Starting phenix.real_space_refine on Wed Aug 5 11:44:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5g_38934/08_2026/8y5g_38934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5g_38934/08_2026/8y5g_38934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y5g_38934/08_2026/8y5g_38934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5g_38934/08_2026/8y5g_38934.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y5g_38934/08_2026/8y5g_38934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5g_38934/08_2026/8y5g_38934.map" } resolution = 3.0 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= 0.003 sd= 0.042 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: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 60 5.16 5 C 6388 2.51 5 N 1649 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9860 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2876 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2862 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 13, 'TRANS': 344} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.85, per 1000 atoms: 0.19 Number of scatterers: 9860 At special positions: 0 Unit cell: (84.36, 93.48, 139.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 4 11.99 O 1759 8.00 N 1649 7.00 C 6388 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: 0.70 Conformation dependent library (CDL) restraints added in 229.8 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 50.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.541A pdb=" N VAL A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.908A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.724A pdb=" N VAL A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 Processing helix chain 'A' and resid 179 through 198 removed outlier: 3.579A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.506A pdb=" N ALA A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.534A pdb=" N ILE B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 58 through 91 removed outlier: 4.136A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Proline residue: B 85 - end of helix Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 111 Proline residue: B 108 - end of helix removed outlier: 3.508A pdb=" N THR B 111 " --> pdb=" O PRO B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 111' Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.884A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 149 through 175 removed outlier: 3.764A pdb=" N VAL B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Proline residue: B 163 - end of helix removed outlier: 3.534A pdb=" N MET B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.727A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.717A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 229 removed outlier: 4.286A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.760A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 279 removed outlier: 3.519A pdb=" N GLY B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 28 Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.618A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 88 removed outlier: 4.003A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 127 through 152 Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 156 through 165 removed outlier: 4.235A pdb=" N GLU C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 176 through 199 removed outlier: 3.708A pdb=" N LEU C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Proline residue: C 183 - end of helix Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.944A pdb=" N LYS C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 253 removed outlier: 3.767A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.600A pdb=" N ARG D 89 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 4.964A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 135 removed outlier: 3.638A pdb=" N VAL D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 179 through 198 removed outlier: 3.821A pdb=" N ASN D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.568A pdb=" N ALA D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 removed outlier: 3.517A pdb=" N TYR D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.548A pdb=" N LEU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 40 removed outlier: 6.636A pdb=" N VAL A 32 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N CYS A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A 24 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 36 