7810 (m-40) cc_final: 0.7006 (t0) REVERT: D 67 MET cc_start: 0.7196 (ttp) cc_final: 0.6897 (ttp) REVERT: D 77 ASN cc_start: 0.7945 (m-40) cc_final: 0.7636 (m-40) REVERT: D 148 MET cc_start: 0.7817 (tpp) cc_final: 0.6897 (mtt) REVERT: D 268 TYR cc_start: 0.6071 (m-10) cc_final: 0.5820 (m-10) REVERT: D 281 GLN cc_start: 0.7471 (pp30) cc_final: 0.7240 (tm-30) REVERT: D 288 VAL cc_start: 0.7144 (OUTLIER) cc_final: 0.6881 (p) REVERT: D 329 SER cc_start: 0.7404 (m) cc_final: 0.7042 (p) REVERT: A 16 LEU cc_start: 0.8588 (mm) cc_final: 0.8322 (mm) REVERT: A 141 SER cc_start: 0.8424 (OUTLIER) cc_final: 0.7744 (t) REVERT: A 170 SER cc_start: 0.8616 (m) cc_final: 0.8119 (t) REVERT: A 174 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 235 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7911 (pt) outliers start: 23 outliers final: 15 residues processed: 152 average time/residue: 0.0868 time to fit residues: 19.3014 Evaluate side-chains 150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118013 restraints weight = 12711.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120735 restraints weight = 10379.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121972 restraints weight = 6949.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122282 restraints weight = 5963.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122751 restraints weight = 5674.715| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10225 Z= 0.160 Angle : 0.578 9.544 14063 Z= 0.310 Chirality : 0.044 0.299 1618 Planarity : 0.003 0.043 1595 Dihedral : 21.203 170.236 1923 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.27 % Allowed : 17.34 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1108 helix: 0.79 (0.29), residues: 324 sheet: -1.33 (0.28), residues: 295 loop : -1.31 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.011 0.001 TYR C 211 PHE 0.013 0.001 PHE D 126 TRP 0.023 0.002 TRP D 274 HIS 0.003 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (10223) covalent geometry : angle 0.57790 / 0.31 (14059) SS BOND : bond 0.00196 / 0.10 ( 2) SS BOND : angle 0.48342 / 0.25 ( 4) hydrogen bonds : bond 0.03519 / 2.25 ( 455) hydrogen bonds : angle 5.90817 / 4.05 ( 1271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.365 Fit side-chains REVERT: B 10 SER cc_start: 0.8452 (m) cc_final: 0.8112 (m) REVERT: B 75 MET cc_start: 0.8369 (ttt) cc_final: 0.7852 (ttt) REVERT: B 84 ASN cc_start: 0.7827 (m-40) cc_final: 0.7051 (t0) REVERT: D 77 ASN cc_start: 0.7958 (m-40) cc_final: 0.7645 (m-40) REVERT: D 148 MET cc_start: 0.7859 (tpp) cc_final: 0.7061 (mtt) REVERT: D 281 GLN cc_start: 0.7501 (pp30) cc_final: 0.7262 (tm-30) REVERT: D 288 VAL cc_start: 0.7244 (OUTLIER) cc_final: 0.6974 (p) REVERT: D 329 SER cc_start: 0.7474 (m) cc_final: 0.7121 (p) REVERT: A 16 LEU cc_start: 0.8639 (mm) cc_final: 0.8368 (mm) REVERT: A 141 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 170 SER cc_start: 0.8633 (m) cc_final: 0.8144 (t) REVERT: A 174 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6827 (tm-30) REVERT: A 235 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7952 (pt) outliers start: 22 outliers final: 16 residues processed: 147 average time/residue: 0.0902 time to fit residues: 19.6078 Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.117285 restraints weight = 12579.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118773 restraints weight = 8882.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119807 restraints weight = 8471.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120686 restraints weight = 6361.