Starting phenix.real_space_refine on Sat Jun 7 14:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfy_61444/06_2025/9jfy_61444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfy_61444/06_2025/9jfy_61444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jfy_61444/06_2025/9jfy_61444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfy_61444/06_2025/9jfy_61444.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfy_61444/06_2025/9jfy_61444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfy_61444/06_2025/9jfy_61444.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 66 5.16 5 C 5635 2.51 5 N 1482 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8805 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2323 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 97 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1631 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2568 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 414 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 5.68, per 1000 atoms: 0.65 Number of scatterers: 8805 At special positions: 0 Unit cell: (92.4, 119.7, 133.35, 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 66 16.00 O 1622 8.00 N 1482 7.00 C 5635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.1% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'R' and resid 41 through 73 removed outlier: 3.782A pdb=" N ILE R 55 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 98 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 114 through 149 removed outlier: 3.667A pdb=" N GLY R 126 " --> pdb=" O GLY R 122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 136 " --> pdb=" O SER R 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 181 Proline residue: R 177 - end of helix Processing helix chain 'R' and resid 212 through 228 Processing helix chain 'R' and resid 228 through 248 removed outlier: 3.571A pdb=" N LEU R 232 " --> pdb=" O TYR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 300 removed outlier: 3.647A pdb=" N TRP R 287 " --> pdb=" O PHE R 283 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'R' and resid 314 through 336 removed outlier: 3.566A pdb=" N SER R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN R 329 " --> pdb=" O ASN R 325 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 337 through 342 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.642A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.616A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.110A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.091A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.863A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.936A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.802A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 33 through 35 removed outlier: 6.284A pdb=" N THR R 33 " --> pdb=" O ARG R 191 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG R 193 " --> pdb=" O THR R 33 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL R 35 " --> pdb=" O ARG R 193 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL R 203 " --> pdb=" O GLU R 187 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N TYR R 189 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N SER R 201 " --> pdb=" O TYR R 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.882A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.332A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.833A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.957A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.139A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.961A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.604A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.760A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.793A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.400A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.592A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1266 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: 2.53 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2824 1.35 - 1.46: 2221 1.46 - 1.58: 3850 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 8994 Sorted by residual: bond pdb=" CA SER R 176 " pdb=" C SER R 176 " ideal model delta sigma weight residual 1.522 1.532 -0.010 1.26e-02 6.30e+03 6.85e-01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.78e-01 bond pdb=" C PHE L 11 " pdb=" O PHE L 11 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.16e-01 bond pdb=" N GLN R 197 " pdb=" CA GLN R 197 " ideal model delta sigma weight residual 1.462 1.473 -0.011 1.48e-02 4.57e+03 5.91e-01 bond pdb=" CB PHE L 11 " pdb=" CG