Starting phenix.real_space_refine on Thu Jul 2 19:51:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjw_39352/07_2026/8yjw_39352.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjw_39352/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yjw_39352/07_2026/8yjw_39352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjw_39352/07_2026/8yjw_39352.map" model { file = "/net/cci-nas-00/data/ceres_data/8yjw_39352/07_2026/8yjw_39352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjw_39352/07_2026/8yjw_39352.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.17, per 1000 atoms: 0.22 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: 0.86 Conformation dependent library (CDL) restraints added in 320.7 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: 1.09 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: 1.38 Time building geometry restraints manager: 1.12 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: 13511 2.46 - 4.93: 441 4.93 - 7.39: 79 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=" 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 angle pdb=" CA GLN D 281 " pdb=" CB GLN D 281 " pdb=" CG GLN D 281 " ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+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: 3.600 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: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- 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 : 1.085 12.323 14063 Z= 0.654 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 1.08470 / 0.65 (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 : 0.481 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: 0.0851 time to fit residues: 20.3949 Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 315 GLN A 179 ASN A 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122578 restraints weight = 12773.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123565 restraints weight = 10007.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124840 restraints weight = 9622.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124940 restraints weight = 7694.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126310 restraints weight = 7092.598| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10225 Z= 0.196 Angle : 0.693 10.152 14063 Z= 0.370 Chirality : 0.048 0.244 1618 Planarity : 0.005 0.045 1595 Dihedral : 21.507 169.602 1923 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.03 % Allowed : 9.18 % Favored : 89.78 % 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: -2.29 (0.23), residues: 1108 helix: -1.09 (0.26), residues: 330 sheet: -1.36 (0.28), residues: 312 loop : -1.80 (0.24), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 53 TYR 0.014 0.002 TYR D 40 PHE 0.014 0.002 PHE C 169 TRP 0.006 0.001 TRP B 28 HIS 0.009 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (10223) covalent geometry : angle 0.69255 / 0.37 (14059) SS BOND : bond 0.00242 / 0.12 ( 2) SS BOND : angle 0.63551 / 0.31 ( 4) hydrogen bonds : bond 0.05158 / 3.38 ( 455) hydrogen bonds : angle 7.03329 / 4.81 ( 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 166 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.356 Fit side-chains REVERT: B 10 SER cc_start: 0.8426 (m) cc_final: 0.7994 (m) REVERT: B 84 ASN cc_start: 0.7736 (m-40) cc_final: 0.7084 (t0) REVERT: B 207 PHE cc_start: 0.8532 (m-10) cc_final: 0.8311 (m-10) REVERT: D 108 GLU cc_start: 0.7307 (tp30) cc_final: 0.6579 (tp30) REVERT: D 325 VAL cc_start: 0.7284 (t) cc_final: 0.7067 (t) REVERT: A 170 SER cc_start: 0.8519 (m) cc_final: 0.8078 (t) outliers start: 10 outliers final: 4 residues processed: 160 average time/residue: 0.0927 time to fit residues: 21.1055 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.0000 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 ASN ** C 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.153594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120502 restraints weight = 12745.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.120739 restraints weight = 9828.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121363 restraints weight = 10416.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122061 restraints weight = 8582.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122310 restraints weight = 8133.744| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2050 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= 0.171 Angle : 0.615 10.265 14063 Z= 0.329 Chirality : 0.046 0.266 1618 Planarity : 0.004 0.042 1595 Dihedral : 21.561 167.665 1923 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.44 % Allowed : 13.42 % Favored : 85.14 % 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: -1.74 (0.24), residues: 1108 helix: -0.11 (0.28), residues: 324 sheet: -1.35 (0.29), residues: 297 loop : -1.67 (0.25), residues: 487 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 0.014 0.002 PHE D 126 TRP 0.030 0.002 TRP D 274 HIS 0.007 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (10223) covalent geometry : angle 0.61485 / 0.33 (14059) SS BOND : bond 0.00172 / 0.09 ( 2) SS BOND : angle 0.55423 / 0.28 ( 4) hydrogen bonds : bond 0.04336 / 2.75 ( 455) hydrogen bonds : angle 