Starting phenix.real_space_refine on Sun Apr 27 17:19:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgj_44514/04_2025/9bgj_44514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgj_44514/04_2025/9bgj_44514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgj_44514/04_2025/9bgj_44514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgj_44514/04_2025/9bgj_44514.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgj_44514/04_2025/9bgj_44514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgj_44514/04_2025/9bgj_44514.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.069 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 50 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 3849 2.51 5 N 1145 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6361 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2669 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 19, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 517 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "B" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2640 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 19, 'TRANS': 314} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 524 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.24, per 1000 atoms: 0.82 Number of scatterers: 6361 At special positions: 0 Unit cell: (82.17, 83.83, 100.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 50 15.00 Mg 2 11.99 O 1297 8.00 N 1145 7.00 C 3849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.81 Conformation dependent library (CDL) restraints added in 841.4 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1258 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 51.0% alpha, 6.0% beta 19 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.643A pdb=" N ARG A 18 " --> pdb=" O THR A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.528A pdb=" N GLY A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 90 through 123 removed outlier: 3.912A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 143 Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.595A pdb=" N VAL A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.556A pdb=" N ARG A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 206 " --> pdb=" O MET A 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 206' Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 222 through 227 removed outlier: 3.835A pdb=" N ARG A 225 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.982A pdb=" N ILE A 235 " --> pdb=" O PRO A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.680A pdb=" N LEU A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 318 through 335 removed outlier: 3.854A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.744A pdb=" N ARG B 18 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.526A pdb=" N GLY B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 90 through 123 removed outlier: 3.941A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 143 Processing helix chain 'B' and resid 161 through 177 removed outlier: 5.264A pdb=" N VAL B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.259A pdb=" N ARG B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.726A pdb=" N LEU B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 318 through 335 removed outlier: 3.891A pdb=" N LEU B 322 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 148 removed outlier: 6.316A pdb=" N ALA A 238 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N HIS A 278 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 240 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N TYR A 314 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL A 277 " --> pdb=" O TYR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 148 removed outlier: 6.777A pdb=" N VAL B 193 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 235 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N GLU B 276 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 238 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS B 278 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 240 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TYR B 314 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 277 " --> pdb=" O TYR B 314 " (cutoff:3.500A) 213 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1687 1.33 - 1.45: 1379 1.45 - 1.57: 3395 1.57 - 1.69: 99 1.69 - 1.80: 32 Bond restraints: 6592 Sorted by residual: bond pdb=" N ASP A 63 " pdb=" CA ASP A 63 " ideal model delta sigma weight residual 1.456 1.479 -0.023 1.23e-02 6.61e+03 3.39e+00 bond pdb=" N ASP B 63 " pdb=" CA ASP B 63 " ideal model delta sigma weight residual 1.456 1.477 -0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C3' DT C 24 " pdb=" O3' DT C 24 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C