Starting phenix.real_space_refine on Thu Jul 2 03:18:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgj_44514/07_2026/9bgj_44514.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgj_44514/07_2026/9bgj_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bgj_44514/07_2026/9bgj_44514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgj_44514/07_2026/9bgj_44514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bgj_44514/07_2026/9bgj_44514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgj_44514/07_2026/9bgj_44514.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.67, per 1000 atoms: 0.26 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: 0.56 Conformation dependent library (CDL) restraints added in 358.8 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: 0.82 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: 1.27 Time building geometry restraints manager: 0.73 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=" C5' DG C 25 " pdb=" C4' DG C 25 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.14e+01 bond pdb=" C3' DA D 3 " pdb=" C2' DA D 3 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.11e+00 bond pdb=" C3' DA D 11 " pdb=" C2' DA D 11 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.99e+00 bond pdb=" C3' DA C 11 " pdb=" C2' DA C 11 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.12e+00 bond pdb=" C3' DT C 24 " pdb=" C2' DT C 24 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.49e+00 ... (remaining 6587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 8580 1.10 - 2.20: 438 2.20 - 3.29: 110 3.29 - 4.39: 20 4.39 - 5.49: 12 Bond angle restraints: 9160 Sorted by residual: angle pdb=" O5' DG C 25 " pdb=" C5' DG C 25 " pdb=" C4' DG C 25 " ideal model delta sigma weight residual 109.40 112.84 -3.44 8.00e-01 1.56e+00 1.85e+01 angle pdb=" N3 DT C 7 " pdb=" C4 DT C 7 " pdb=" O4 DT C 7 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O4' DG C 23 " pdb=" C4' DG C 23 " pdb=" C3' DG C 23 " ideal model delta sigma weight residual 106.00 103.49 2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT C 6 " pdb=" C4 DT C 6 " pdb=" O4 DT C 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT C 24 " pdb=" C4 DT C 24 " pdb=" O4 DT C 24 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (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: 615 0.033 - 0.066: 271 0.066 - 0.099: 76 0.099 - 0.131: 42 0.131 - 0.164: 4 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=" C3' DT D 16 " pdb=" C4' DT D 16 " pdb=" O3' DT D 16 " pdb=" C2' DT D 16 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.14e-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 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: 2.560 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.004 0.030 6592 Z= 0.310 Angle : 0.607 5.488 9160 Z= 0.434 Chirality : 0.044 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (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 ARG 0.005 0.000 ARG B 225 TYR 0.017 0.001 TYR A 297 PHE 0.021 0.001 PHE B 171 TRP 0.011 0.001 TRP A 117 HIS 0.001 0.000 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.31 ( 6592) covalent geometry : angle 0.60722 / 0.43 ( 9160) hydrogen bonds : bond 0.15872 / 10.46 ( 264) hydrogen bonds : angle 5.41762 / 3.77 ( 699) *********************** 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 : 0.146 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: 0.0977 time to fit residues: 9.6952 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 : 0.226 ------------------------------------------------------------------------------- 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 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3855 r_free = 0.3855 target = 0.162301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.117473 restraints weight = 6590.190| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.96 r_work: 0.3176 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6592 Z= 0.183 Angle : 0.567 5.728 9160 Z= 0.303 Chirality : 0.043 0.169 1008 Planarity : 0.004 0.036 1028 Dihedral : 23.696 97.817 1325 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.36 % Allowed : 24.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.35), residues: 666 helix: 1.56 (0.33), residues: 267 sheet: -1.45 (0.72), residues: 44 loop : -0.52 (0.37), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.006 0.001 PHE A 288 TRP 0.012 0.002 TRP A 117 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 6592) covalent geometry : angle 0.56711 / 0.30 ( 9160) hydrogen bonds : bond 0.04719 / 3.16 ( 264) hydrogen bonds : angle 4.00112 / 2.83 ( 699) *********************** 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 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.209 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: 0.7930 (OUTLIER) cc_final: 0.7441 (tm-30) REVERT: A 24 ARG cc_start: 0.6567 (tmt170) cc_final: 0.5721 (tpt-90) REVERT: A 85 ASP cc_start: 0.7437 (t0) cc_final: 0.7207 (t0) REVERT: A 103 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8118 (tt0) REVERT: A 124 GLU cc_start: 0.8334 (mp0) cc_final: 0.8129 (mp0) REVERT: A 196 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8584 (mm-30) REVERT: B 24 ARG cc_start: 0.6087 (tmt170) cc_final: 0.2257 (mtm180) REVERT: B 85 ASP cc_start: 0.7876 (t0) cc_final: 0.7569 (t0) REVERT: B 166 GLU cc_start: 0.7570 (tp30) cc_final: 0.7207 (mt-10) REVERT: B 202 GLU cc_start: 0.7653 (mt-10) cc_final: 0.6945 (mp0) outliers start: 30 outliers final: 20 residues processed: 90 average time/residue: 0.0874 time to fit residues: 10.5001 Evaluate side-chains 85 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 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 145 VAL 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 49 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.118518 restraints weight = 6548.102| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.97 r_work: 0.3186 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.150 Angle : 0.536 5.467 9160 Z= 0.287 Chirality : 0.042 0.168 1008 Planarity : 0.004 0.035 1028 Dihedral : 23.669 97.641 1312 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 6.43 % Allowed : 23.75 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.35), residues: 666 helix: 1.68 (0.33), residues: 267 sheet: -1.44 (0.76), residues: 41 loop : -0.51 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6592) covalent geometry : angle 0.53589 / 0.29 ( 9160) hydrogen bonds : bond 0.04227 / 2.85 ( 264) hydrogen bonds : angle 3.82158 / 2.70 ( 699) *********************** 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 103 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.271 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 24 ARG cc_start: 0.6504 (tmt170) cc_final: 0.5675 (tpt-90) REVERT: A 103 GLU cc_start: 0.8746 (tm-30) cc_final: 0.8110 (tt0) REVERT: A 124 GLU cc_start: 0.8349 (mp0) cc_final: 0.8102 (mp0) REVERT: A 196 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8539 (mm-30) REVERT: B 24 ARG cc_start: 0.6029 (tmt170) cc_final: 0.2178 (mtm180) REVERT: B 85 ASP cc_start: 0.7860 (t0) cc_final: 0.7526 (t0) REVERT: B 142 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7713 (mtp-110) REVERT: B 166 GLU cc_start: 0.7541 (tp30) cc_final: 0.7166 (mt-10) REVERT: B 202 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6951 (mp0) REVERT: B 225 ARG cc_start: 0.8583 (mtt90) cc_final: 0.8304 (mpt-90) REVERT: B 264 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7292 (mp) outliers start: 36 outliers final: 22 residues processed: 97 average time/residue: 0.0852 time to fit residues: 11.0106 Evaluate side-chains 90 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 65 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 264 LEU 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 41 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 54 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120661 restraints weight = 6564.174| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.96 r_work: 0.3213 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.126 Angle : 0.515 5.662 9160 Z= 0.276 Chirality : 0.042 0.166 1008 Planarity : 0.004 0.033 1028 Dihedral : 23.498 96.666 1309 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.89 % Allowed : 23.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.35), residues: 666 helix: 1.83 (0.33), residues: 267 sheet: -1.43 (0.76), residues: 41 loop : -0.46 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.016 0.001 TYR A 297 PHE 0.006 0.001 PHE B 171 TRP 0.010 0.001 TRP A 117 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 6592) covalent geometry : angle 0.51518 / 0.28 ( 9160) hydrogen bonds : bond 0.03762 / 2.53 ( 264) hydrogen bonds : angle 3.62701 / 2.58 ( 699) *********************** 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 99 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.195 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: A 24 ARG cc_start: 0.6437 (tmt170) cc_final: 0.5592 (tpt-90) REVERT: A 103 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8078 (tt0) REVERT: A 124 GLU cc_start: 0.8250 (mp0) cc_final: 0.7987 (mp0) REVERT: A 196 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8552 (mm-30) REVERT: B 24 ARG cc_start: 0.5967 (tmt170) cc_final: 0.2114 (mtm180) REVERT: B 85 ASP cc_start: 0.7812 (t0) cc_final: 0.7455 (t0) REVERT: B 142 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7986 (mtm180) REVERT: B 166 GLU cc_start: 0.7543 (tp30) cc_final: 0.7160 (mt-10) REVERT: B 202 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6894 (mp0) REVERT: B 225 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8128 (mtt90) REVERT: B 264 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7278 (mp) REVERT: B 312 GLU cc_start: 0.8819 (tt0) cc_final: 0.8293 (tt0) outliers start: 33 outliers final: 21 residues processed: 92 average time/residue: 0.0897 time to fit residues: 10.9043 Evaluate side-chains 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 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 212 THR 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 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 145 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 289 VAL 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 18 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** 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 = 0.3890 r_free = 0.3890 target = 0.165703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120708 restraints weight = 6668.044| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.97 r_work: 0.3219 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.126 Angle : 0.508 5.630 9160 Z= 0.271 Chirality : 0.041 0.168 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.459 95.958 1309 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.36 % Allowed : 23.