Starting phenix.real_space_refine on Wed Jul 1 23:28:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.map" model { file = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dlr_27512/07_2026/8dlr_27512.cif" } resolution = 2.51 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= -0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2567 2.51 5 N 656 2.21 5 O 788 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: 4027 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2218 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 14, 'TRANS': 259} Chain breaks: 2 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.09, per 1000 atoms: 0.27 Number of scatterers: 4027 At special positions: 0 Unit cell: (92, 64, 108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 788 8.00 N 656 7.00 C 2567 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 42 " - pdb=" SG CYS L 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG A1306 " - " ASN A 282 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 164.9 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 7.9% alpha, 56.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'H' and resid 46 through 50 removed outlier: 3.696A pdb=" N SER H 49 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.966A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 129 removed outlier: 4.142A pdb=" N LYS H 127 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 98 through 102 removed outlier: 4.143A pdb=" N GLU L 102 " --> pdb=" O ALA L 99 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.012A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.979A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.663A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.835A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.146A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N TYR A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.272A pdb=" N PHE A 157 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 11.025A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.318A pdb=" N GLU H 29 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE H 53 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ARG H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.318A pdb=" N GLU H 29 " --> pdb=" O THR H 141 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL H 133 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AA9, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.403A pdb=" N TRP L 54 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 29 through 32 165 hydrogen bonds defined for protein. 405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1253 1.34 - 1.47: 1107 1.47 - 1.59: 1744 1.59 - 1.71: 0 1.71 - 1.84: 21 Bond restraints: 4125 Sorted by residual: bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.93e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.90e+00 ... (remaining 4120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 5349 1.80 - 3.59: 228 3.59 - 5.39: 26 5.39 - 7.19: 3 7.19 - 8.98: 3 Bond angle restraints: 5609 Sorted by residual: angle pdb=" C GLN L 69 " pdb=" N ASP L 70 " pdb=" CA ASP L 70 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" CA ASN A 280 " pdb=" CB ASN A 280 " pdb=" CG ASN A 280 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.00e+00 1.00e+00 8.16e+00 angle pdb=" N GLY H 75 " pdb=" CA GLY H 75 " pdb=" C GLY H 75 " ideal model delta sigma weight residual 113.18 119.45 -6.27 2.37e+00 1.78e-01 7.00e+00 angle pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" C ASP A 287 " ideal model delta sigma weight residual 108.79 104.81 3.98 1.53e+00 4.27e-01 6.76e+00 angle pdb=" CA LEU H 74 " pdb=" CB LEU H 74 " pdb=" CG LEU H 74 " ideal model delta sigma weight residual 116.30 125.28 -8.98 3.50e+00 8.16e-02 6.59e+00 ... (remaining 5604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 2180 16.63 - 33.26: 160 33.26 - 49.90: 25 49.90 - 66.53: 3 66.53 - 83.16: 8 Dihedral angle restraints: 2376 sinusoidal: 912 harmonic: 1464 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -41.28 -44.72 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU H 74 " pdb=" C LEU H 74 " pdb=" N GLY H 75 " pdb=" CA GLY H 75 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 466 0.054 - 0.109: 135 0.109 - 0.163: 34 0.163 - 0.217: 3 0.217 - 0.271: 3 Chirality restraints: 641 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB THR A 63 " pdb=" CA THR A 63 " pdb=" OG1 THR A 63 " pdb=" CG2 THR A 63 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL A 227 " pdb=" CA VAL A 227 " pdb=" CG1 VAL A 227 " pdb=" CG2 VAL A 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 638 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO A 295 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO A 230 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 48 " -0.014 2.00e-02 2.50e+03 1.35e-02 3.20e+00 pdb=" CG PHE H 48 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 48 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE H 48 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 48 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 48 " -0.001 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1131 2.81 - 3.33: 3161 3.33 - 3.86: 6983 3.86 - 4.38: 8076 4.38 - 4.90: 14213 Nonbonded interactions: 33564 Sorted by model distance: nonbonded pdb=" OH TYR A 144 " pdb=" OH TYR H 129 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR H 52 " pdb=" O THR H 120 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OG1 THR A 114 " model vdw 2.342 3.040 nonbonded pdb=" O ASP L 111 " pdb=" OG1 THR L 114 " model vdw 2.346 3.040 nonbonded pdb=" NE2 GLN A 14 " pdb=" O TYR A 160 " model vdw 2.347 3.120 ... (remaining 33559 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.740 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4136 Z= 0.281 Angle : 0.834 8.983 5637 Z= 0.444 Chirality : 0.057 0.271 641 Planarity : 0.007 0.070 705 Dihedral : 12.631 83.158 1425 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.36), residues: 495 helix: -0.46 (1.50), residues: 11 sheet: -0.36 (0.33), residues: 221 loop : -0.59 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 246 TYR 0.017 0.002 TYR H 79 PHE 0.030 0.003 PHE H 48 TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.28 ( 4125) covalent geometry : angle 0.81081 / 0.44 ( 5609) SS BOND : bond 0.00469 / 0.24 ( 5) SS BOND : angle 1.85266 / 0.95 ( 10) hydrogen bonds : bond 0.13212 / 8.91 ( 150) hydrogen bonds : angle 6.94746 / 4.67 ( 405) link_NAG-ASN : bond 0.00442 / 0.23 ( 6) link_NAG-ASN : angle 3.35917 / 2.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.097 Fit side-chains REVERT: H 86 ARG cc_start: 0.8319 (mtp180) cc_final: 0.8006 (ttt180) REVERT: L 88 ASN cc_start: 0.8039 (m-40) cc_final: 0.7835 (m110) REVERT: L 102 GLU cc_start: 0.8303 (tt0) cc_final: 0.8042 (tt0) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.4713 time to fit residues: 40.4981 Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 207 HIS L 85 ASN L 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.075173 restraints weight = 6313.824| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.53 r_work: 0.2875 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4136 Z= 0.156 Angle : 0.566 6.558 5637 Z= 0.295 Chirality : 0.045 0.222 641 Planarity : 0.005 0.049 705 Dihedral : 4.806 17.825 544 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.92 % Allowed : 8.26 % Favored : 90.83 % 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: -0.55 (0.37), residues: 495 helix: -1.40 (1.23), residues: 17 sheet: -0.14 (0.34), residues: 210 loop : -0.38 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.010 0.001 TYR L 105 PHE 0.013 0.001 PHE A 175 TRP 0.004 0.001 TRP H 134 HIS 0.001 0.001 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 4125) covalent geometry : angle 0.54858 / 0.29 ( 5609) SS BOND : bond 0.00453 / 0.23 ( 5) SS BOND : angle 1.07229 / 0.59 ( 10) hydrogen bonds : bond 0.02926 / 1.86 ( 150) hydrogen bonds : angle 5.71637 / 3.84 ( 405) link_NAG-ASN : bond 0.00252 / 0.14 ( 6) link_NAG-ASN : angle 2.45494 / 1.