ASP B 63 " pdb=" N TYR B 64 " ideal model delta sigma weight residual 1.335 1.319 0.016 1.38e-02 5.25e+03 1.35e+00 bond pdb=" C ASP A 63 " pdb=" N TYR A 64 " ideal model delta sigma weight residual 1.335 1.322 0.014 1.38e-02 5.25e+03 9.63e-01 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8755 1.10 - 2.20: 309 2.20 - 3.29: 66 3.29 - 4.39: 18 4.39 - 5.49: 12 Bond angle restraints: 9160 Sorted by residual: angle pdb=" N VAL B 157 " pdb=" CA VAL B 157 " pdb=" C VAL B 157 " ideal model delta sigma weight residual 113.39 108.20 5.19 1.47e+00 4.63e-01 1.25e+01 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 113.72 108.46 5.26 1.52e+00 4.33e-01 1.20e+01 angle pdb=" N VAL B 28 " pdb=" CA VAL B 28 " pdb=" C VAL B 28 " ideal model delta sigma weight residual 110.21 106.45 3.76 1.13e+00 7.83e-01 1.11e+01 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" CB ASP A 85 " ideal model delta sigma weight residual 113.65 109.55 4.10 1.47e+00 4.63e-01 7.78e+00 angle pdb=" CA VAL B 157 " pdb=" C VAL B 157 " pdb=" N SER B 158 " ideal model delta sigma weight residual 118.55 116.48 2.07 8.60e-01 1.35e+00 5.78e+00 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.21: 3028 19.21 - 38.41: 474 38.41 - 57.62: 273 57.62 - 76.82: 32 76.82 - 96.03: 11 Dihedral angle restraints: 3818 sinusoidal: 1871 harmonic: 1947 Sorted by residual: dihedral pdb=" CA GLN B 129 " pdb=" C GLN B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual 180.00 162.82 17.18 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA GLN A 129 " pdb=" C GLN A 129 " pdb=" N PRO A 130 " pdb=" CA PRO A 130 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CG ARG B 308 " pdb=" CD ARG B 308 " pdb=" NE ARG B 308 " pdb=" CZ ARG B 308 " ideal model delta sinusoidal sigma weight residual -180.00 -135.52 -44.48 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 3815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 680 0.033 - 0.066: 231 0.066 - 0.099: 60 0.099 - 0.131: 35 0.131 - 0.164: 2 Chirality restraints: 1008 Sorted by residual: chirality pdb=" CA TYR A 297 " pdb=" N TYR A 297 " pdb=" C TYR A 297 " pdb=" CB TYR A 297 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA VAL B 161 " pdb=" N VAL B 161 " pdb=" C VAL B 161 " pdb=" CB VAL B 161 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO B 162 " pdb=" N PRO B 162 " pdb=" C PRO B 162 " pdb=" CB PRO B 162 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1005 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 85 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CG ASP A 85 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP A 85 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 85 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 231 " 0.024 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO B 232 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 231 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 232 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.019 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 55 2.52 - 3.11: 4509 3.11 - 3.71: 10089 3.71 - 4.30: 14248 4.30 - 4.90: 23596 Nonbonded interactions: 52497 Sorted by model distance: nonbonded pdb=" OP1 DC D 12 " pdb="MG MG B 401 " model vdw 1.922 2.170 nonbonded pdb=" OP1 DC C 12 " pdb="MG MG A 401 " model vdw 1.925 2.170 nonbonded pdb=" O PHE B 241 " pdb="MG MG B 401 " model vdw 2.117 2.170 nonbonded pdb=" O PHE A 241 " pdb="MG MG A 401 " model vdw 2.182 2.170 nonbonded pdb=" OD2 ASP B 188 " pdb="MG MG B 401 " model vdw 2.216 2.170 ... (remaining 52492 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' and (resid 2 through 299 or resid 304 through 339 or resid 401)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.220 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.003 0.038 6592 Z= 0.148 Angle : 0.542 5.488 9160 Z= 0.300 Chirality : 0.040 0.164 1008 Planarity : 0.004 0.037 1028 Dihedral : 22.775 96.030 2560 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.93 % Allowed : 26.43 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.35), residues: 666 helix: 0.95 (0.33), residues: 282 sheet: -1.23 (0.73), residues: 43 loop : -0.78 (0.37), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS A 81 PHE 0.021 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.005 0.000 ARG B 225 Details of bonding type rmsd hydrogen bonds : bond 0.15872 ( 264) hydrogen bonds : angle 5.41762 ( 699) covalent geometry : bond 0.00338 ( 6592) covalent geometry : angle 0.54153 ( 9160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.600 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 24 ARG cc_start: 0.6699 (tmt170) cc_final: 0.5822 (tpt-90) REVERT: A 103 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8099 (tt0) REVERT: A 196 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8514 (mm-30) REVERT: B 24 ARG cc_start: 0.6069 (tmt170) cc_final: 0.2271 (mtm180) REVERT: B 85 ASP cc_start: 0.7848 (t0) cc_final: 0.7435 (t0) REVERT: B 142 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7780 (mtp-110) REVERT: B 166 GLU cc_start: 0.7609 (tp30) cc_final: 0.7327 (mt-10) REVERT: B 202 GLU cc_start: 0.7588 (mt-10) cc_final: 0.6892 (mp0) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.2177 time to fit residues: 21.4169 Evaluate side-chains 80 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.161087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116026 restraints weight = 6545.363| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.97 r_work: 0.3159 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6592 Z= 0.202 Angle : 0.546 5.638 9160 Z= 0.291 Chirality : 0.042 0.169 1008 Planarity : 0.004 0.036 1028 Dihedral : 23.562 95.789 1325 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 6.61 % Allowed : 23.39 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.35), residues: 666 helix: 1.53 (0.33), residues: 267 sheet: -1.54 (0.71), residues: 44 loop : -0.48 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.005 0.001 PHE A 288 TYR 0.017 0.001 TYR A 297 ARG 0.004 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 264) hydrogen bonds : angle 3.88570 ( 699) covalent geometry : bond 0.00489 ( 6592) covalent geometry : angle 0.54629 ( 9160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.632 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 24 ARG cc_start: 0.6545 (tmt170) cc_final: 0.5755 (tpt-90) REVERT: A 103 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8126 (tt0) REVERT: A 124 GLU cc_start: 0.8301 (mp0) cc_final: 0.8090 (mp0) REVERT: A 196 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8496 (mm-30) REVERT: B 24 ARG cc_start: 0.6116 (tmt170) cc_final: 0.2180 (mtm180) REVERT: B 85 ASP cc_start: 0.7890 (t0) cc_final: 0.7619 (t0) REVERT: B 166 GLU cc_start: 0.7551 (tp30) cc_final: 0.7232 (mt-10) REVERT: B 202 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6970 (mp0) outliers start: 37 outliers final: 19 residues processed: 98 average time/residue: 0.1977 time to fit residues: 25.6581 Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 2 optimal weight: 0.0670 chunk 18 optimal weight: 0.0980 overall best weight: 2.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.169500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123743 restraints weight = 6666.892| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3311 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6592 Z= 0.152 Angle : 0.512 5.492 9160 Z= 0.270 Chirality : 0.040 0.167 1008 Planarity : 0.004 0.034 1028 Dihedral : 23.287 94.167 1309 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 6.07 % Allowed : 23.57 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.35), residues: 666 helix: 1.79 (0.33), residues: 267 sheet: -1.40 (0.75), residues: 41 loop : -0.47 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.015 0.001 PHE B 171 TYR 0.019 0.001 TYR A 297 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 264) hydrogen bonds : angle 3.69990 ( 699) covalent geometry : bond 0.00362 ( 6592) covalent geometry : angle 0.51170 ( 9160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.531 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: A 24 ARG cc_start: 0.6468 (tmt170) cc_final: 0.5618 (tpt-90) REVERT: A 103 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8153 (tt0) REVERT: A 124 GLU cc_start: 0.8265 (mp0) cc_final: 0.8048 (mp0) REVERT: A 196 GLU cc_start: 0.8854 (tt0) cc_final: 0.8522 (mm-30) REVERT: B 24 ARG cc_start: 0.6111 (tmt170) cc_final: 0.2140 (mtm180) REVERT: B 85 ASP cc_start: 0.7813 (t0) cc_final: 0.7464 (t0) REVERT: B 166 GLU cc_start: 0.7656 (tp30) cc_final: 0.7320 (mt-10) REVERT: B 202 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7002 (tp30) REVERT: B 289 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8842 (p) outliers start: 34 outliers final: 22 residues processed: 94 average time/residue: 0.2158 time to fit residues: 26.3580 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.164415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119639 restraints weight = 6671.915| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.95 r_work: 0.3202 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6592 Z= 0.147 Angle : 0.502 5.497 9160 Z= 0.266 Chirality : 0.040 0.167 1008 Planarity : 0.004 0.033 1028 Dihedral : 23.168 95.969 1306 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.36 % Allowed : 24.29 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.36), residues: 666 helix: 1.86 (0.34), residues: 267 sheet: -1.37 (0.76), residues: 41 loop : -0.42 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.011 