PHE L 11 " ideal model delta sigma weight residual 1.502 1.485 0.017 2.30e-02 1.89e+03 5.63e-01 ... (remaining 8989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 11849 1.16 - 2.32: 283 2.32 - 3.47: 52 3.47 - 4.63: 12 4.63 - 5.79: 6 Bond angle restraints: 12202 Sorted by residual: angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.90 3.30 9.60e-01 1.09e+00 1.18e+01 angle pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" C TYR S 235 " ideal model delta sigma weight residual 109.81 115.60 -5.79 2.21e+00 2.05e-01 6.86e+00 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 109.80 4.10 1.80e+00 3.09e-01 5.19e+00 angle pdb=" C SER R 196 " pdb=" N GLN R 197 " pdb=" CA GLN R 197 " ideal model delta sigma weight residual 122.61 126.06 -3.45 1.56e+00 4.11e-01 4.89e+00 angle pdb=" CA PHE L 11 " pdb=" CB PHE L 11 " pdb=" CG PHE L 11 " ideal model delta sigma weight residual 113.80 111.72 2.08 1.00e+00 1.00e+00 4.31e+00 ... (remaining 12197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4670 17.55 - 35.09: 496 35.09 - 52.64: 127 52.64 - 70.19: 20 70.19 - 87.73: 6 Dihedral angle restraints: 5319 sinusoidal: 2024 harmonic: 3295 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 149.88 -56.88 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CA MET R 175 " pdb=" C MET R 175 " pdb=" N SER R 176 " pdb=" CA SER R 176 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 162.68 17.32 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 985 0.038 - 0.075: 287 0.075 - 0.113: 103 0.113 - 0.151: 17 0.151 - 0.188: 1 Chirality restraints: 1393 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE S 157 " pdb=" N ILE S 157 " pdb=" C ILE S 157 " pdb=" CB ILE S 157 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1390 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO S 236 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 205 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C TRP R 205 " -0.025 2.00e-02 2.50e+03 pdb=" O TRP R 205 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS R 206 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER R 303 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO R 304 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.019 5.00e-02 4.00e+02 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 879 2.75 - 3.29: 8226 3.29 - 3.82: 14519 3.82 - 4.36: 16574 4.36 - 4.90: 30510 Nonbonded interactions: 70708 Sorted by model distance: nonbonded pdb=" O LEU R 288 " pdb=" OG1 THR R 292 " model vdw 2.208 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.222 3.040 nonbonded pdb=" NE1 TRP R 287 " pdb=" OD1 ASN R 325 " model vdw 2.234 3.120 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.286 3.040 nonbonded pdb=" ND2 ASN B 155 " pdb=" OD1 ASP B 170 " model vdw 2.290 3.120 ... (remaining 70703 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: 2.030 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.480 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8998 Z= 0.131 Angle : 0.464 5.790 12208 Z= 0.254 Chirality : 0.041 0.188 1393 Planarity : 0.004 0.059 1541 Dihedral : 15.557 87.735 3182 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 20.30 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1113 helix: 2.51 (0.27), residues: 388 sheet: 0.71 (0.30), residues: 297 loop : -0.37 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 205 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR S 235 ARG 0.003 0.000 ARG R 207 Details of bonding type rmsd hydrogen bonds : bond 0.10903 ( 445) hydrogen bonds : angle 4.95434 ( 1266) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.00565 ( 6) covalent geometry : bond 0.00251 ( 8994) covalent geometry : angle 0.46323 (12202) Misc. bond : bond 0.06228 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 GLN cc_start: 0.7668 (mt0) cc_final: 0.7375 (mt0) REVERT: B 258 ASP cc_start: 0.7014 (t0) cc_final: 0.6691 (t70) REVERT: S 93 MET cc_start: 0.7019 (tpp) cc_final: 0.6797 (ttm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2486 time to fit residues: 61.0397 Evaluate side-chains 142 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN B 88 ASN B 259 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.201935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158701 restraints weight = 9656.167| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.65 r_work: 0.3540 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8998 Z= 0.141 Angle : 0.566 11.407 12208 Z= 0.299 Chirality : 0.043 0.198 1393 Planarity : 0.004 0.067 1541 Dihedral : 4.406 67.541 1222 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 19.