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120793 restraints weight = 6487.295| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10225 Z= 0.171 Angle : 0.589 9.337 14063 Z= 0.315 Chirality : 0.044 0.300 1618 Planarity : 0.003 0.043 1595 Dihedral : 21.166 171.346 1923 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.17 % Allowed : 18.06 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.25), residues: 1108 helix: 0.79 (0.29), residues: 325 sheet: -1.38 (0.29), residues: 285 loop : -1.26 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.012 0.002 TYR C 211 PHE 0.014 0.002 PHE D 126 TRP 0.024 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10223) covalent geometry : angle 0.58883 / 0.31 (14059) SS BOND : bond 0.00218 / 0.11 ( 2) SS BOND : angle 0.48539 / 0.26 ( 4) hydrogen bonds : bond 0.03515 / 2.24 ( 455) hydrogen bonds : angle 5.91009 / 4.05 ( 1271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.351 Fit side-chains REVERT: B 10 SER cc_start: 0.8499 (m) cc_final: 0.8154 (m) REVERT: B 75 MET cc_start: 0.8376 (ttt) cc_final: 0.7879 (ttt) REVERT: B 84 ASN cc_start: 0.7853 (m-40) cc_final: 0.7047 (t0) REVERT: D 77 ASN cc_start: 0.8000 (m-40) cc_final: 0.7694 (m-40) REVERT: D 148 MET cc_start: 0.7820 (tpp) cc_final: 0.7110 (mtt) REVERT: D 160 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: D 281 GLN cc_start: 0.7493 (pp30) cc_final: 0.7243 (tm-30) REVERT: D 288 VAL cc_start: 0.7394 (OUTLIER) cc_final: 0.7133 (p) REVERT: D 329 SER cc_start: 0.7529 (m) cc_final: 0.7199 (p) REVERT: A 16 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 141 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.7845 (t) REVERT: A 170 SER cc_start: 0.8621 (m) cc_final: 0.8133 (t) REVERT: A 235 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8030 (pt) outliers start: 21 outliers final: 16 residues processed: 154 average time/residue: 0.0866 time to fit residues: 19.6129 Evaluate side-chains 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.118604 restraints weight = 12552.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120068 restraints weight = 8768.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121535 restraints weight = 7829.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122063 restraints weight = 6034.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122293 restraints weight = 6111.360| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10225 Z= 0.141 Angle : 0.575 8.834 14063 Z= 0.307 Chirality : 0.044 0.305 1618 Planarity : 0.003 0.046 1595 Dihedral : 21.140 171.334 1923 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.27 % Allowed : 17.85 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1108 helix: 0.86 (0.29), residues: 325 sheet: -1.42 (0.29), residues: 277 loop : -1.24 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.012 0.001 TYR C 211 PHE 0.016 0.001 PHE D 126 TRP 0.026 0.002 TRP D 274 HIS 0.002 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10223) covalent geometry : angle 0.57517 / 0.31 (14059) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 0.43632 / 0.22 ( 4) hydrogen bonds : bond 0.03376 / 2.19 ( 455) hydrogen bonds : angle 5.82910 / 4.00 ( 1271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.452 Fit side-chains REVERT: B 10 SER cc_start: 0.8460 (m) cc_final: 0.8131 (m) REVERT: B 75 MET cc_start: 0.8390 (ttt) cc_final: 0.7896 (ttt) REVERT: B 84 ASN cc_start: 0.7843 (m-40) cc_final: 0.7046 (t0) REVERT: D 77 ASN cc_start: 0.7971 (m-40) cc_final: 0.7666 (m-40) REVERT: D 148 MET cc_start: 0.7868 (tpp) cc_final: 0.7208 (ttm) REVERT: D 160 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6914 (pm20) REVERT: D 281 GLN cc_start: 0.7463 (pp30) cc_final: 0.7223 (tm-30) REVERT: D 288 VAL cc_start: 0.7365 (OUTLIER) cc_final: 0.7108 (p) REVERT: D 329 SER cc_start: 0.7502 (m) cc_final: 0.7193 (p) REVERT: A 16 LEU cc_start: 0.8585 (mm) cc_final: 0.8308 (mm) REVERT: A 141 SER cc_start: 0.8511 (OUTLIER) cc_final: 0.7841 (t) REVERT: A 170 SER cc_start: 0.8644 (m) cc_final: 0.8105 (t) outliers start: 22 outliers final: 16 residues processed: 157 average time/residue: 0.0934 time to fit residues: 21.4624 Evaluate side-chains 154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 43 optimal weight: 0.0050 chunk 4 optimal weight: 0.0770 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 113 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.2752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.154741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120359 restraints weight = 12393.