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 264) hydrogen bonds : angle 3.61902 ( 699) covalent geometry : bond 0.00352 ( 6592) covalent geometry : angle 0.50206 ( 9160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 1.138 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: A 24 ARG cc_start: 0.6429 (tmt170) cc_final: 0.5621 (tpt-90) REVERT: A 103 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8106 (tt0) REVERT: A 124 GLU cc_start: 0.8099 (mp0) cc_final: 0.7812 (mp0) REVERT: A 196 GLU cc_start: 0.8838 (tt0) cc_final: 0.8532 (mm-30) REVERT: B 17 GLU cc_start: 0.8065 (tt0) cc_final: 0.7757 (mt-10) REVERT: B 24 ARG cc_start: 0.6024 (tmt170) cc_final: 0.2148 (mtm180) REVERT: B 85 ASP cc_start: 0.7778 (t0) cc_final: 0.7541 (t0) REVERT: B 166 GLU cc_start: 0.7564 (tp30) cc_final: 0.7151 (mt-10) REVERT: B 289 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8920 (p) REVERT: B 312 GLU cc_start: 0.8774 (tt0) cc_final: 0.8420 (tt0) outliers start: 30 outliers final: 19 residues processed: 90 average time/residue: 0.2182 time to fit residues: 25.4894 Evaluate side-chains 83 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 289 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.162438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116893 restraints weight = 6601.060| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.99 r_work: 0.3176 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6592 Z= 0.173 Angle : 0.520 5.586 9160 Z= 0.273 Chirality : 0.041 0.167 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.222 97.603 1306 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.43 % Allowed : 23.57 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.35), residues: 666 helix: 1.82 (0.33), residues: 267 sheet: -1.39 (0.77), residues: 41 loop : -0.43 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.019 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 264) hydrogen bonds : angle 3.61101 ( 699) covalent geometry : bond 0.00416 ( 6592) covalent geometry : angle 0.52006 ( 9160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.739 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: A 24 ARG cc_start: 0.6449 (tmt170) cc_final: 0.5649 (tpt-90) REVERT: A 85 ASP cc_start: 0.7412 (t0) cc_final: 0.7205 (t0) REVERT: A 103 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8073 (tt0) REVERT: A 124 GLU cc_start: 0.8117 (mp0) cc_final: 0.7759 (mp0) REVERT: A 196 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: B 17 GLU cc_start: 0.8077 (tt0) cc_final: 0.7769 (mt-10) REVERT: B 24 ARG cc_start: 0.6029 (tmt170) cc_final: 0.2117 (mtm180) REVERT: B 85 ASP cc_start: 0.7823 (t0) cc_final: 0.7593 (t0) REVERT: B 166 GLU cc_start: 0.7574 (tp30) cc_final: 0.7150 (mt-10) REVERT: B 169 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7084 (tm-30) REVERT: B 312 GLU cc_start: 0.8754 (tt0) cc_final: 0.8373 (tt0) outliers start: 36 outliers final: 22 residues processed: 96 average time/residue: 0.2242 time to fit residues: 28.1163 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 200 ASN B 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115872 restraints weight = 6643.708| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.94 r_work: 0.3153 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6592 Z= 0.210 Angle : 0.545 5.401 9160 Z= 0.286 Chirality : 0.042 0.168 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.330 99.393 1302 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 6.61 % Allowed : 22.86 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.35), residues: 666 helix: 1.74 (0.33), residues: 267 sheet: -1.52 (0.75), residues: 44 loop : -0.41 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 156 HIS 0.001 0.001 HIS B 307 PHE 0.014 0.001 PHE B 171 TYR 0.018 0.001 TYR A 297 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 264) hydrogen bonds : angle 3.71725 ( 699) covalent geometry : bond 0.00510 ( 6592) covalent geometry : angle 0.54492 ( 9160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 0.642 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 17 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: A 24 ARG cc_start: 0.6496 (tmt170) cc_final: 0.5685 (tpt-90) REVERT: A 103 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8041 (tt0) REVERT: A 124 GLU cc_start: 0.8148 (mp0) cc_final: 0.7764 (mp0) REVERT: A 142 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8079 (mtm180) REVERT: A 163 GLU cc_start: 0.8468 (mp0) cc_final: 0.8238 (mp0) REVERT: A 196 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8608 (mm-30) REVERT: B 17 GLU cc_start: 0.8111 (tt0) cc_final: 0.7802 (mt-10) REVERT: B 24 ARG cc_start: 0.6056 (tmt170) cc_final: 0.2090 (mtm180) REVERT: B 169 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7184 (tm-30) REVERT: B 312 GLU cc_start: 