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.35), residues: 666 helix: 1.84 (0.33), residues: 267 sheet: -1.30 (0.78), residues: 41 loop : -0.43 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.018 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.009 0.001 TRP A 117 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 6592) covalent geometry : angle 0.50836 / 0.27 ( 9160) hydrogen bonds : bond 0.03581 / 2.41 ( 264) hydrogen bonds : angle 3.58274 / 2.53 ( 699) *********************** 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 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.213 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: 0.7851 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: A 24 ARG cc_start: 0.6382 (tmt170) cc_final: 0.5539 (tpt-90) REVERT: A 103 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8034 (tt0) REVERT: A 124 GLU cc_start: 0.8162 (mp0) cc_final: 0.7878 (mp0) REVERT: A 196 GLU cc_start: 0.8877 (tt0) cc_final: 0.8545 (mm-30) REVERT: B 24 ARG cc_start: 0.5906 (tmt170) cc_final: 0.2078 (mtm180) REVERT: B 85 ASP cc_start: 0.7790 (t0) cc_final: 0.7444 (t0) REVERT: B 142 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7977 (mtm180) REVERT: B 202 GLU cc_start: 0.7596 (mt-10) cc_final: 0.6881 (mp0) REVERT: B 264 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7222 (mp) outliers start: 30 outliers final: 21 residues processed: 91 average time/residue: 0.0765 time to fit residues: 9.3379 Evaluate side-chains 88 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 212 THR Chi-restraints excluded: chain A residue 236 SER 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 142 ARG Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 264 LEU 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 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 331 ASN ** 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 = 0.3903 r_free = 0.3903 target = 0.166899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121934 restraints weight = 6598.503| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.97 r_work: 0.3236 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6592 Z= 0.115 Angle : 0.498 5.727 9160 Z= 0.267 Chirality : 0.041 0.167 1008 Planarity : 0.003 0.031 1028 Dihedral : 23.385 95.399 1305 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.36 % Allowed : 23.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.35), residues: 666 helix: 1.96 (0.33), residues: 267 sheet: -1.25 (0.77), residues: 41 loop : -0.43 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.005 0.001 PHE B 87 TRP 0.011 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 6592) covalent geometry : angle 0.49821 / 0.27 ( 9160) hydrogen bonds : bond 0.03362 / 2.26 ( 264) hydrogen bonds : angle 3.51591 / 2.48 ( 699) *********************** 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 95 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.190 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: 0.7872 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: A 24 ARG cc_start: 0.6371 (tmt170) cc_final: 0.5514 (tpt-90) REVERT: A 103 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8077 (tt0) REVERT: A 124 GLU cc_start: 0.8151 (mp0) cc_final: 0.7846 (mp0) REVERT: A 196 GLU cc_start: 0.8858 (tt0) cc_final: 0.8543 (mm-30) REVERT: B 17 GLU cc_start: 0.7916 (tt0) cc_final: 0.7604 (mt-10) REVERT: B 24 ARG cc_start: 0.5896 (tmt170) cc_final: 0.2055 (mtm180) REVERT: B 85 ASP cc_start: 0.7778 (t0) cc_final: 0.7432 (t0) REVERT: B 142 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: B 166 GLU cc_start: 0.7500 (tp30) cc_final: 0.7124 (mt-10) REVERT: B 180 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7691 (mp) REVERT: B 202 GLU cc_start: 0.7625 (mt-10) cc_final: 0.6866 (tp30) REVERT: B 312 GLU cc_start: 0.8695 (tt0) cc_final: 0.8323 (tt0) outliers start: 30 outliers final: 22 residues processed: 90 average time/residue: 0.0777 time to fit residues: 9.2766 Evaluate side-chains 87 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 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 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 SER 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 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 161 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 180 LEU 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 68 optimal weight: 50.0000 chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.2980 chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 0.0670 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.164478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.119622 restraints weight = 6613.386| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.93 r_work: 0.3198 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6592 Z= 0.158 Angle : 0.520 5.574 9160 Z= 0.276 Chirality : 0.042 0.168 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.523 95.516 1305 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.89 % Allowed : 22.50 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.35), residues: 666 helix: 1.89 (0.33), residues: 267 sheet: -1.26 (0.79), residues: 41 loop : -0.41 