6.46495 / 4.44 ( 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: 14 poor density : 153 time to evaluate : 0.277 Fit side-chains REVERT: B 10 SER cc_start: 0.8457 (m) cc_final: 0.8018 (m) REVERT: B 84 ASN cc_start: 0.7738 (m-40) cc_final: 0.6985 (t0) REVERT: D 67 MET cc_start: 0.7075 (ttm) cc_final: 0.6795 (ttp) REVERT: D 108 GLU cc_start: 0.7273 (tp30) cc_final: 0.7003 (tm-30) REVERT: A 141 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7679 (t) REVERT: A 170 SER cc_start: 0.8531 (m) cc_final: 0.8124 (t) REVERT: A 235 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7813 (pt) outliers start: 14 outliers final: 10 residues processed: 159 average time/residue: 0.0658 time to fit residues: 15.4839 Evaluate side-chains 147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 232 ASP 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: 8.9990 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 HIS D 77 ASN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.153692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118955 restraints weight = 12818.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122594 restraints weight = 9823.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123894 restraints weight = 6077.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124172 restraints weight = 5367.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124384 restraints weight = 5049.733| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2422 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= 0.163 Angle : 0.587 9.621 14063 Z= 0.316 Chirality : 0.045 0.278 1618 Planarity : 0.004 0.042 1595 Dihedral : 21.438 164.767 1923 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.75 % Allowed : 14.65 % Favored : 83.59 % 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: -1.39 (0.24), residues: 1108 helix: 0.37 (0.28), residues: 324 sheet: -1.30 (0.28), residues: 323 loop : -1.46 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.013 0.002 TYR C 211 PHE 0.019 0.002 PHE B 207 TRP 0.022 0.002 TRP D 274 HIS 0.005 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (10223) covalent geometry : angle 0.58684 / 0.32 (14059) SS BOND : bond 0.00157 / 0.08 ( 2) SS BOND : angle 0.30557 / 0.16 ( 4) hydrogen bonds : bond 0.03757 / 2.42 ( 455) hydrogen bonds : angle 6.18134 / 4.24 ( 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 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.206 Fit side-chains REVERT: B 10 SER cc_start: 0.8467 (m) cc_final: 0.8084 (m) REVERT: B 84 ASN cc_start: 0.7814 (m-40) cc_final: 0.7058 (t0) REVERT: C 72 LEU cc_start: 0.8328 (mt) cc_final: 0.8076 (mt) REVERT: D 69 TYR cc_start: 0.7193 (m-10) cc_final: 0.6848 (m-80) REVERT: D 160 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: D 263 LEU cc_start: 0.6988 (tt) cc_final: 0.6620 (tp) REVERT: D 329 SER cc_start: 0.7303 (m) cc_final: 0.6978 (p) REVERT: A 170 SER cc_start: 0.8580 (m) cc_final: 0.8123 (t) REVERT: A 235 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7896 (pt) outliers start: 17 outliers final: 10 residues processed: 152 average time/residue: 0.0690 time to fit residues: 15.4835 Evaluate side-chains 144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 134 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 177 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: 1.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 44 optimal weight: 0.5980 chunk 114 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.154749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120089 restraints weight = 12563.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121729 restraints weight = 8733.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122819 restraints weight = 8153.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123547 restraints weight = 6158.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123714 restraints weight = 6338.419| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10225 Z= 0.141 Angle : 0.581 9.612 14063 Z= 0.310 Chirality : 0.043 0.281 1618 Planarity : 0.003 0.043 1595 Dihedral : 21.387 164.074 1923 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.06 % Allowed : 16.31 % Favored : 81.63 % 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: 0.55 (0.29), residues: 324 sheet: -1.24 (0.28), residues: 321 loop : -1.41 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.009 0.001 TYR C 211 PHE 0.015 0.001 PHE D 126 TRP 0.021 0.001 TRP D 274 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (10223) covalent geometry : angle 0.58143 / 0.31 (14059) SS BOND : bond 0.00183 / 0.09 ( 2) SS BOND : angle 0.42846 / 0.22 ( 4) hydrogen bonds : bond 0.03623 / 2.31 ( 455) hydrogen bonds : angle 6.06306 / 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 158 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.253 Fit side-chains REVERT: B 10 SER cc_start: 0.8470 (m) cc_final: 0.8106 (m) REVERT: B 84 ASN cc_start: 0.7797 (m-40) cc_final: 0.7026 (t0) REVERT: D 69 TYR cc_start: 0.7072 (m-10) cc_final: 0.6563 (m-80) REVERT: D 263 LEU cc_start: 0.6997 (tt) cc_final: 0.6664 (tp) REVERT: D 329 SER cc_start: 0.7341 (m) cc_final: 0.6973 (p) REVERT: A 16 LEU cc_start: 0.8610 (mm) cc_final: 0.8353 (mm) REVERT: A 141 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7740 (t) REVERT: A 170 SER cc_start: 0.8612 (m) cc_final: 0.8160 (t) REVERT: A 174 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6953 (tm-30) REVERT: A 235 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (pt) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.0753 time to fit residues: 16.4026 Evaluate side-chains 145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 121 LEU 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 72 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 0.0570 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 44 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 78 optimal weight: 0.6980 chunk 89 optimal weight: 0.0570 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.2616 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.155085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120407 restraints weight = 12617.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123451 restraints weight = 9605.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.124797 restraints weight = 6260.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125251 restraints weight = 5633.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.125630 restraints weight = 5112.567| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10225 Z= 0.115 Angle : 0.550 8.545 14063 Z= 0.296 Chirality : 0.043 0.285 1618 Planarity : 0.003 0.044 1595 Dihedral : 21.271 162.674 1923 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.96 % Allowed : 17.03 % Favored : 81.01 % 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: -1.03 (0.25), residues: 1108 helix: 0.87 (0.29), residues: 325 sheet: -1.11 (0.28), residues: 311 loop : -1.41 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.009 0.001 TYR C 211 PHE 0.014 0.001 PHE D 126 TRP 0.022 0.001 TRP D 274 HIS 0.002 0.000 HIS B 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (10223) covalent geometry : angle 0.54996 / 0.30 (14059) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.23841 / 0.11 ( 4) hydrogen bonds : bond 0.03358 / 2.18 ( 455) hydrogen bonds : angle 5.87817 / 4.04 ( 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: 19 poor density : 144 time to evaluate : 0.245 Fit side-chains REVERT: B 10 SER cc_start: 0.8493 (m) cc_final: 0.8138 (m) REVERT: B 84 ASN cc_start: 0.7768 (m-40) cc_final: 0.6959 (t0) REVERT: C 72 LEU cc_start: 0.8255 (mt) cc_final: 0.7980 (mt) REVERT: C 207 PHE cc_start: 0.8885 (m-80) cc_final: 0.8557 (m-80) REVERT: D 69 TYR cc_start: 0.6919 (m-10) cc_final: 0.6350 (m-80) REVERT: D 160 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6845 (pm20) REVERT: D 263 LEU cc_start: 0.7053 (tt) cc_final: 0.6715 (tp) REVERT: D 281 GLN cc_start: 0.7454 (pp30) cc_final: 0.7238 (tm-30) REVERT: D 288 VAL cc_start: 0.7066 (OUTLIER) cc_final: 0.6807 (p) REVERT: D 329 SER cc_start: 0.7370 (m) cc_final: 0.7026 (p) REVERT: A 16 LEU cc_start: 0.8546 (mm) cc_final: 0.8265 (mm) REVERT: A 170 SER cc_start: 0.8613 (m) cc_final: 0.8093 (t) REVERT: A 235 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7834 (pt) outliers start: 19 outliers final: 12 residues processed: 155 average time/residue: 0.0717 time to fit residues: 16.4132 Evaluate side-chains 149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 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 232 ASP Chi-restraints excluded: chain C residue 255 ILE 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 160 GLU 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 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: 0.5980 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.152332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.117368 restraints weight = 12686.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120756 restraints weight = 9961.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121502 restraints weight = 6581.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121923 restraints weight = 5866.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122042 restraints weight = 5450.160| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10225 Z= 0.177 Angle : 0.601 9.737 14063 Z= 0.320 Chirality : 0.044 0.281 1618 Planarity : 0.004 0.043 1595 Dihedral : 21.196 166.513 1923 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % 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: -1.08 (0.25), residues: 1108 helix: 0.81 (0.29), residues: 324 sheet: -1.15 (0.28), residues: 315 loop : -1.42 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 91 TYR 0.015 0.002 TYR D 83 PHE 0.012 0.002 PHE D 126 TRP 0.024 0.002 TRP D 274 HIS 0.004 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (10223) covalent geometry : angle 0.60069 / 0.32 (14059) SS BOND : bond 0.00229 / 0.12 ( 2) SS BOND : angle 0.56107 / 0.29 ( 4) hydrogen bonds : bond 0.03561 / 2.28 ( 455) hydrogen bonds : angle 5.89696 / 4.04 ( 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 161 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.344 Fit side-chains REVERT: B 10 SER cc_start: 0.8527 (m) cc_final: 0.8157 (m) REVERT: B 84 ASN cc_start: 0.7801 (m-40) cc_final: 