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.161 Fit side-chains REVERT: A 154 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8647 (mt-10) REVERT: H 82 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8748 (tmtm) REVERT: H 86 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7922 (ttp-170) REVERT: L 88 ASN cc_start: 0.8142 (m-40) cc_final: 0.7802 (m110) REVERT: L 102 GLU cc_start: 0.8742 (tt0) cc_final: 0.8346 (tt0) outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.5554 time to fit residues: 41.9334 Evaluate side-chains 62 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.071878 restraints weight = 6042.814| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.63 r_work: 0.2765 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4136 Z= 0.214 Angle : 0.581 5.544 5637 Z= 0.302 Chirality : 0.045 0.236 641 Planarity : 0.004 0.044 705 Dihedral : 4.811 17.457 544 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.38 % Allowed : 9.63 % Favored : 88.99 % 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: -0.37 (0.37), residues: 495 helix: -0.97 (1.34), residues: 17 sheet: -0.01 (0.34), residues: 203 loop : -0.28 (0.38), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 80 TYR 0.011 0.001 TYR L 105 PHE 0.019 0.002 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 4125) covalent geometry : angle 0.56256 / 0.30 ( 5609) SS BOND : bond 0.00360 / 0.20 ( 5) SS BOND : angle 1.31413 / 0.69 ( 10) hydrogen bonds : bond 0.03158 / 1.99 ( 150) hydrogen bonds : angle 5.61304 / 3.79 ( 405) link_NAG-ASN : bond 0.00188 / 0.11 ( 6) link_NAG-ASN : angle 2.46656 / 1.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.098 Fit side-chains REVERT: A 52 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: H 82 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8675 (tmtm) REVERT: H 86 ARG cc_start: 0.8370 (mtp180) cc_final: 0.8054 (ttp-170) REVERT: L 23 GLU cc_start: 0.8339 (pp20) cc_final: 0.8110 (pp20) REVERT: L 88 ASN cc_start: 0.8277 (m-40) cc_final: 0.7900 (m110) REVERT: L 102 GLU cc_start: 0.8768 (tt0) cc_final: 0.8497 (tt0) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.6118 time to fit residues: 42.8728 Evaluate side-chains 66 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.072130 restraints weight = 6010.198| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.62 r_work: 0.2775 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4136 Z= 0.191 Angle : 0.582 7.352 5637 Z= 0.302 Chirality : 0.044 0.228 641 Planarity : 0.004 0.041 705 Dihedral : 4.836 26.807 544 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.38 % Allowed : 10.78 % Favored : 87.84 % 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: -0.40 (0.37), residues: 495 helix: -0.76 (1.39), residues: 17 sheet: -0.04 (0.36), residues: 194 loop : -0.30 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.010 0.001 TYR A 269 PHE 0.016 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 4125) covalent geometry : angle 0.55769 / 0.30 ( 5609) SS BOND : bond 0.00383 / 0.20 ( 5) SS BOND : angle 2.38924 / 1.40 ( 10) hydrogen bonds : bond 0.02938 / 1.86 ( 150) hydrogen bonds : angle 5.49216 / 3.71 ( 405) link_NAG-ASN : bond 0.00218 / 0.12 ( 6) link_NAG-ASN : angle 2.44016 / 1.54 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.160 Fit side-chains REVERT: A 52 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: H 25 GLN cc_start: 0.9222 (mt0) cc_final: 0.8972 (mt0) REVERT: H 86 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8108 (ttm170) REVERT: L 23 GLU cc_start: 0.8366 (pp20) cc_final: 0.8114 (pp20) REVERT: L 88 ASN cc_start: 0.8208 (m-40) cc_final: 0.7895 (m110) REVERT: L 102 GLU cc_start: 0.8729 (tt0) cc_final: 0.8274 (tt0) outliers start: 6 outliers final: 3 residues processed: 71 average time/residue: 0.5945 time to fit residues: 43.6055 Evaluate side-chains 68 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.071799 restraints weight = 6008.687| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.61 r_work: 0.2766 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 4136 Z= 0.198 Angle : 0.590 7.149 