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.018 0.001 TYR A 297 PHE 0.006 0.001 PHE B 171 TRP 0.011 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 6592) covalent geometry : angle 0.52036 / 0.28 ( 9160) hydrogen bonds : bond 0.03674 / 2.47 ( 264) hydrogen bonds : angle 3.56868 / 2.52 ( 699) *********************** 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 98 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 65 time to evaluate : 0.210 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: 0.7888 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: A 24 ARG cc_start: 0.6450 (tmt170) cc_final: 0.5643 (tpt-90) REVERT: A 103 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8088 (tt0) REVERT: A 124 GLU cc_start: 0.8143 (mp0) cc_final: 0.7783 (mp0) REVERT: A 196 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8555 (mm-30) REVERT: B 17 GLU cc_start: 0.7985 (tt0) cc_final: 0.7683 (mt-10) REVERT: B 24 ARG cc_start: 0.5998 (tmt170) cc_final: 0.2150 (mtm180) REVERT: B 85 ASP cc_start: 0.7822 (t0) cc_final: 0.7517 (t0) REVERT: B 142 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7931 (mtm180) REVERT: B 166 GLU cc_start: 0.7545 (tp30) cc_final: 0.7149 (mt-10) REVERT: B 202 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7012 (tp30) REVERT: B 260 MET cc_start: 0.8464 (ttt) cc_final: 0.8244 (ttt) REVERT: B 312 GLU cc_start: 0.8689 (tt0) cc_final: 0.8336 (tt0) outliers start: 33 outliers final: 25 residues processed: 91 average time/residue: 0.0907 time to fit residues: 10.8180 Evaluate side-chains 91 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 212 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 280 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 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 318 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.165631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120784 restraints weight = 6534.516| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.95 r_work: 0.3216 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.131 Angle : 0.508 5.621 9160 Z= 0.270 Chirality : 0.041 0.168 1008 Planarity : 0.003 0.031 1028 Dihedral : 23.498 95.049 1305 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 5.54 % Allowed : 23.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.35), residues: 666 helix: 1.96 (0.33), residues: 267 sheet: -1.22 (0.79), residues: 41 loop : -0.43 (0.37), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.004 0.001 PHE B 87 TRP 0.009 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 6592) covalent geometry : angle 0.50769 / 0.27 ( 9160) hydrogen bonds : bond 0.03476 / 2.34 ( 264) hydrogen bonds : angle 3.51788 / 2.49 ( 699) *********************** 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 97 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.213 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 24 ARG cc_start: 0.6384 (tmt170) cc_final: 0.5546 (tpt-90) REVERT: A 37 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 103 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8078 (tt0) REVERT: A 124 GLU cc_start: 0.8129 (mp0) cc_final: 0.7785 (mp0) REVERT: A 163 GLU cc_start: 0.8438 (mp0) cc_final: 0.8209 (mp0) REVERT: A 196 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8545 (mm-30) REVERT: B 17 GLU cc_start: 0.7962 (tt0) cc_final: 0.7655 (mt-10) REVERT: B 24 ARG cc_start: 0.5922 (tmt170) cc_final: 0.2066 (mtm180) REVERT: B 85 ASP cc_start: 0.7767 (t0) cc_final: 0.7489 (t0) REVERT: B 142 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7913 (mtm180) REVERT: B 166 GLU cc_start: 0.7541 (tp30) cc_final: 0.7124 (mt-10) REVERT: B 202 GLU cc_start: 0.7729 (mt-10) cc_final: 0.6996 (tp30) REVERT: B 225 ARG cc_start: 0.8549 (mtt90) cc_final: 0.8256 (mtt90) REVERT: B 312 GLU cc_start: 0.8706 (tt0) cc_final: 0.8363 (tt0) outliers start: 31 outliers final: 23 residues processed: 90 average time/residue: 0.0872 time to fit residues: 10.2940 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 : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 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 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 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 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 161 VAL Chi-restraints excluded: chain B residue 167 VAL 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 47 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.161805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116826 restraints weight = 6709.565| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.94 r_work: 0.3163 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6592 Z= 0.205 Angle : 0.553 5.468 9160 Z= 0.290 Chirality : 0.043 0.168 1008 Planarity : 0.004 0.032 1028 Dihedral : 23.669 95.497 1305 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 5.00 % Allowed : 24.