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 23 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 71 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.479A pdb=" N PHE A 45 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 219 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR A 47 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N MET A 221 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 49 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 218 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 229 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 220 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 279 removed outlier: 6.598A pdb=" N ASN A 270 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 removed outlier: 5.661A pdb=" N VAL A 317 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 319 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 40 removed outlier: 6.690A pdb=" N VAL D 32 " --> pdb=" O CYS D 26 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N CYS D 26 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG D 24 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 36 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE D 23 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER D 71 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.440A pdb=" N PHE D 45 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 219 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR D 47 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N MET D 221 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU D 49 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 218 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP D 229 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 220 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 274 through 279 removed outlier: 7.503A pdb=" N ARG D 266 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG D 261 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG D 268 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 300 through 302 removed outlier: 4.234A pdb=" N ALA D 361 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 321 through 322 502 hydrogen bonds defined for protein. 1446 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: 1.00 Time building geometry restraints manager: 0.89 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: 3187 1.34 - 1.46: 2193 1.46 - 1.58: 4559 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10050 Sorted by residual: bond pdb=" CA VAL D 330 " pdb=" CB VAL D 330 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.16e-02 7.43e+03 1.31e+00 bond pdb=" CB ASN A 270 " pdb=" CG ASN A 270 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" N GLU D 366 " pdb=" CA GLU D 366 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.37e-02 5.33e+03 1.13e+00 bond pdb=" CG ARG A 233 " pdb=" CD ARG A 233 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 10045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 13467 2.62 - 5.25: 144 5.25 - 7.87: 8 7.87 - 10.50: 4 10.50 - 13.12: 1 Bond angle restraints: 13624 Sorted by residual: angle pdb=" CB MET D 360 " pdb=" CG MET D 360 " pdb=" SD MET D 360 " ideal model delta sigma weight residual 112.70 125.82 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C SER A 97 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ASN A 270 " pdb=" CA ASN A 270 " pdb=" CB ASN A 270 " ideal model delta sigma weight residual 109.48 115.46 -5.98 1.68e+00 3.54e-01 1.27e+01 angle pdb=" C VAL B 107 " pdb=" CA VAL B 107 " pdb=" CB VAL B 107 " ideal model delta sigma weight residual 114.35 110.60 3.75 1.06e+00 8.90e-01 1.25e+01 angle pdb=" N HIS D 146 " pdb=" CA HIS D 146 " pdb=" C HIS D 146 " ideal model delta sigma weight residual 114.64 109.27 5.37 1.52e+00 4.33e-01 1.25e+01 ... (remaining 13619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 5196 17.69 - 35.38: 629 35.38 - 53.06: 189 53.06 - 70.75: 37 70.75 - 88.44: 6 Dihedral angle restraints: 6057 sinusoidal: 2457 harmonic: 3600 Sorted by residual: dihedral pdb=" CA TRP D 364 " pdb=" C TRP D 364 " pdb=" N VAL D 365 " pdb=" CA VAL D 365 " ideal model delta harmonic sigma weight residual 180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA D 99 " pdb=" C ALA D 99 " pdb=" N LEU D 100 " pdb=" CA LEU D 100 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR A 213 " pdb=" C THR A 213 " pdb=" N MET A 214 " pdb=" CA MET A 214 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 924 0.032 - 0.063: 474 0.063 - 0.095: 109 0.095 - 0.127: 81 0.127 - 0.159: 9 