5637 Z= 0.305 Chirality : 0.045 0.232 641 Planarity : 0.004 0.040 705 Dihedral : 4.839 27.982 544 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.29 % Allowed : 11.93 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.37), residues: 495 helix: -0.73 (1.39), residues: 17 sheet: -0.12 (0.35), residues: 205 loop : -0.29 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 246 TYR 0.010 0.001 TYR H 114 PHE 0.017 0.001 PHE A 175 TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 4125) covalent geometry : angle 0.56624 / 0.30 ( 5609) SS BOND : bond 0.00362 / 0.19 ( 5) SS BOND : angle 2.34687 / 1.37 ( 10) hydrogen bonds : bond 0.02937 / 1.85 ( 150) hydrogen bonds : angle 5.43854 / 3.67 ( 405) link_NAG-ASN : bond 0.00214 / 0.11 ( 6) link_NAG-ASN : angle 2.42292 / 1.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.157 Fit side-chains REVERT: A 52 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8182 (tp40) REVERT: H 86 ARG cc_start: 0.8466 (mtp180) cc_final: 0.8133 (ttm170) REVERT: L 23 GLU cc_start: 0.8376 (pp20) cc_final: 0.8119 (pp20) REVERT: L 88 ASN cc_start: 0.8124 (m-40) cc_final: 0.7710 (m110) REVERT: L 102 GLU cc_start: 0.8722 (tt0) cc_final: 0.8308 (tt0) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.5806 time to fit residues: 41.3927 Evaluate side-chains 69 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 40 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 38 optimal weight: 0.1980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN H 25 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.072419 restraints weight = 6128.999| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.66 r_work: 0.2780 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4136 Z= 0.131 Angle : 0.552 7.421 5637 Z= 0.287 Chirality : 0.043 0.215 641 Planarity : 0.004 0.039 705 Dihedral : 4.591 27.045 544 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.83 % Allowed : 13.53 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.37), residues: 495 helix: -0.76 (1.36), residues: 17 sheet: 0.01 (0.35), residues: 202 loop : -0.17 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.009 0.001 TYR H 114 PHE 0.010 0.001 PHE A 133 TRP 0.006 0.001 TRP H 66 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 4125) covalent geometry : angle 0.53051 / 0.28 ( 5609) SS BOND : bond 0.00408 / 0.21 ( 5) SS BOND : angle 2.04440 / 1.20 ( 10) hydrogen bonds : bond 0.02562 / 1.62 ( 150) hydrogen bonds : angle 5.26539 / 3.55 ( 405) link_NAG-ASN : bond 0.00280 / 0.14 ( 6) link_NAG-ASN : angle 2.31146 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.159 Fit side-chains REVERT: A 154 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8416 (mt-10) REVERT: H 67 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7969 (mtp) REVERT: H 86 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8069 (ttm170) REVERT: H 106 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7877 (mtm-85) REVERT: H 127 LYS cc_start: 0.9078 (pttm) cc_final: 0.8839 (pttt) REVERT: L 88 ASN cc_start: 0.8032 (m-40) cc_final: 0.7602 (m110) REVERT: L 102 GLU cc_start: 0.8685 (tt0) cc_final: 0.8241 (tt0) REVERT: L 122 LYS cc_start: 0.8390 (ttpp) cc_final: 0.8126 (tttt) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.6568 time to fit residues: 47.3374 Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.072161 restraints weight = 6106.376| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.58 r_work: 0.2771 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4136 Z= 0.176 Angle : 0.582 8.912 5637 Z= 0.301 Chirality : 0.044 0.229 641 Planarity : 0.004 0.039 705 Dihedral : 4.685 27.469 544 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.29 % Allowed : 13.30 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.37), residues: 495 helix: -0.58 (1.39), residues: 17 sheet: -0.06 (0.35), residues: 205 loop : -0.29 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 69 TYR 0.010 0.001 TYR H 114 PHE 0.015 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 4125) covalent geometry : angle 0.55995 / 0.29 ( 