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122732 restraints weight = 9874.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123718 restraints weight = 6986.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124146 restraints weight = 6553.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.124605 restraints weight = 5815.912| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10225 Z= 0.121 Angle : 0.570 8.459 14063 Z= 0.304 Chirality : 0.044 0.308 1618 Planarity : 0.003 0.045 1595 Dihedral : 21.105 171.587 1923 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.65 % Allowed : 18.78 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1108 helix: 1.00 (0.29), residues: 325 sheet: -1.38 (0.29), residues: 285 loop : -1.16 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.008 0.001 TYR C 211 PHE 0.017 0.001 PHE D 126 TRP 0.033 0.002 TRP D 274 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (10223) covalent geometry : angle 0.57019 / 0.30 (14059) SS BOND : bond 0.00051 / 0.03 ( 2) SS BOND : angle 0.29271 / 0.15 ( 4) hydrogen bonds : bond 0.03244 / 2.12 ( 455) hydrogen bonds : angle 5.72946 / 3.92 ( 1271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.395 Fit side-chains REVERT: B 10 SER cc_start: 0.8465 (m) cc_final: 0.8142 (m) REVERT: B 75 MET cc_start: 0.8363 (ttt) cc_final: 0.7837 (ttt) REVERT: B 84 ASN cc_start: 0.7791 (m-40) cc_final: 0.7006 (t0) REVERT: C 41 ASP cc_start: 0.8299 (t0) cc_final: 0.8094 (t70) REVERT: D 67 MET cc_start: 0.7046 (ttm) cc_final: 0.6617 (ttp) REVERT: D 77 ASN cc_start: 0.7929 (m-40) cc_final: 0.7652 (m-40) REVERT: D 148 MET cc_start: 0.7840 (tpp) cc_final: 0.7142 (ttm) REVERT: D 160 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: D 281 GLN cc_start: 0.7470 (pp30) cc_final: 0.7246 (tm-30) REVERT: D 288 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.7020 (p) REVERT: D 329 SER cc_start: 0.7520 (m) cc_final: 0.7206 (p) REVERT: A 16 LEU cc_start: 0.8539 (mm) cc_final: 0.8273 (mm) REVERT: A 141 SER cc_start: 0.8528 (OUTLIER) cc_final: 0.7792 (t) outliers start: 16 outliers final: 13 residues processed: 152 average time/residue: 0.0875 time to fit residues: 19.3916 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 73 ARG Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 91 optimal weight: 0.1980 chunk 99 optimal weight: 0.0020 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 23 optimal weight: 0.0980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120475 restraints weight = 12543.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.124022 restraints weight = 9645.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.125069 restraints weight = 6106.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.125340 restraints weight = 5288.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125628 restraints weight = 5113.917| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10225 Z= 0.125 Angle : 0.565 8.507 14063 Z= 0.301 Chirality : 0.044 0.309 1618 Planarity : 0.003 0.045 1595 Dihedral : 21.078 172.809 1923 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.96 % Allowed : 18.68 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1108 helix: 1.07 (0.29), residues: 325 sheet: -1.34 (0.29), residues: 285 loop : -1.12 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.009 0.001 TYR C 211 PHE 0.018 0.001 PHE D 126 TRP 0.031 0.002 TRP D 274 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10223) covalent geometry : angle 0.56522 / 0.30 (14059) SS BOND : bond 0.00089 / 0.05 ( 2) SS BOND : angle 0.33135 / 0.17 ( 4) hydrogen bonds : bond 0.03252 / 2.11 ( 455) hydrogen bonds : angle 5.68096 / 3.88 ( 1271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1600.90 seconds wall clock time: 28 minutes 29.63 seconds (1709.63 seconds total)