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1113 helix: 2.55 (0.27), residues: 386 sheet: 0.60 (0.30), residues: 299 loop : -0.35 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS S 232 PHE 0.015 0.002 PHE B 253 TYR 0.014 0.001 TYR S 190 ARG 0.005 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 445) hydrogen bonds : angle 4.36227 ( 1266) SS BOND : bond 0.00561 ( 3) SS BOND : angle 0.92796 ( 6) covalent geometry : bond 0.00323 ( 8994) covalent geometry : angle 0.56550 (12202) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7862 (m170) cc_final: 0.7490 (m-70) REVERT: A 197 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8197 (mtpp) REVERT: B 19 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7205 (tpt170) REVERT: S 46 GLU cc_start: 0.7594 (tt0) cc_final: 0.7157 (mt-10) REVERT: S 142 GLN cc_start: 0.6385 (mm-40) cc_final: 0.6009 (mt0) outliers start: 27 outliers final: 15 residues processed: 165 average time/residue: 0.2308 time to fit residues: 51.6247 Evaluate side-chains 139 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 226 ASN R 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.195964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.152067 restraints weight = 9712.164| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.48 r_work: 0.3523 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8998 Z= 0.175 Angle : 0.582 7.696 12208 Z= 0.309 Chirality : 0.043 0.248 1393 Planarity : 0.004 0.062 1541 Dihedral : 4.629 71.850 1222 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.36 % Allowed : 19.13 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1113 helix: 2.38 (0.27), residues: 386 sheet: 0.39 (0.29), residues: 303 loop : -0.47 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE B 199 TYR 0.019 0.002 TYR S 235 ARG 0.008 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 445) hydrogen bonds : angle 4.38176 ( 1266) SS BOND : bond 0.00683 ( 3) SS BOND : angle 1.06859 ( 6) covalent geometry : bond 0.00419 ( 8994) covalent geometry : angle 0.58212 (12202) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 183 HIS cc_start: 0.4922 (OUTLIER) cc_final: 0.4236 (p-80) REVERT: R 191 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.7586 (mmt-90) REVERT: R 193 ARG cc_start: 0.6094 (mpt-90) cc_final: 0.5881 (mpt-90) REVERT: R 241 ARG cc_start: 0.7832 (mtt90) cc_final: 0.7536 (mtt-85) REVERT: A 188 HIS cc_start: 0.8015 (m170) cc_final: 0.7772 (m-70) REVERT: A 297 GLU cc_start: 0.6419 (tm-30) cc_final: 0.5229 (mt-10) REVERT: A 298 GLU cc_start: 0.6547 (tp30) cc_final: 0.6268 (tp30) REVERT: B 175 GLN cc_start: 0.8352 (pp30) cc_final: 0.7762 (mm-40) REVERT: B 239 ASN cc_start: 0.8007 (m-40) cc_final: 0.7718 (m110) REVERT: S 18 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7793 (tpt170) REVERT: S 38 ARG cc_start: 0.8314 (ptt180) cc_final: 0.8068 (ptt180) REVERT: S 76 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7590 (mtmm) REVERT: S 142 GLN cc_start: 0.6521 (mm-40) cc_final: 0.6179 (mt0) REVERT: S 179 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.6852 (tp40) outliers start: 41 outliers final: 25 residues processed: 171 average time/residue: 0.2248 time to fit residues: 51.8591 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 1 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN R 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.199611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155090 restraints weight = 9629.691| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.50 r_work: 0.3569 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8998 Z= 0.102 Angle : 0.513 6.898 12208 Z= 0.270 Chirality : 0.041 0.183 1393 Planarity : 0.004 0.064 1541 Dihedral : 4.310 67.588 1222 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.08 % Allowed : 20.40 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.26), residues: 1113 helix: 2.62 (0.28), residues: 377 sheet: 0.38 (0.29), residues: 297 loop : -0.48 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 205 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE R 56 TYR 0.016 0.001 TYR S 60 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 445) hydrogen bonds : angle 4.11363 ( 1266) SS BOND : bond 0.00541 ( 3) SS BOND : angle 1.20832 ( 6) covalent geometry : bond 0.00222 ( 8994) covalent geometry : angle 0.51262 (12202) Misc. bond : bond 0.00031 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 191 ARG cc_start: 0.7975 (mmt-90) cc_final: 0.7573 (mmt-90) REVERT: R 193 ARG cc_start: 0.6079 (mpt-90) cc_final: 0.5847 (mpt-90) REVERT: A 260 THR cc_start: 0.8113 (t) cc_final: 0.7737 (p) REVERT: A 297 GLU cc_start: 0.6416 (tm-30) cc_final: 0.5267 (mt-10) REVERT: A 298 