5609) SS BOND : bond 0.00446 / 0.23 ( 5) SS BOND : angle 2.20768 / 1.30 ( 10) hydrogen bonds : bond 0.02786 / 1.76 ( 150) hydrogen bonds : angle 5.27862 / 3.56 ( 405) link_NAG-ASN : bond 0.00194 / 0.10 ( 6) link_NAG-ASN : angle 2.36285 / 1.49 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.164 Fit side-chains REVERT: A 52 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8119 (tp40) REVERT: A 154 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8544 (mt-10) REVERT: H 67 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7858 (mtp) REVERT: H 86 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8016 (ttm170) REVERT: H 106 ARG cc_start: 0.8358 (mtt180) cc_final: 0.7864 (mtm-85) REVERT: L 88 ASN cc_start: 0.8070 (m-40) cc_final: 0.7602 (m110) REVERT: L 102 GLU cc_start: 0.8663 (tt0) cc_final: 0.8158 (mt-10) REVERT: L 122 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8078 (tttt) outliers start: 10 outliers final: 4 residues processed: 66 average time/residue: 0.6178 time to fit residues: 42.0676 Evaluate side-chains 66 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.100247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.072482 restraints weight = 6020.408| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.65 r_work: 0.2777 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4136 Z= 0.148 Angle : 0.568 9.440 5637 Z= 0.295 Chirality : 0.044 0.220 641 Planarity : 0.004 0.038 705 Dihedral : 4.605 26.295 544 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.61 % Allowed : 13.99 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.37), residues: 495 helix: -0.57 (1.38), residues: 17 sheet: -0.06 (0.34), residues: 205 loop : -0.29 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 69 TYR 0.010 0.001 TYR H 114 PHE 0.012 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 4125) covalent geometry : angle 0.54789 / 0.29 ( 5609) SS BOND : bond 0.00457 / 0.23 ( 5) SS BOND : angle 1.96509 / 1.15 ( 10) hydrogen bonds : bond 0.02624 / 1.65 ( 150) hydrogen bonds : angle 5.18444 / 3.51 ( 405) link_NAG-ASN : bond 0.00233 / 0.12 ( 6) link_NAG-ASN : angle 2.35019 / 1.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.181 Fit side-chains REVERT: A 154 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 86 ARG cc_start: 0.8480 (mtp180) cc_final: 0.8069 (ttm170) REVERT: H 106 ARG cc_start: 0.8393 (mtt180) cc_final: 0.7859 (mtm-85) REVERT: H 127 LYS cc_start: 0.9099 (pttm) cc_final: 0.8833 (pttt) REVERT: L 88 ASN cc_start: 0.8142 (m-40) cc_final: 0.7680 (m110) REVERT: L 102 GLU cc_start: 0.8639 (tt0) cc_final: 0.8146 (mt-10) REVERT: L 122 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8141 (tttt) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.6897 time to fit residues: 44.0319 Evaluate side-chains 63 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.099643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.071848 restraints weight = 6087.143| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.65 r_work: 0.2769 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4136 Z= 0.164 Angle : 0.573 8.925 5637 Z= 0.298 Chirality : 0.044 0.229 641 Planarity : 0.004 0.038 705 Dihedral : 4.616 25.908 544 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.38 % Allowed : 14.91 % Favored : 83.72 % 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: -0.36 (0.37), residues: 495 helix: -0.56 (1.39), residues: 17 sheet: -0.05 (0.35), residues: 205 loop : -0.26 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 69 TYR 0.011 0.001 TYR H 114 PHE 0.014 0.001 PHE A 175 TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 4125) covalent geometry : angle 0.55329 / 0.29 ( 5609) SS BOND : bond 0.00438 / 0.22 ( 5) SS BOND : angle 1.89112 / 1.11 ( 10) hydrogen bonds : bond 0.02745 / 1.73 ( 150) hydrogen bonds : angle 5.15368 / 3.49 ( 405) link_NAG-ASN : bond 0.00209 / 0.11 ( 6) link_NAG-ASN : angle 2.33744 / 1.