Starting phenix.real_space_refine on Sat May 10 12:41:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgj_44514/05_2025/9bgj_44514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgj_44514/05_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_44514/05_2025/9bgj_44514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgj_44514/05_2025/9bgj_44514.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgj_44514/05_2025/9bgj_44514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgj_44514/05_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-5687/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: 4.97, per 1000 atoms: 0.78 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: 2.58 Conformation dependent library (CDL) restraints added in 990.0 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: 2.01 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: 1.97 Time building geometry restraints manager: 2.54 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.750 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- 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 : 0.568 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: 0.2201 time to fit residues: 21.5835 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 : 0.629 ------------------------------------------------------------------------------- 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: 5.9990 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 = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116027 restraints weight = 6545.363| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.97 r_work: 0.3159 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- 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 : 0.611 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: 0.6550 (tmt170) cc_final: 0.5755 (tpt-90) REVERT: A 103 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8122 (tt0) REVERT: A 124 GLU cc_start: 0.8301 (mp0) cc_final: 0.8091 (mp0) REVERT: A 196 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8493 (mm-30) REVERT: B 24 ARG cc_start: 0.6117 (tmt170) cc_final: 0.2183 (mtm180) REVERT: B 85 ASP cc_start: 0.7887 (t0) cc_final: 0.7617 (t0) REVERT: B 166 GLU cc_start: 0.7548 (tp30) cc_final: 0.7230 (mt-10) REVERT: B 202 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6966 (mp0) outliers start: 37 outliers final: 19 residues processed: 98 average time/residue: 0.1841 time to fit residues: 24.0488 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 : 0.490 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113546 restraints weight = 6654.654| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.96 r_work: 0.3124 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6592 Z= 0.263 Angle : 0.589 6.062 9160 Z= 0.310 Chirality : 0.044 0.170 1008 Planarity : 0.005 0.036 1028 Dihedral : 23.716 95.953 1309 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 7.86 % Allowed : 22.14 % 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: 0.26 (0.35), residues: 666 helix: 1.46 (0.33), residues: 267 sheet: -1.72 (0.71), residues: 44 loop : -0.55 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 156 HIS 0.002 0.001 HIS B 307 PHE 0.017 0.001 PHE B 171 TYR 0.019 0.002 TYR A 297 ARG 0.004 0.001 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 264) hydrogen bonds : angle 3.95288 ( 699) covalent geometry : bond 0.00640 ( 6592) covalent geometry : angle 0.58920 ( 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 110 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 66 time to evaluate : 0.665 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: 0.7906 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: A 24 ARG cc_start: 0.6522 (tmt170) cc_final: 0.4991 (tpt90) REVERT: A 37 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 103 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8126 (tt0) REVERT: A 124 GLU cc_start: 0.8314 (mp0) cc_final: 0.8020 (mp0) REVERT: A 131 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7513 (mtp-110) REVERT: A 197 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8546 (pm20) REVERT: B 24 ARG cc_start: 0.6049 (tmt170) cc_final: 0.2088 (mtm180) REVERT: B 85 ASP cc_start: 0.8021 (t0) cc_final: 0.7790 (t0) REVERT: B 169 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7121 (tm-30) outliers start: 44 outliers final: 22 residues processed: 102 average time/residue: 0.2138 time to fit residues: 28.0673 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 131 ARG 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 185 SER Chi-restraints excluded: chain A residue 197 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 50 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 56 SER 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 203 MET Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 64 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3873 r_free = 0.3873 target = 0.164206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119302 restraints weight = 6666.496| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.97 r_work: 0.3201 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6592 Z= 0.138 Angle : 0.505 5.475 9160 Z= 0.268 Chirality : 0.040 0.164 1008 Planarity : 0.004 0.033 1028 Dihedral : 23.177 95.682 1302 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.71 % Allowed : 22.86 % Favored : 71.43 % 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: 0.53 (0.35), residues: 666 helix: 1.79 (0.33), residues: 267 sheet: -1.55 (0.76), residues: 41 loop : -0.50 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS B 307 PHE 0.017 0.001 PHE B 171 TYR 0.018 0.001 TYR A 297 ARG 0.003 0.000 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 264) hydrogen bonds : angle 3.62362 ( 699) covalent geometry : bond 0.00326 ( 6592) covalent geometry : angle 0.50547 ( 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 103 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.658 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: 0.7870 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: A 24 ARG cc_start: 0.6370 (tmt170) cc_final: 0.5528 (tpt-90) REVERT: A 103 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8010 (tt0) REVERT: A 124 GLU cc_start: 0.8167 (mp0) cc_final: 0.7849 (mp0) REVERT: A 163 GLU cc_start: 0.8433 (mp0) cc_final: 0.8191 (mp0) REVERT: A 196 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8588 (mm-30) REVERT: B 17 GLU cc_start: 0.8088 (tt0) cc_final: 0.7779 (mt-10) REVERT: B 24 ARG cc_start: 0.5962 (tmt170) cc_final: 0.2051 (mtm180) REVERT: B 85 ASP cc_start: 0.7837 (t0) cc_final: 0.7593 (t0) REVERT: B 166 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6915 (mt-10) REVERT: B 169 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7105 (tm-30) REVERT: B 312 GLU cc_start: 0.8766 (tt0) cc_final: 0.8398 (tt0) outliers start: 32 outliers final: 20 residues processed: 95 average time/residue: 0.2093 time to fit residues: 26.4799 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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 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 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 318 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 199 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 = 0.3838 r_free = 0.3838 target = 0.161207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.116442 restraints weight = 6618.258| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.93 r_work: 0.3158 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1303 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= 0.195 Angle : 0.534 5.448 9160 Z= 0.282 Chirality : 0.041 0.169 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.307 97.016 1302 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 6.25 % Allowed : 22.50 % Favored : 71.25 % 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: 0.50 (0.35), residues: 666 helix: 1.72 (0.33), residues: 267 sheet: -1.50 (0.77), residues: 41 loop : -0.50 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 117 HIS 0.001 0.000 HIS B 307 PHE 0.012 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 0.03848 ( 264) hydrogen bonds : angle 3.70616 ( 699) covalent geometry : bond 0.00472 ( 6592) covalent geometry : angle 0.53416 ( 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 103 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.590 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: 0.7883 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 24 ARG cc_start: 0.6481 (tmt170) cc_final: 0.5688 (tpt-90) REVERT: A 103 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8082 (tt0) REVERT: A 124 GLU cc_start: 0.8171 (mp0) cc_final: 0.7821 (mp0) REVERT: A 142 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8033 (mtm180) REVERT: A 163 GLU cc_start: 0.8453 (mp0) cc_final: 0.8208 (mp0) REVERT: A 196 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8638 (mm-30) REVERT: B 17 GLU cc_start: 0.8116 (tt0) cc_final: 0.7802 (mt-10) REVERT: B 24 ARG cc_start: 0.6029 (tmt170) cc_final: 0.2074 (mtm180) REVERT: B 166 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7026 (mt-10) REVERT: B 169 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7142 (tm-30) REVERT: B 312 GLU cc_start: 0.8752 (tt0) cc_final: 0.8383 (tt0) outliers start: 35 outliers final: 23 residues processed: 95 average time/residue: 0.2019 time to fit residues: 25.0431 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 291 TYR 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 203 MET Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 318 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: 0.8980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 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 = 0.3882 r_free = 0.3882 target = 0.165178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.120155 restraints weight = 6583.081| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.96 r_work: 0.3211 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6592 Z= 0.129 Angle : 0.500 5.597 9160 Z= 0.265 Chirality : 0.039 0.166 1008 Planarity : 0.004 0.031 1028 Dihedral : 23.055 97.315 1302 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.54 % Allowed : 23.39 % 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: 0.66 (0.36), residues: 666 helix: 1.92 (0.33), residues: 267 sheet: -1.34 (0.74), residues: 46 loop : -0.46 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.009 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 0.03223 ( 264) hydrogen bonds : angle 3.55229 ( 699) covalent geometry : bond 0.00302 ( 6592) covalent geometry : angle 0.49994 ( 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 100 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.579 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: 0.7836 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: A 24 ARG cc_start: 0.6335 (tmt170) cc_final: 0.5513 (tpt-90) REVERT: A 103 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8044 (tt0) REVERT: A 124 GLU cc_start: 0.8071 (mp0) cc_final: 0.7747 (mp0) REVERT: A 142 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8029 (mtm180) REVERT: A 163 GLU cc_start: 0.8449 (mp0) cc_final: 0.8208 (mp0) REVERT: A 196 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8567 (mm-30) REVERT: B 17 GLU cc_start: 0.8099 (tt0) cc_final: 0.7793 (mt-10) REVERT: B 24 ARG cc_start: 0.6008 (tmt170) cc_final: 0.2097 (mtm180) REVERT: B 166 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7014 (mt-10) REVERT: B 169 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7136 (tm-30) REVERT: B 312 GLU cc_start: 0.8768 (tt0) cc_final: 0.8430 (tt0) outliers start: 31 outliers final: 23 residues processed: 94 average time/residue: 0.2033 time to fit residues: 24.8722 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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 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 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: 5.