GLU cc_start: 0.6521 (tp30) cc_final: 0.6300 (tp30) REVERT: B 175 GLN cc_start: 0.8279 (pp30) cc_final: 0.7693 (mm-40) REVERT: S 38 ARG cc_start: 0.8269 (ptt180) cc_final: 0.7948 (ptt180) REVERT: S 93 MET cc_start: 0.7924 (ttm) cc_final: 0.7446 (ttm) REVERT: S 140 MET cc_start: 0.8527 (mmm) cc_final: 0.8122 (mmm) REVERT: S 142 GLN cc_start: 0.6324 (mm-40) cc_final: 0.5840 (mt0) outliers start: 29 outliers final: 15 residues processed: 165 average time/residue: 0.2383 time to fit residues: 52.6204 Evaluate side-chains 140 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 61 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 226 ASN R 308 GLN A 195 HIS A 311 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.199102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155354 restraints weight = 9638.590| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.42 r_work: 0.3571 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8998 Z= 0.112 Angle : 0.514 7.440 12208 Z= 0.271 Chirality : 0.041 0.177 1393 Planarity : 0.004 0.065 1541 Dihedral : 4.272 67.997 1222 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.51 % Allowed : 21.25 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1113 helix: 2.40 (0.28), residues: 390 sheet: 0.46 (0.28), residues: 295 loop : -0.43 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 205 HIS 0.004 0.001 HIS S 35 PHE 0.028 0.001 PHE S 68 TYR 0.013 0.001 TYR S 235 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 445) hydrogen bonds : angle 4.11181 ( 1266) SS BOND : bond 0.00556 ( 3) SS BOND : angle 1.05494 ( 6) covalent geometry : bond 0.00253 ( 8994) covalent geometry : angle 0.51381 (12202) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 193 ARG cc_start: 0.6171 (mpt-90) cc_final: 0.5926 (mpt-90) REVERT: A 20 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 243 MET cc_start: 0.6290 (tmm) cc_final: 0.5953 (tmm) REVERT: A 260 THR cc_start: 0.8175 (t) cc_final: 0.7836 (p) REVERT: A 297 GLU cc_start: 0.6488 (tm-30) cc_final: 0.5390 (mt-10) REVERT: A 322 HIS cc_start: 0.5680 (OUTLIER) cc_final: 0.4440 (m-70) REVERT: B 175 GLN cc_start: 0.8309 (pp30) cc_final: 0.7719 (mm-40) REVERT: S 38 ARG cc_start: 0.8250 (ptt180) cc_final: 0.7976 (ptt180) REVERT: S 93 MET cc_start: 0.7878 (ttm) cc_final: 0.7428 (ttm) REVERT: S 142 GLN cc_start: 0.6425 (mm-40) cc_final: 0.5973 (mt0) REVERT: S 179 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6830 (tp40) outliers start: 33 outliers final: 25 residues processed: 155 average time/residue: 0.2252 time to fit residues: 47.0853 Evaluate side-chains 157 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154225 restraints weight = 9535.247| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.33 r_work: 0.3559 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8998 Z= 0.128 Angle : 0.532 7.627 12208 Z= 0.283 Chirality : 0.042 0.195 1393 Planarity : 0.004 0.064 1541 Dihedral : 4.360 68.438 1222 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.04 % Allowed : 21.25 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1113 helix: 2.27 (0.27), residues: 388 sheet: 0.42 (0.28), residues: 300 loop : -0.44 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.002 PHE S 68 TYR 0.015 0.001 TYR S 60 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 445) hydrogen bonds : angle 4.21825 ( 1266) SS BOND : bond 0.00571 ( 3) SS BOND : angle 1.01909 ( 6) covalent geometry : bond 0.00299 ( 8994) covalent geometry : angle 0.53115 (12202) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.6221 (t0) cc_final: 0.5083 (m-40) REVERT: R 191 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7547 (mmt-90) REVERT: R 193 ARG cc_start: 0.6211 (mpt-90) cc_final: 0.5986 (mpt-90) REVERT: A 20 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 243 MET cc_start: 0.6357 (tmm) cc_final: 0.5960 (tmm) REVERT: A 260 THR cc_start: 0.8169 (t) cc_final: 0.7862 (p) REVERT: A 297 GLU cc_start: 0.6461 (tm-30) cc_final: 0.5355 (mt-10) REVERT: A 298 GLU cc_start: 0.6841 (tp30) cc_final: 0.6425 (tp30) REVERT: A 322 HIS cc_start: 0.5672 (OUTLIER) cc_final: 0.4332 (m-70) REVERT: B 175 GLN cc_start: 0.8405 (pp30) cc_final: 0.7767 (mm-40) REVERT: B 219 ARG cc_start: 0.8221 (mpt180) cc_final: 0.7929 (mmt180) REVERT: B 335 PHE cc_start: 0.8188 (m-80) cc_final: 0.7795 (m-80) REVERT: S 19 LYS cc_start: 0.8164 (tttm) cc_final: 0.7835 (tttt) REVERT: S 38 ARG cc_start: 0.8235 (ptt180) cc_final: 0.7963 (ptt180) REVERT: S 93 MET cc_start: 0.7890 (ttm) cc_final: 0.7467 (ttm) REVERT: S 140 MET cc_start: 0.8522 (mmm) cc_final: 0.8164 (mmm) REVERT: S 142 GLN cc_start: 0.6611 (mt0) cc_final: 0.6181 (mt0) REVERT: S 179 