0.7007 (t0) REVERT: D 160 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: D 263 LEU cc_start: 0.7086 (tt) cc_final: 0.6753 (tp) REVERT: D 281 GLN cc_start: 0.7512 (pp30) cc_final: 0.7277 (tm-30) REVERT: D 288 VAL cc_start: 0.7271 (OUTLIER) cc_final: 0.7003 (p) REVERT: D 329 SER cc_start: 0.7438 (m) cc_final: 0.7095 (p) REVERT: A 16 LEU cc_start: 0.8670 (mm) cc_final: 0.8395 (mm) REVERT: A 141 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.7797 (t) REVERT: A 170 SER cc_start: 0.8626 (m) cc_final: 0.8138 (t) REVERT: A 235 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7961 (pt) outliers start: 22 outliers final: 15 residues processed: 153 average time/residue: 0.0756 time to fit residues: 17.0708 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain C residue 121 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 68 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.153035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118419 restraints weight = 12540.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120529 restraints weight = 8832.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121314 restraints weight = 8193.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.121867 restraints weight = 6057.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122882 restraints weight = 5609.134| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2935 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= 0.142 Angle : 0.573 9.349 14063 Z= 0.307 Chirality : 0.043 0.287 1618 Planarity : 0.003 0.045 1595 Dihedral : 21.166 166.470 1923 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.17 % Allowed : 18.27 % 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: -1.03 (0.25), residues: 1108 helix: 0.91 (0.29), residues: 325 sheet: -1.13 (0.28), residues: 307 loop : -1.43 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.011 0.001 TYR C 211 PHE 0.015 0.001 PHE D 126 TRP 0.025 0.002 TRP D 274 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10223) covalent geometry : angle 0.57344 / 0.31 (14059) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.43042 / 0.22 ( 4) hydrogen bonds : bond 0.03361 / 2.17 ( 455) hydrogen bonds : angle 5.79980 / 3.97 ( 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 159 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.226 Fit side-chains REVERT: B 10 SER cc_start: 0.8462 (m) cc_final: 0.8122 (m) REVERT: B 84 ASN cc_start: 0.7828 (m-40) cc_final: 0.7032 (t0) REVERT: D 148 MET cc_start: 0.7777 (tpp) cc_final: 0.6837 (mtt) REVERT: D 160 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: D 263 LEU cc_start: 0.7090 (tt) cc_final: 0.6767 (tp) REVERT: D 281 GLN cc_start: 0.7481 (pp30) cc_final: 0.7246 (tm-30) REVERT: D 288 VAL cc_start: 0.7252 (OUTLIER) cc_final: 0.6976 (p) REVERT: D 329 SER cc_start: 0.7460 (m) cc_final: 0.7121 (p) REVERT: A 16 LEU cc_start: 0.8598 (mm) cc_final: 0.8313 (mm) REVERT: A 141 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 170 SER cc_start: 0.8606 (m) cc_final: 0.8114 (t) REVERT: A 235 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7955 (pt) outliers start: 21 outliers final: 14 residues processed: 153 average time/residue: 0.0668 time to fit residues: 15.1084 Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 121 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.152827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118126 restraints weight = 12529.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119752 restraints weight = 8850.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121144 restraints weight = 7834.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.121630 restraints weight = 6021.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121937 restraints weight = 6107.653| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10225 Z= 0.153 Angle : 0.581 9.039 14063 Z= 0.310 Chirality : 0.043 0.291 1618 Planarity : 0.003 0.043 1595 Dihedral : 21.132 168.296 1923 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.17 % Allowed : 18.27 % 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: -1.05 (0.25), residues: 1108 helix: 0.91 (0.29), residues: 325 sheet: -1.34 (0.29), residues: 287 loop : -1.32 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.014 0.001 TYR D 40 PHE 0.015 0.001 PHE D 126 TRP 0.027 0.002 TRP D 274 HIS 0.003 0.001 HIS C 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10223) covalent geometry : angle 0.58071 / 0.31 (14059) SS BOND : bond 0.00207 / 0.11 ( 2) SS BOND : angle 0.48834 / 0.26 ( 4) hydrogen bonds : bond 0.03379 / 2.18 ( 455) hydrogen bonds : angle 5.79568 / 3.96 ( 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 162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.436 Fit side-chains REVERT: B 10 SER cc_start: 0.8478 (m) cc_final: 0.8131 (m) REVERT: B 84 ASN cc_start: 0.7841 (m-40) cc_final: 0.7030 (t0) REVERT: D 148 MET cc_start: 0.7776 (tpp) cc_final: 0.6918 (mtt) REVERT: D 160 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: D 263 LEU cc_start: 0.7113 (tt) cc_final: 0.6792 (tp) REVERT: D 281 GLN cc_start: 0.7493 (pp30) cc_final: 0.7261 (tm-30) REVERT: D 288 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7077 (p) REVERT: D 329 SER cc_start: 0.7535 (m) cc_final: 0.7222 (p) REVERT: A 16 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 141 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.7818 (t) REVERT: A 170 SER cc_start: 0.8600 (m) cc_final: 0.8109 (t) REVERT: A 235 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.8007 (pt) outliers start: 21 outliers final: 16 residues processed: 155 average time/residue: 0.0791 time to fit residues: 18.3274 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 : 0.209 ------------------------------------------------------------------------------- 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 121 LEU 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 230 LEU 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 216 THR Chi-restraints excluded: chain A residue 233 VAL 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 43 optimal weight: 0.0870 chunk 4 optimal weight: 0.0970 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.4156 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.153725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118750 restraints weight = 12431.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120538 restraints weight = 8755.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.121811 restraints weight = 7734.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.122335 restraints weight = 5952.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122569 restraints weight = 6061.772| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3082 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= 0.132 Angle : 0.570 8.600 14063 Z= 0.305 Chirality : 0.043 0.293 1618 Planarity : 0.003 0.045 1595 Dihedral : 21.112 168.601 1923 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.06 % Allowed : 18.99 % Favored : 78.95 % 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: -1.00 (0.25), residues: 1108 helix: 1.00 (0.29), residues: 325 sheet: -1.35 (0.29), residues: 289 loop : -1.30 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 91 TYR 0.010 0.001 TYR C 211 PHE 0.017 0.001 PHE D 126 TRP 0.032 0.002 TRP D 274 HIS 0.002 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (10223) covalent geometry : angle 0.57034 / 0.31 (14059) SS BOND : bond 0.00083 / 0.04 ( 2) SS BOND : angle 0.38601 / 0.19 ( 4) hydrogen bonds : bond 0.03240 / 2.10 ( 455) hydrogen bonds : angle 5.73997 / 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 156 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.360 Fit side-chains REVERT: B 10 SER cc_start: 0.8453 (m) cc_final: 0.8117 (m) REVERT: B 84 ASN cc_start: 0.7818 (m-40) cc_final: 0.7019 (t0) REVERT: D 148 MET cc_start: 0.7780 (tpp) cc_final: 0.6968 (mtt) REVERT: D 160 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6884 (pm20) REVERT: D 263 LEU cc_start: 0.7149 (tt) cc_final: 0.6832 (tp) REVERT: D 281 GLN cc_start: 0.7487 (pp30) cc_final: 0.7262 (tm-30) REVERT: D 288 VAL cc_start: 0.7303 (OUTLIER) cc_final: 0.7027 (p) REVERT: D 329 SER cc_start: 0.7534 (m) cc_final: 0.7210 (p) REVERT: A 16 LEU cc_start: 0.8571 (mm) cc_final: 0.8285 (mm) REVERT: A 141 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.7792 (t) outliers start: 20 outliers final: 15 residues processed: 150 average time/residue: 0.0729 time to fit residues: 16.2424 Evaluate side-chains 152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 121 LEU 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 230 LEU 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 233 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 0.0040 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 23 optimal weight: 0.0270 overall best weight: 0.2850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 21 ASN ** 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 = 0.3865 r_free = 0.3865 target = 0.155412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120911 restraints weight = 12549.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122539 restraints weight = 8900.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.123994 restraints weight = 7804.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124469 restraints weight = 5976.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124744 restraints weight = 6126.680| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10225 Z= 0.124 Angle : 0.568 8.228 14063 Z= 0.302 Chirality : 0.043 0.298 1618 Planarity : 0.003 0.045 1595 Dihedral : 21.086 169.395 1923 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.86 % Allowed : 19.20 % Favored : 78.95 % 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: 1.04 (0.29), residues: 325 sheet: -1.35 (0.29), residues: 295 loop : -1.20 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.016 0.001 TYR D 40 PHE 0.017 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 0.00267 / 0.12 (10223) covalent geometry : angle 0.56766 / 0.30 (14059) SS BOND : bond 0.00036 / 0.02 ( 2) SS BOND : angle 0.32744 / 0.17 ( 4) hydrogen bonds : bond 0.03206 / 2.08 ( 455) hydrogen bonds : angle 5.67276 / 3.88 ( 1271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.49 seconds wall clock time: 25 minutes 47.27 seconds (1547.27 seconds total)