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CG LEU D 313 " pdb=" CB LEU D 313 " pdb=" CD1 LEU D 313 " pdb=" CD2 LEU D 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA PHE C 138 " pdb=" N PHE C 138 " pdb=" C PHE C 138 " pdb=" CB PHE C 138 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA GLU A 189 " pdb=" N GLU A 189 " pdb=" C GLU A 189 " pdb=" CB GLU A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1594 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 285 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO D 286 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 167 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 168 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 208 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO C 209 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.032 5.00e-02 4.00e+02 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 134 2.68 - 3.24: 9027 3.24 - 3.79: 13908 3.79 - 4.35: 18484 4.35 - 4.90: 31962 Nonbonded interactions: 73515 Sorted by model distance: nonbonded pdb=" OD2 ASP D 348 " pdb="MG MG D 402 " model vdw 2.131 2.170 nonbonded pdb=" O PHE D 345 " pdb="MG MG D 401 " model vdw 2.191 2.170 nonbonded pdb=" N ASP C 108 " pdb=" OD1 ASP C 108 " model vdw 2.269 3.120 nonbonded pdb=" O ILE B 146 " pdb=" OG1 THR B 149 " model vdw 2.278 3.040 nonbonded pdb=" NE2 GLN D 154 " pdb=" O SER D 174 " model vdw 2.305 3.120 ... (remaining 73510 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 16 through 373 or resid 401 through 402)) selection = chain 'D' } 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: 0.940 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.080 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:5.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 0.038 10050 Z= 0.184 Angle : 0.674 13.122 13624 Z= 0.365 Chirality : 0.044 0.159 1597 Planarity : 0.006 0.078 1723 Dihedral : 16.922 88.441 3725 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 2.40 % Allowed : 24.70 % Favored : 72.90 % 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: -0.20 (0.24), residues: 1232 helix: 0.80 (0.22), residues: 575 sheet: 0.63 (0.39), residues: 199 loop : -1.70 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 233 TYR 0.013 0.001 TYR D 98 PHE 0.029 0.002 PHE B 48 TRP 0.009 0.001 TRP D 368 HIS 0.007 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (10050) covalent geometry : angle 0.67438 / 0.37 (13624) hydrogen bonds : bond 0.23991 / 16.27 ( 502) hydrogen bonds : angle 6.97190 / 4.98 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.274 Fit side-chains REVERT: A 28 ASP cc_start: 0.7274 (t70) cc_final: 0.7039 (t70) REVERT: A 75 MET cc_start: 0.7675 (mpt) cc_final: 0.7430 (mmt) REVERT: A 152 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: A 185 GLN cc_start: 0.7572 (tt0) cc_final: 0.7026 (tt0) REVERT: A 186 MET cc_start: 0.8160 (mtm) cc_final: 0.7864 (mtm) REVERT: A 189 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6806 (mp0) REVERT: A 297 GLU cc_start: 0.8268 (pm20) cc_final: 0.8057 (mp0) REVERT: A 343 GLU cc_start: 0.7349 (pt0) cc_final: 0.7096 (pt0) REVERT: C 173 LEU cc_start: 0.7477 (mp) cc_final: 0.7266 (mp) REVERT: D 129 MET cc_start: 0.8584 (mmm) cc_final: 0.8369 (mmt) outliers start: 26 outliers final: 20 residues processed: 288 average time/residue: 0.4849 time to fit residues: 149.5702 Evaluate side-chains 286 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 206 HIS A 358 GLN D 42 ASN D 255 ASN D 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104255 restraints weight = 13597.661| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.19 r_work: 0.3205 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.005 0.037 10050 Z= 0.200 Angle : 0.626 10.861 13624 Z= 0.327 Chirality : 0.045 0.153 1597 Planarity : 0.006 0.062 1723 Dihedral : 7.000 59.190 1391 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 4.88 % Allowed : 20.65 % Favored : 74.47 % 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 (0.24), residues: 1232 helix: 1.72 (0.22), residues: 582 sheet: 0.50 (0.38), residues: 203 loop : -1.75 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 233 TYR 0.015 0.001 TYR B 223 PHE 0.027 0.002 PHE B 133 TRP 0.012 0.001 TRP B 136 HIS 0.009 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (10050) covalent geometry : angle 0.62551 / 0.33 (13624) hydrogen bonds : bond 0.06742 / 4.45 ( 502) hydrogen bonds : angle 4.85531 / 3.48 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 250 time to evaluate : 0.299 Fit side-chains REVERT: A 143 