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 199 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 = 0.3900 r_free = 0.3900 target = 0.166804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121895 restraints weight = 6546.238| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.96 r_work: 0.3233 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 0.043 6592 Z= 0.122 Angle : 0.490 6.744 9160 Z= 0.257 Chirality : 0.039 0.168 1008 Planarity : 0.003 0.031 1028 Dihedral : 22.911 98.568 1301 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.25 % Allowed : 22.68 % 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 (0.36), residues: 666 helix: 2.06 (0.34), residues: 267 sheet: -1.25 (0.75), residues: 46 loop : -0.40 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 117 HIS 0.000 0.000 HIS A 81 PHE 0.021 0.001 PHE B 171 TYR 0.018 0.001 TYR A 297 ARG 0.003 0.000 ARG A 29 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 264) hydrogen bonds : angle 3.46114 ( 699) covalent geometry : bond 0.00285 ( 6592) covalent geometry : angle 0.48990 ( 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 106 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 71 time to evaluate : 0.678 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: 0.7792 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: A 24 ARG cc_start: 0.6298 (tmt170) cc_final: 0.5370 (tpt-90) REVERT: A 29 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: A 85 ASP cc_start: 0.7241 (t0) cc_final: 0.7032 (t0) REVERT: A 103 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8081 (tt0) REVERT: A 124 GLU cc_start: 0.8172 (mp0) cc_final: 0.7909 (mp0) REVERT: A 142 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8024 (mtm180) REVERT: A 196 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8574 (mm-30) REVERT: B 17 GLU cc_start: 0.8009 (tt0) cc_final: 0.7702 (mt-10) REVERT: B 24 ARG cc_start: 0.6016 (tmt170) cc_final: 0.2133 (mtm180) REVERT: B 169 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7166 (tm-30) REVERT: B 202 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7322 (tp30) REVERT: B 312 GLU cc_start: 0.8835 (tt0) cc_final: 0.8504 (tt0) outliers start: 35 outliers final: 23 residues processed: 96 average time/residue: 0.2113 time to fit residues: 26.3388 Evaluate side-chains 94 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 68 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 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 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 161 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 199 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 = 0.3883 r_free = 0.3883 target = 0.165245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120072 restraints weight = 6522.115| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.95 r_work: 0.3210 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6592 Z= 0.141 Angle : 0.499 5.686 9160 Z= 0.262 Chirality : 0.040 0.168 1008 Planarity : 0.003 0.030 1028 Dihedral : 22.991 99.976 1300 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.89 % Allowed : 22.86 % Favored : 71.25 % 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 (0.36), residues: 666 helix: 2.01 (0.33), residues: 267 sheet: -1.20 (0.76), residues: 46 loop : -0.37 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.017 0.001 PHE B 171 TYR 0.018 0.001 TYR A 297 ARG 0.004 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 264) hydrogen bonds : angle 3.45918 ( 699) covalent geometry : bond 0.00337 ( 6592) covalent geometry : angle 0.49850 ( 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 100 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.604 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: 0.7796 (OUTLIER) cc_final: 0.7332 (tm-30) REVERT: A 24 ARG cc_start: 0.6300 (tmt170) cc_final: 0.5487 (tpt-90) REVERT: A 29 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: A 103 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8081 (tt0) REVERT: A 124 GLU cc_start: 0.8146 (mp0) cc_final: 0.7863 (mp0) REVERT: A 142 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8030 (mtm180) REVERT: A 196 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: A 332 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: B 17 GLU cc_start: 0.8073 (tt0) cc_final: 0.7771 (mt-10) REVERT: B 24 ARG cc_start: 0.6016 (tmt170) cc_final: 0.2137 (mtm180) REVERT: B 166 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6994 (mt-10) REVERT: B 169 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7197 (tm-30) REVERT: B 202 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7318 (tp30) REVERT: B 312 GLU cc_start: 0.8866 (tt0) cc_final: 0.8538 (tt0) outliers start: 33 outliers final: 25 residues processed: 93 average time/residue: 0.1889 time to fit residues: 23.1759 Evaluate side-chains 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 332 GLU 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 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=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: 6.9990 chunk 57 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 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 = 0.3825 r_free = 0.3825 target = 0.159974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114628 restraints weight = 6657.571| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.96 r_work: 0.3142 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6592 Z= 0.243 Angle : 0.567 