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.158 Fit side-chains REVERT: A 52 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8130 (tp40) REVERT: A 154 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8477 (mt-10) REVERT: H 38 LYS cc_start: 0.8904 (tptm) cc_final: 0.8535 (tptp) REVERT: H 86 ARG cc_start: 0.8464 (mtp180) cc_final: 0.8035 (ttm170) REVERT: H 106 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7825 (mtm-85) REVERT: H 127 LYS cc_start: 0.9078 (pttm) cc_final: 0.8801 (pttt) REVERT: L 88 ASN cc_start: 0.8137 (m-40) cc_final: 0.7695 (m110) REVERT: L 102 GLU cc_start: 0.8625 (tt0) cc_final: 0.8153 (mt-10) REVERT: L 122 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8132 (tttt) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 0.6154 time to fit residues: 41.8861 Evaluate side-chains 66 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 0.0570 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.072502 restraints weight = 5981.597| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.55 r_work: 0.2779 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4136 Z= 0.162 Angle : 0.572 8.604 5637 Z= 0.297 Chirality : 0.044 0.226 641 Planarity : 0.004 0.038 705 Dihedral : 4.607 25.907 544 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.15 % Allowed : 15.14 % Favored : 83.72 % 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 (0.37), residues: 495 helix: -0.57 (1.38), residues: 17 sheet: -0.08 (0.35), residues: 205 loop : -0.27 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 69 TYR 0.011 0.001 TYR H 114 PHE 0.013 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.001 0.000 HIS A 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 4125) covalent geometry : angle 0.55346 / 0.29 ( 5609) SS BOND : bond 0.00433 / 0.22 ( 5) SS BOND : angle 1.74128 / 1.02 ( 10) hydrogen bonds : bond 0.02714 / 1.72 ( 150) hydrogen bonds : angle 5.11815 / 3.47 ( 405) link_NAG-ASN : bond 0.00202 / 0.11 ( 6) link_NAG-ASN : angle 2.31036 / 1.46 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.154 Fit side-chains REVERT: A 52 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8131 (tp40) REVERT: A 154 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8410 (mt-10) REVERT: H 38 LYS cc_start: 0.8865 (tptm) cc_final: 0.8474 (tptp) REVERT: H 86 ARG cc_start: 0.8436 (mtp180) cc_final: 0.7998 (ttm170) REVERT: H 106 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7817 (mtm-85) REVERT: H 127 LYS cc_start: 0.9031 (pttm) cc_final: 0.8749 (pttt) REVERT: L 88 ASN cc_start: 0.8144 (m-40) cc_final: 0.7685 (m110) REVERT: L 102 GLU cc_start: 0.8625 (tt0) cc_final: 0.8139 (mt-10) REVERT: L 122 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8070 (tttt) outliers start: 5 outliers final: 3 residues processed: 63 average time/residue: 0.6486 time to fit residues: 42.0496 Evaluate side-chains 65 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain L residue 71 ASN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN L 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.069821 restraints weight = 6159.181| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.51 r_work: 0.2724 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 4136 Z= 0.296 Angle : 0.652 9.629 5637 Z= 0.337 Chirality : 0.047 0.244 641 Planarity : 0.004 0.040 705 Dihedral : 4.998 29.307 544 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.92 % Allowed : 15.37 % Favored : 83.72 % 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: -0.40 (0.37), residues: 495 helix: -0.57 (1.42), residues: 17 sheet: -0.05 (0.35), residues: 206 loop : -0.31 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.012 0.002 TYR H 128 PHE 0.024 0.002 PHE A 175 TRP 0.011 0.001 TRP H 66 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.30 ( 4125) covalent geometry : angle 0.63089 / 0.33 ( 5609) SS BOND : bond 0.00565 / 0.28 ( 5) SS BOND : angle 2.29289 / 1.34 ( 10) hydrogen bonds : bond 0.03347 / 2.12 ( 150) hydrogen bonds : angle 5.37471 / 3.65 ( 405) link_NAG-ASN : bond 0.00154 / 0.09 ( 6) link_NAG-ASN : angle 2.46711 / 1.56 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.32 seconds wall clock time: 33 minutes 43.21 seconds (2023.21 seconds total)