ARG cc_start: 0.8345 (mtp85) cc_final: 0.8116 (mmm160) REVERT: B 133 PHE cc_start: 0.8107 (t80) cc_final: 0.7779 (t80) REVERT: B 137 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8227 (mp) REVERT: C 43 THR cc_start: 0.8300 (t) cc_final: 0.7923 (m) REVERT: C 121 LEU cc_start: 0.8359 (tt) cc_final: 0.8095 (tt) REVERT: D 140 PHE cc_start: 0.8175 (m-10) cc_final: 0.7861 (m-80) REVERT: D 207 ASP cc_start: 0.7789 (t0) cc_final: 0.7587 (t0) REVERT: D 371 VAL cc_start: 0.8329 (t) cc_final: 0.8026 (m) outliers start: 53 outliers final: 27 residues processed: 281 average time/residue: 0.4768 time to fit residues: 143.7007 Evaluate side-chains 261 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 233 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 331 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 185 GLN A 187 GLN A 358 GLN D 42 ASN D 147 GLN D 255 ASN D 321 ASN D 335 ASN D 346 ASN D 358 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106521 restraints weight = 13592.262| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.17 r_work: 0.3236 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10050 Z= 0.129 Angle : 0.567 11.358 13624 Z= 0.289 Chirality : 0.043 0.217 1597 Planarity : 0.005 0.055 1723 Dihedral : 5.428 57.390 1360 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 5.16 % Allowed : 21.01 % Favored : 73.82 % 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: 0.66 (0.25), residues: 1232 helix: 2.03 (0.23), residues: 580 sheet: 0.34 (0.38), residues: 205 loop : -1.75 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 233 TYR 0.009 0.001 TYR B 223 PHE 0.024 0.001 PHE C 138 TRP 0.008 0.001 TRP B 136 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (10050) covalent geometry : angle 0.56736 / 0.29 (13624) hydrogen bonds : bond 0.05046 / 3.34 ( 502) hydrogen bonds : angle 4.44961 / 3.21 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.370 Fit side-chains REVERT: A 28 ASP cc_start: 0.7462 (t70) cc_final: 0.7206 (t70) REVERT: B 133 PHE cc_start: 0.8100 (t80) cc_final: 0.7723 (t80) REVERT: B 137 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8179 (mp) REVERT: D 37 ASP cc_start: 0.8424 (m-30) cc_final: 0.8194 (m-30) REVERT: D 140 PHE cc_start: 0.8131 (m-10) cc_final: 0.7862 (m-80) REVERT: D 207 ASP cc_start: 0.7715 (t0) cc_final: 0.7455 (t0) REVERT: D 330 VAL cc_start: 0.8741 (p) cc_final: 0.8516 (m) outliers start: 56 outliers final: 24 residues processed: 276 average time/residue: 0.4746 time to fit residues: 140.7227 Evaluate side-chains 259 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 142 GLN A 358 GLN D 42 ASN D 255 ASN D 277 ASN D 321 ASN D 335 ASN D 358 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.121815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103632 restraints weight = 13603.991| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.14 r_work: 0.3197 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 10050 Z= 0.232 Angle : 0.627 12.210 13624 Z= 0.321 Chirality : 0.046 0.234 1597 Planarity : 0.006 0.053 1723 Dihedral : 4.910 57.183 1348 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 5.44 % Allowed : 21.57 % Favored : 73.00 % 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: 0.46 (0.24), residues: 1232 helix: 1.85 (0.22), residues: 585 sheet: 0.25 (0.38), residues: 200 loop : -1.84 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 24 TYR 0.017 0.001 TYR B 223 PHE 0.028 0.002 PHE C 138 TRP 0.009 0.001 TRP C 129 HIS 0.007 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.23 (10050) covalent geometry : angle 0.62748 / 0.32 (13624) hydrogen bonds : bond 0.06282 / 4.17 ( 502) hydrogen bonds : angle 4.50269 / 3.25 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 251 time to evaluate : 0.291 Fit side-chains REVERT: A 28 ASP cc_start: 0.7537 (t70) cc_final: 0.7296 (t70) REVERT: A 75 MET cc_start: 0.7972 (mpt) cc_final: 0.7650 (mpt) REVERT: B 133 PHE cc_start: 0.8195 (t80) cc_final: 0.7815 (t80) REVERT: B 137 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 215 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7594 (tmm) REVERT: D 37 ASP cc_start: 0.8442 (m-30) cc_final: 0.8225 (m-30) REVERT: D 67 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8468 (mt-10) REVERT: D 140 PHE cc_start: 0.8056 (m-10) cc_final: 0.7782 (m-80) REVERT: D 207 ASP cc_start: 0.7787 (t0) cc_final: 0.7530 (t0) REVERT: D 330 VAL cc_start: 0.8835 (p) cc_final: 0.8604 (m) REVERT: D 371 VAL cc_start: 0.8392 (t) cc_final: 0.8056 (m) outliers start: 59 outliers final: 33 residues processed: 285 