5.478 9160 Z= 0.298 Chirality : 0.043 0.169 1008 Planarity : 0.004 0.033 1028 Dihedral : 23.390 102.024 1300 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.71 % Allowed : 22.86 % Favored : 71.43 % 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: 0.46 (0.35), residues: 666 helix: 1.58 (0.33), residues: 273 sheet: -1.35 (0.74), residues: 49 loop : -0.45 (0.38), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 156 HIS 0.001 0.001 HIS B 307 PHE 0.016 0.001 PHE B 171 TYR 0.018 0.001 TYR A 297 ARG 0.005 0.000 ARG B 333 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 264) hydrogen bonds : angle 3.69206 ( 699) covalent geometry : bond 0.00592 ( 6592) covalent geometry : angle 0.56725 ( 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 99 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.578 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: A 24 ARG cc_start: 0.6450 (tmt170) cc_final: 0.4858 (tpt90) REVERT: A 103 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8066 (tt0) REVERT: A 124 GLU cc_start: 0.8059 (mp0) cc_final: 0.7671 (mp0) REVERT: A 142 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8106 (mtm180) REVERT: A 196 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8656 (mm-30) REVERT: A 332 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: B 17 GLU cc_start: 0.8109 (tt0) cc_final: 0.7802 (mt-10) REVERT: B 24 ARG cc_start: 0.6059 (tmt170) cc_final: 0.2117 (mtm180) REVERT: B 169 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7199 (tm-30) REVERT: B 202 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7357 (tp30) REVERT: B 312 GLU cc_start: 0.8784 (tt0) cc_final: 0.8449 (tt0) outliers start: 32 outliers final: 23 residues processed: 90 average time/residue: 0.2039 time to fit residues: 23.8247 Evaluate side-chains 92 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 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 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 332 GLU 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 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 Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 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 = 0.3906 r_free = 0.3906 target = 0.167260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122120 restraints weight = 6622.778| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.98 r_work: 0.3235 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1693 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= 0.119 Angle : 0.504 5.751 9160 Z= 0.268 Chirality : 0.039 0.168 1008 Planarity : 0.003 0.031 1028 Dihedral : 22.898 102.341 1300 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.29 % Allowed : 23.93 % Favored : 71.79 % 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: 0.69 (0.35), residues: 666 helix: 1.87 (0.33), residues: 273 sheet: -1.27 (0.76), residues: 47 loop : -0.41 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 156 HIS 0.000 0.000 HIS B 278 PHE 0.016 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 0.03031 ( 264) hydrogen bonds : angle 3.43874 ( 699) covalent geometry : bond 0.00271 ( 6592) covalent geometry : angle 0.50357 ( 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 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.590 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: A 24 ARG cc_start: 0.6345 (tmt170) cc_final: 0.5378 (tpt-90) REVERT: A 103 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8034 (tt0) REVERT: A 124 GLU cc_start: 0.8162 (mp0) cc_final: 0.7885 (mp0) REVERT: A 142 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8022 (mtm180) REVERT: A 203 MET cc_start: 0.8596 (ttt) cc_final: 0.8387 (ttt) REVERT: A 332 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7733 (tm-30) REVERT: B 17 GLU cc_start: 0.8101 (tt0) cc_final: 0.7818 (mt-10) REVERT: B 24 ARG cc_start: 0.5900 (tmt170) cc_final: 0.2051 (mtm180) REVERT: B 166 GLU cc_start: 0.7482 (mm-30) cc_final: 0.6981 (mt-10) REVERT: B 169 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7184 (tm-30) REVERT: B 202 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7306 (tp30) REVERT: B 225 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8280 (mtt90) REVERT: B 312 GLU cc_start: 0.8814 (tt0) cc_final: 0.8516 (tt0) outliers start: 24 outliers final: 15 residues processed: 86 average time/residue: 0.2120 time to fit residues: 23.5802 Evaluate side-chains 82 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 97 VAL 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 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 161 VAL Chi-restraints excluded: chain B residue 337 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: 0.9990 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** B 199 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 = 0.3870 r_free = 0.3870 target = 0.163989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119137 restraints weight = 6725.249| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.97 r_work: 0.3195 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6592 Z= 0.157 Angle : 0.516 5.588 9160 Z= 0.271 Chirality : 0.040 0.169 1008 Planarity : 0.004 0.030 1028 Dihedral : 23.005 104.155 1300 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 3.93 % Allowed : 24.11 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.78 (0.33), residues: 273 sheet: -1.20 (0.77), residues: 47 loop : -0.41 (0.37), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 156 HIS 0.001 0.000 HIS B 307 PHE 0.015 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 0.03341 ( 264) hydrogen bonds : angle 3.50735 ( 699) covalent geometry : bond 0.00377 ( 6592) covalent geometry : angle 0.51581 ( 9160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.89 seconds wall clock time: 56 minutes 17.94 seconds (3377.94 seconds total)