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.35), residues: 666 helix: 1.61 (0.33), residues: 273 sheet: -1.19 (0.76), residues: 46 loop : -0.47 (0.38), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 29 TYR 0.017 0.001 TYR A 297 PHE 0.007 0.001 PHE B 102 TRP 0.012 0.002 TRP B 156 HIS 0.001 0.000 HIS B 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 ( 6592) covalent geometry : angle 0.55261 / 0.29 ( 9160) hydrogen bonds : bond 0.03996 / 2.68 ( 264) hydrogen bonds : angle 3.66193 / 2.59 ( 699) *********************** 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 96 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 0.178 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: A 24 ARG cc_start: 0.6469 (tmt170) cc_final: 0.5668 (tpt-90) REVERT: A 37 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 103 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8042 (tt0) REVERT: A 124 GLU cc_start: 0.8139 (mp0) cc_final: 0.7760 (mp0) REVERT: A 163 GLU cc_start: 0.8449 (mp0) cc_final: 0.8220 (mp0) REVERT: A 196 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8577 (mm-30) REVERT: B 17 GLU cc_start: 0.8072 (tt0) cc_final: 0.7769 (mt-10) REVERT: B 24 ARG cc_start: 0.6010 (tmt170) cc_final: 0.2106 (mtm180) REVERT: B 85 ASP cc_start: 0.7866 (t0) cc_final: 0.7648 (t0) REVERT: B 142 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7949 (mtm180) REVERT: B 166 GLU cc_start: 0.7580 (tp30) cc_final: 0.7156 (mt-10) REVERT: B 202 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7072 (tp30) REVERT: B 225 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8296 (mtt90) REVERT: B 312 GLU cc_start: 0.8740 (tt0) cc_final: 0.8395 (tt0) outliers start: 28 outliers final: 20 residues processed: 90 average time/residue: 0.0862 time to fit residues: 10.2042 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 : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 37 LEU 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 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 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 56 SER 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 318 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 68 optimal weight: 50.0000 chunk 4 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.121964 restraints weight = 6555.903| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.95 r_work: 0.3231 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6592 Z= 0.113 Angle : 0.506 5.499 9160 Z= 0.270 Chirality : 0.041 0.167 1008 Planarity : 0.003 0.031 1028 Dihedral : 23.419 94.552 1305 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.29 % Allowed : 24.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.35), residues: 666 helix: 1.98 (0.33), residues: 267 sheet: -1.10 (0.76), residues: 46 loop : -0.43 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.017 0.001 TYR A 297 PHE 0.007 0.001 PHE B 87 TRP 0.015 0.001 TRP B 156 HIS 0.001 0.000 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6592) covalent geometry : angle 0.50600 / 0.27 ( 9160) hydrogen bonds : bond 0.03340 / 2.24 ( 264) hydrogen bonds : angle 3.50390 / 2.48 ( 699) ********************** 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 89 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.149 Fit side-chains TARDY: cannot create tardy model for: "TRP B 126 " (corrupted residue). Skipping it. REVERT: A 17 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: A 24 ARG cc_start: 0.6309 (tmt170) cc_final: 0.5461 (tpt-90) REVERT: A 37 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 103 GLU cc_start: 0.8674 (tm-30) cc_final: 0.7963 (tt0) REVERT: A 124 GLU cc_start: 0.8100 (mp0) cc_final: 0.7803 (mp0) REVERT: A 163 GLU cc_start: 0.8457 (mp0) cc_final: 0.8226 (mp0) REVERT: A 196 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8528 (mm-30) REVERT: B 17 GLU cc_start: 0.8045 (tt0) cc_final: 0.7737 (mt-10) REVERT: B 24 ARG cc_start: 0.5840 (tmt170) cc_final: 0.1976 (mtm180) REVERT: B 85 ASP cc_start: 0.7788 (t0) cc_final: 0.7496 (t0) REVERT: B 142 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7928 (mtm180) REVERT: B 166 GLU cc_start: 0.7539 (tp30) cc_final: 0.7125 (mt-10) REVERT: B 202 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7019 (tp30) REVERT: B 225 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8264 (mtt90) REVERT: B 312 GLU cc_start: 0.8772 (tt0) cc_final: 0.8422 (tt0) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.0904 time to fit residues: 9.7792 Evaluate side-chains 86 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR 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 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 167 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 230 VAL 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 64 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120610 restraints weight = 6613.350| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.94 r_work: 0.3215 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6592 Z= 0.134 Angle : 0.510 5.637 9160 Z= 0.271 Chirality : 0.041 0.169 1008 Planarity : 0.004 0.030 1028 Dihedral : 23.395 94.720 1305 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.75 % Allowed : 25.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.35), residues: 666 helix: 1.80 (0.33), residues: 273 sheet: -1.05 (0.77), residues: 46 loop : -0.45 (0.37), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 29 TYR 0.017 0.001 TYR A 297 PHE 0.004 0.001 PHE B 54 TRP 0.012 0.001 TRP B 156 HIS 0.001 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 6592) covalent geometry : angle 0.51011 / 0.27 ( 9160) hydrogen bonds : bond 0.03409 / 2.28 ( 264) hydrogen bonds : angle 3.51350 / 2.48 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1659.69 seconds wall clock time: 29 minutes 7.15 seconds (1747.15 seconds total)