average time/residue: 0.4771 time to fit residues: 145.5959 Evaluate side-chains 277 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 331 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 chunk 118 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 358 GLN D 321 ASN D 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.124446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106257 restraints weight = 13574.468| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.17 r_work: 0.3235 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10050 Z= 0.129 Angle : 0.572 12.498 13624 Z= 0.289 Chirality : 0.042 0.183 1597 Planarity : 0.005 0.049 1723 Dihedral : 4.728 58.826 1348 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 5.16 % Allowed : 23.41 % 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: 0.60 (0.25), residues: 1232 helix: 2.01 (0.23), residues: 587 sheet: 0.20 (0.38), residues: 200 loop : -1.80 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 24 TYR 0.011 0.001 TYR B 223 PHE 0.022 0.001 PHE C 138 TRP 0.009 0.001 TRP D 368 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10050) covalent geometry : angle 0.57209 / 0.29 (13624) hydrogen bonds : bond 0.04733 / 3.14 ( 502) hydrogen bonds : angle 4.25345 / 3.08 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 247 time to evaluate : 0.311 Fit side-chains REVERT: A 28 ASP cc_start: 0.7566 (t70) cc_final: 0.7322 (t70) REVERT: A 75 MET cc_start: 0.7929 (mpt) cc_final: 0.7685 (mpt) REVERT: B 133 PHE cc_start: 0.8111 (t80) cc_final: 0.7759 (t80) REVERT: B 137 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 215 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7488 (tmm) REVERT: C 173 LEU cc_start: 0.7967 (mp) cc_final: 0.7637 (mp) REVERT: D 37 ASP cc_start: 0.8418 (m-30) cc_final: 0.8198 (m-30) REVERT: D 60 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7958 (mp) REVERT: D 148 LEU cc_start: 0.8555 (mp) cc_final: 0.8336 (mt) REVERT: D 207 ASP cc_start: 0.7742 (t0) cc_final: 0.7482 (t0) REVERT: D 330 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8507 (m) REVERT: D 371 VAL cc_start: 0.8388 (t) cc_final: 0.8047 (m) outliers start: 56 outliers final: 33 residues processed: 279 average time/residue: 0.4324 time to fit residues: 130.0321 Evaluate side-chains 274 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 110 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.8768 > 50:) chunk 52 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 358 GLN D 42 ASN D 321 ASN D 335 ASN D 346 ASN D 358 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105512 restraints weight = 13653.805| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.20 r_work: 0.3225 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10050 Z= 0.148 Angle : 0.583 13.048 13624 Z= 0.295 Chirality : 0.043 0.182 1597 Planarity : 0.005 0.048 1723 Dihedral : 4.720 59.343 1348 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 5.16 % Allowed : 24.15 % Favored : 70.69 % 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: 0.62 (0.25), residues: 1232 helix: 2.03 (0.22), residues: 587 sheet: 0.21 (0.38), residues: 198 loop : -1.79 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 24 TYR 0.012 0.001 TYR B 223 PHE 0.023 0.001 PHE C 138 TRP 0.007 0.001 TRP C 129 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (10050) covalent geometry : angle 0.58270 / 0.29 (13624) hydrogen bonds : bond 0.04953 / 3.29 ( 502) hydrogen bonds : angle 4.24308 / 3.08 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 249 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7593 (t70) cc_final: 0.7349 (t70) REVERT: A 116 MET cc_start: 0.8300 (mpp) cc_final: 0.7935 (mpp) REVERT: B 137 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 215 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7585 (tmm) REVERT: C 173 LEU cc_start: 0.8003 (mp) cc_final: 0.7691 (mp) REVERT: D 37 ASP cc_start: 0.8446 (m-30) cc_final: 0.8222 (m-30) REVERT: D 60 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7940 (mp) REVERT: D 148 LEU cc_start: 0.8564 (mp) cc_final: 0.8338 (mt) REVERT: D 330 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8543 (m) outliers start: 56 outliers final: 35 residues processed: 283 average time/residue: 0.4584 time to fit residues: 139.0020 Evaluate side-chains 277 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.0870 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 185 GLN A 358 GLN D 42 ASN D 255 ASN D 321 ASN D 335 ASN D 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105413 restraints