0.8758 (tt0) cc_final: 0.8383 (tt0) outliers start: 37 outliers final: 27 residues processed: 98 average time/residue: 0.2297 time to fit residues: 29.1173 Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 67 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 12 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.122722 restraints weight = 6534.389| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.95 r_work: 0.3242 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6592 Z= 0.114 Angle : 0.492 5.609 9160 Z= 0.262 Chirality : 0.039 0.166 1008 Planarity : 0.003 0.031 1028 Dihedral : 22.910 99.513 1302 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.46 % Allowed : 24.82 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.35), residues: 666 helix: 1.99 (0.33), residues: 267 sheet: -1.20 (0.75), residues: 46 loop : -0.43 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS B 278 PHE 0.022 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 264) hydrogen bonds : angle 3.49228 ( 699) covalent geometry : bond 0.00259 ( 6592) covalent geometry : angle 0.49228 ( 9160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.694 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7361 (tm-30) REVERT: A 24 ARG cc_start: 0.6282 (tmt170) cc_final: 0.5433 (tpt-90) REVERT: A 103 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8049 (tt0) REVERT: A 124 GLU cc_start: 0.8157 (mp0) cc_final: 0.7857 (mp0) REVERT: A 163 GLU cc_start: 0.8430 (mp0) cc_final: 0.8190 (mp0) REVERT: A 196 GLU cc_start: 0.8820 (tt0) cc_final: 0.8527 (mm-30) REVERT: B 17 GLU cc_start: 0.8079 (tt0) cc_final: 0.7779 (mt-10) REVERT: B 24 ARG cc_start: 0.5904 (tmt170) cc_final: 0.2052 (mtm180) REVERT: B 169 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7132 (tm-30) REVERT: B 225 ARG cc_start: 0.8532 (mtt90) cc_final: 0.8279 (mtt90) REVERT: B 312 GLU cc_start: 0.8772 (tt0) cc_final: 0.8426 (tt0) outliers start: 25 outliers final: 17 residues processed: 88 average time/residue: 0.2366 time to fit residues: 28.3188 Evaluate side-chains 85 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116885 restraints weight = 6568.631| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.94 r_work: 0.3171 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6592 Z= 0.203 Angle : 0.538 5.459 9160 Z= 0.283 Chirality : 0.042 0.169 1008 Planarity : 0.004 0.031 1028 Dihedral : 23.230 101.282 1301 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.54 % Allowed : 23.93 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.35), residues: 666 helix: 1.81 (0.33), residues: 267 sheet: -1.19 (0.76), residues: 46 loop : -0.43 (0.38), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.018 0.001 PHE B 171 TYR 0.018 0.001 TYR A 297 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 264) hydrogen bonds : angle 3.66112 ( 699) covalent geometry : bond 0.00493 ( 6592) covalent geometry : angle 0.53754 ( 9160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.666 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: A 24 ARG cc_start: 0.6397 (tmt170) cc_final: 0.5602 (tpt-90) REVERT: A 103 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8026 (tt0) REVERT: A 124 GLU cc_start: 0.8089 (mp0) cc_final: 0.7787 (mp0) REVERT: A 142 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8060 (mtm180) REVERT: A 163 GLU cc_start: 0.8450 (mp0) cc_final: 0.8213 (mp0) REVERT: A 196 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8607 (mm-30) REVERT: B 17 GLU cc_start: 0.8094 (tt0) cc_final: 0.7796 (mt-10) REVERT: B 24 ARG cc_start: 0.6054 (tmt170) cc_final: 0.2132 (mtm180) REVERT: B 169 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7155 (tm-30) REVERT: B 225 ARG cc_start: 0.8612 (mtt90) cc_final: 0.8290 (mtt90) REVERT: B 312 GLU cc_start: 0.8762 (tt0) cc_final: 0.8407 (tt0) outliers start: 31 outliers final: 20 residues processed: 91 average time/residue: 0.2216 time to fit residues: 26.5674 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 0.4980 chunk 50 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.0470 chunk 58 optimal weight: 4.