weight = 13607.409| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.19 r_work: 0.3225 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10050 Z= 0.151 Angle : 0.592 13.325 13624 Z= 0.299 Chirality : 0.043 0.182 1597 Planarity : 0.005 0.048 1723 Dihedral : 4.412 54.273 1346 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 5.16 % Allowed : 24.24 % Favored : 70.60 % 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: 0.63 (0.25), residues: 1232 helix: 2.04 (0.22), residues: 587 sheet: 0.22 (0.38), residues: 198 loop : -1.78 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 233 TYR 0.012 0.001 TYR B 223 PHE 0.029 0.001 PHE B 133 TRP 0.008 0.001 TRP C 129 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (10050) covalent geometry : angle 0.59187 / 0.30 (13624) hydrogen bonds : bond 0.04961 / 3.29 ( 502) hydrogen bonds : angle 4.23464 / 3.08 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 0.335 Fit side-chains REVERT: A 27 PHE cc_start: 0.7230 (t80) cc_final: 0.6892 (t80) REVERT: A 28 ASP cc_start: 0.7594 (t70) cc_final: 0.7318 (t70) REVERT: A 116 MET cc_start: 0.8292 (mpp) cc_final: 0.7956 (mpp) REVERT: B 133 PHE cc_start: 0.8059 (t80) cc_final: 0.7707 (t80) REVERT: B 137 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8130 (mp) REVERT: B 215 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7588 (tmm) REVERT: C 173 LEU cc_start: 0.8034 (mp) cc_final: 0.7716 (mp) REVERT: D 37 ASP cc_start: 0.8452 (m-30) cc_final: 0.8221 (m-30) REVERT: D 60 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7959 (mp) REVERT: D 148 LEU cc_start: 0.8544 (mp) cc_final: 0.8316 (mt) REVERT: D 330 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8536 (m) REVERT: D 371 VAL cc_start: 0.8389 (t) cc_final: 0.8051 (m) outliers start: 56 outliers final: 31 residues processed: 283 average time/residue: 0.4247 time to fit residues: 128.9415 Evaluate side-chains 276 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 10 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 42 ASN A 142 GLN A 154 GLN A 185 GLN A 358 GLN D 42 ASN D 321 ASN D 335 ASN D 346 ASN D 358 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108486 restraints weight = 13334.789| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.15 r_work: 0.3266 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10050 Z= 0.113 Angle : 0.578 13.378 13624 Z= 0.290 Chirality : 0.042 0.152 1597 Planarity : 0.005 0.052 1723 Dihedral : 4.261 54.138 1346 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 3.78 % Allowed : 25.71 % Favored : 70.51 % 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: 0.76 (0.25), residues: 1232 helix: 2.21 (0.23), residues: 584 sheet: 0.17 (0.38), residues: 198 loop : -1.74 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 233 TYR 0.009 0.001 TYR A 322 PHE 0.024 0.001 PHE B 133 TRP 0.012 0.001 TRP D 368 HIS 0.004 0.000 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10050) covalent geometry : angle 0.57812 / 0.29 (13624) hydrogen bonds : bond 0.03910 / 2.60 ( 502) hydrogen bonds : angle 4.06849 / 2.97 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 0.213 Fit side-chains REVERT: A 27 PHE cc_start: 0.7226 (t80) cc_final: 0.6885 (t80) REVERT: A 28 ASP cc_start: 0.7615 (t70) cc_final: 0.7350 (t70) REVERT: A 277 ASN cc_start: 0.8098 (m-40) cc_final: 0.7754 (p0) REVERT: B 133 PHE cc_start: 0.8034 (t80) cc_final: 0.7703 (t80) REVERT: B 137 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8126 (mp) REVERT: D 37 ASP cc_start: 0.8393 (m-30) cc_final: 0.8157 (m-30) REVERT: D 148 LEU cc_start: 0.8476 (mp) cc_final: 0.8261 (mt) REVERT: D 330 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8477 (m) outliers start: 41 outliers final: 21 residues processed: 267 average time/residue: 0.4518 time to fit residues: 129.6424 Evaluate side-chains 270 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 95 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 154 GLN A 358 GLN C 28 ASN D 321 ASN D 335 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107910 restraints weight = 13386.718| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.17 r_work: 0.3258 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10050 Z= 0.121 Angle : 0.585 12.425 13624 Z= 0.292 Chirality : 0.043 0.151 1597 Planarity : 0.005 0.056 1723 Dihedral : 4.192 53.745 1346 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 3.32 % Allowed : 27.10 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1232 helix: 2.24 (0.23), residues: 588 sheet: 0.16 (0.38), residues: 199 loop : -1.71 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 24 TYR 0.011 0.001 TYR B 223 PHE 0.024 0.001 PHE B 133 TRP 0.008 0.001 TRP D 368 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10050) covalent geometry : angle 0.58517 / 0.29 (13624) hydrogen bonds : bond 0.04111 / 2.74 ( 502) hydrogen bonds : angle 4.06273 / 2.97 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.363 Fit side-chains REVERT: A 27 PHE cc_start: 0.7213 (t80) cc_final: 0.6878 (t80) REVERT: A 277 ASN cc_start: 0.8084 (m-40) cc_final: 0.7732 (p0) REVERT: B 137 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 277 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6719 (mm) REVERT: C 25 LEU cc_start: 0.8046 (mp) cc_final: 0.7753 (mt) REVERT: C 173 LEU cc_start: 0.8030 (mp) cc_final: 0.7781 (mp) REVERT: D 37 ASP cc_start: 0.8417 (m-30) cc_final: 0.8182 (m-30) REVERT: D 140 PHE cc_start: 0.8043 (m-10) cc_final: 0.7682 (m-80) REVERT: D 148 LEU cc_start: 0.8470 (mp) cc_final: 0.8251 (mt) REVERT: D 329 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8245 (p) REVERT: D 330 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8512 (m) outliers start: 36 outliers final: 23 residues processed: 268 average time/residue: 0.4678 time to fit residues: 134.4618 Evaluate side-chains 270 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 116 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 51 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN A 42 ASN A 154 GLN D 321 ASN D 335 ASN D 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108091 restraints weight = 13346.678| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.15 r_work: 0.3259 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10050 Z= 0.122 Angle : 0.593 11.302 13624 Z= 0.295 Chirality : 0.043 0.149 1597 Planarity : 0.005 0.060 1723 Dihedral : 4.180 53.537 1346 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.22 % Favored : 95.70 % Rotamer: Outliers : 3.23 % Allowed : 26.91 % Favored : 69.86 % 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: 0.85 (0.25), residues: 1232 helix: 2.29 (0.22), residues: 586 sheet: 0.17 (0.38), residues: 198 loop : -1.70 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 24 TYR 0.010 0.001 TYR B 223 PHE 0.030 0.001 PHE B 133 TRP 0.008 0.001 TRP D 368 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (10050) covalent geometry : angle 0.59282 / 0.30 (13624) hydrogen bonds : bond 0.04075 / 2.71 ( 502) hydrogen bonds : angle 4.06090 / 2.97 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 27 PHE cc_start: 0.7210 (t80) cc_final: 0.6878 (t80) REVERT: A 277 ASN cc_start: 0.8079 (m-40) cc_final: 0.7729 (p0) REVERT: B 137 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8187 (mp) REVERT: B 277 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6707 (mm) REVERT: C 173 LEU cc_start: 0.8026 (mp) cc_final: 0.7763 (mp) REVERT: D 37 ASP cc_start: 0.8428 (m-30) cc_final: 0.8194 (m-30) REVERT: D 140 PHE cc_start: 0.8029 (m-10) cc_final: 0.7686 (m-80) REVERT: D 148 LEU cc_start: 0.8466 (mp) cc_final: 0.8247 (mt) REVERT: D 330 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8501 (m) outliers start: 35 outliers final: 26 residues processed: 267 average time/residue: 0.4590 time to fit residues: 131.4319 Evaluate side-chains 265 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 35 GLN Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 42 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 ASN A 154 GLN A 358 GLN C 28 ASN D 321 ASN D 335 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106364 restraints weight = 13381.395| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.17 r_work: 0.3232 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10050 Z= 0.158 Angle : 0.620 11.824 13624 Z= 0.310 Chirality : 0.044 0.233 1597 Planarity : 0.005 0.061 1723 Dihedral : 4.300 53.642 1346 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 2.86 % Allowed : 27.65 % Favored : 69.49 % 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: 0.78 (0.25), residues: 1232 helix: 2.26 (0.22), residues: 582 sheet: 0.17 (0.38), residues: 198 loop : -1.76 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 24 TYR 0.014 0.001 TYR B 223 PHE 0.031 0.001 PHE B 133 TRP 0.007 0.001 TRP C 129 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (10050) covalent geometry : angle 0.61964 / 0.31 (13624) hydrogen bonds : bond 0.04848 / 3.22 ( 502) hydrogen bonds : angle 4.15778 / 3.03 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.05 seconds wall clock time: 53 minutes 51.29 seconds (3231.29 seconds total)