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120030 restraints weight = 6588.819| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.94 r_work: 0.3213 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6592 Z= 0.142 Angle : 0.509 5.619 9160 Z= 0.270 Chirality : 0.040 0.168 1008 Planarity : 0.004 0.030 1028 Dihedral : 23.001 102.334 1301 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.18 % Allowed : 23.75 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.35), residues: 666 helix: 1.73 (0.33), residues: 273 sheet: -1.19 (0.76), residues: 47 loop : -0.45 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.016 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.004 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.03261 ( 264) hydrogen bonds : angle 3.55442 ( 699) covalent geometry : bond 0.00338 ( 6592) covalent geometry : angle 0.50881 ( 9160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.720 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7333 (tm-30) REVERT: A 24 ARG cc_start: 0.6357 (tmt170) cc_final: 0.5553 (tpt-90) REVERT: A 103 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8031 (tt0) REVERT: A 124 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: A 142 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8031 (mtm180) REVERT: A 163 GLU cc_start: 0.8406 (mp0) cc_final: 0.8168 (mp0) REVERT: A 196 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8574 (mm-30) REVERT: B 17 GLU cc_start: 0.8090 (tt0) cc_final: 0.7801 (mt-10) REVERT: B 24 ARG cc_start: 0.5960 (tmt170) cc_final: 0.2076 (mtm180) REVERT: B 169 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7140 (tm-30) REVERT: B 202 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7309 (tp30) REVERT: B 225 ARG cc_start: 0.8567 (mtt90) cc_final: 0.8292 (mtt90) REVERT: B 312 GLU cc_start: 0.8802 (tt0) cc_final: 0.8447 (tt0) outliers start: 29 outliers final: 24 residues processed: 90 average time/residue: 0.2578 time to fit residues: 30.2328 Evaluate side-chains 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122208 restraints weight = 6640.081| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.96 r_work: 0.3238 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6592 Z= 0.122 Angle : 0.499 5.752 9160 Z= 0.265 Chirality : 0.039 0.170 1008 Planarity : 0.003 0.030 1028 Dihedral : 22.856 103.433 1301 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.64 % Allowed : 24.46 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.35), residues: 666 helix: 1.81 (0.33), residues: 273 sheet: -1.08 (0.78), residues: 47 loop : -0.46 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.016 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.004 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 264) hydrogen bonds : angle 3.48511 ( 699) covalent geometry : bond 0.00286 ( 6592) covalent geometry : angle 0.49940 ( 9160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.657 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: A 24 ARG cc_start: 0.6294 (tmt170) cc_final: 0.5472 (tpt-90) REVERT: A 29 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7737 (mmm-85) REVERT: A 103 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8043 (tt0) REVERT: A 124 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 142 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8025 (mtm180) REVERT: A 163 GLU cc_start: 0.8408 (mp0) cc_final: 0.8166 (mp0) REVERT: A 196 GLU cc_start: 0.8816 (tt0) cc_final: 0.8572 (mm-30) REVERT: A 201 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: A 332 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 17 GLU cc_start: 0.8069 (tt0) cc_final: 0.7776 (mt-10) REVERT: B 24 ARG cc_start: 0.5945 (tmt170) cc_final: 0.2080 (mtm180) REVERT: B 166 GLU cc_start: 0.7478 (tp30) cc_final: 0.7213 (mt-10) REVERT: B 169 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7199 (tm-30) REVERT: B 202 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7326 (tp30) REVERT: B 225 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8303 (mtt90) REVERT: B 312 GLU cc_start: 0.8809 (tt0) cc_final: 0.8453 (tt0) outliers start: 26 outliers final: 19 residues processed: 91 average time/residue: 0.2225 time to fit residues: 25.9422 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain B residue 39 GLN Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 40 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 = 0.3950 r_free = 0.3950 target = 0.171516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127364 restraints weight = 6713.914| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.94 r_work: 0.3304 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6592 Z= 0.108 Angle : 0.487 6.027 9160 Z= 0.259 Chirality : 0.038 0.170 1008 Planarity : 0.003 0.030 1028 Dihedral : 22.615 105.774 1301 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.93 % Allowed : 25.00 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.35), residues: 666 helix: 1.99 (0.33), residues: 273 sheet: -1.02 (0.78), residues: 47 loop : -0.43 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 156 HIS 0.001 0.000 HIS B 278 PHE 0.015 0.001 PHE B 171 TYR 0.017 0.001 TYR A 297 ARG 0.006 0.000 ARG A 65 Details of bonding type rmsd hydrogen bonds : bond 0.02683 ( 264) hydrogen bonds : angle 3.33676 ( 699) covalent geometry : bond 0.00246 ( 6592) covalent geometry : angle 0.48682 ( 9160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4102.09 seconds wall clock time: 73 minutes 20.68 seconds (4400.68 seconds total)