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.6822 (tp40) outliers start: 38 outliers final: 28 residues processed: 169 average time/residue: 0.2401 time to fit residues: 54.9584 Evaluate side-chains 167 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.0270 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 0.0570 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 59 optimal weight: 0.3980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.200911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157037 restraints weight = 9601.241| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.37 r_work: 0.3603 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8998 Z= 0.095 Angle : 0.490 7.026 12208 Z= 0.260 Chirality : 0.041 0.193 1393 Planarity : 0.004 0.064 1541 Dihedral : 4.189 65.471 1222 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.29 % Allowed : 22.00 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1113 helix: 2.40 (0.28), residues: 388 sheet: 0.54 (0.29), residues: 295 loop : -0.39 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.002 0.001 HIS S 35 PHE 0.015 0.001 PHE A 336 TYR 0.015 0.001 TYR S 60 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 445) hydrogen bonds : angle 4.06561 ( 1266) SS BOND : bond 0.00525 ( 3) SS BOND : angle 0.78450 ( 6) covalent geometry : bond 0.00205 ( 8994) covalent geometry : angle 0.48936 (12202) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5839 (t0) cc_final: 0.4890 (m-40) REVERT: A 243 MET cc_start: 0.6189 (tmm) cc_final: 0.5832 (tmm) REVERT: A 260 THR cc_start: 0.8064 (t) cc_final: 0.7770 (p) REVERT: A 297 GLU cc_start: 0.6552 (tm-30) cc_final: 0.5463 (mt-10) REVERT: A 298 GLU cc_start: 0.6837 (tp30) cc_final: 0.6474 (tp30) REVERT: A 322 HIS cc_start: 0.5668 (OUTLIER) cc_final: 0.4341 (m-70) REVERT: B 175 GLN cc_start: 0.8404 (pp30) cc_final: 0.7742 (mm-40) REVERT: B 335 PHE cc_start: 0.8110 (m-80) cc_final: 0.7703 (m-80) REVERT: G 27 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8339 (mtt-85) REVERT: S 19 LYS cc_start: 0.8092 (tttm) cc_final: 0.7796 (tttt) REVERT: S 38 ARG cc_start: 0.8207 (ptt180) cc_final: 0.7980 (ptt180) REVERT: S 46 GLU cc_start: 0.7581 (tt0) cc_final: 0.7049 (mt-10) REVERT: S 93 MET cc_start: 0.7893 (ttm) cc_final: 0.7436 (ttm) REVERT: S 140 MET cc_start: 0.8521 (mmm) cc_final: 0.8146 (mmm) REVERT: S 142 GLN cc_start: 0.6516 (mt0) cc_final: 0.6054 (mt0) REVERT: S 179 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6836 (tp40) outliers start: 31 outliers final: 26 residues processed: 157 average time/residue: 0.3012 time to fit residues: 61.6669 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 62 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.199603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155777 restraints weight = 9826.085| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.64 r_work: 0.3550 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8998 Z= 0.113 Angle : 0.516 6.975 12208 Z= 0.273 Chirality : 0.041 0.169 1393 Planarity : 0.004 0.066 1541 Dihedral : 4.232 66.729 1222 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.61 % Allowed : 21.47 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1113 helix: 2.36 (0.27), residues: 388 sheet: 0.46 (0.29), residues: 295 loop : -0.40 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.022 0.001 PHE S 68 TYR 0.015 0.001 TYR S 60 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 445) hydrogen bonds : angle 4.12764 ( 1266) SS BOND : bond 0.00551 ( 3) SS BOND : angle 0.85301 ( 6) covalent geometry : bond 0.00258 ( 8994) covalent geometry : angle 0.51575 (12202) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5870 (t0) cc_final: 0.4916 (m-40) REVERT: R 47 ILE cc_start: 0.7539 (tp) cc_final: 0.7063 (pt) REVERT: R 191 ARG cc_start: 0.8006 (mmt-90) cc_final: 0.7767 (mmt-90) REVERT: R 193 ARG cc_start: 0.6264 (mpt-90) cc_final: 0.6028 (mpt-90) REVERT: A 243 MET cc_start: 0.6287 (tmm) cc_final: 0.5921 (tmm) REVERT: A 260 THR cc_start: 0.8005 (t) cc_final: 0.7733 (p) REVERT: A 297 GLU cc_start: 0.6730 (tm-30) cc_final: 0.5677 (mt-10) REVERT: A 298 GLU cc_start: 0.6811 (tp30) cc_final: 0.6468 (tp30) REVERT: A 314 LYS cc_start: 0.7634 (mttp) cc_final: 0.7332 (mmmt) REVERT: A 322 HIS cc_start: 0.5695 (OUTLIER) cc_final: 0.4377 (m-70) REVERT: B 217 MET cc_start: 0.7277 (ppp) cc_final: 0.7037 (ppp) REVERT: B 335 PHE cc_start: 0.8102 (m-80) cc_final: 0.7745 (m-80) REVERT: S 38 ARG cc_start: 0.8217 (ptt180) cc_final: 0.7987 (ptt180) REVERT: S 46 GLU cc_start: 0.7644 (tt0) cc_final: 0.7099 (mt-10) REVERT: S 93 MET cc_start: 0.7919 (ttm) cc_final: 0.7508 (ttm) REVERT: S 140 MET cc_start: 0.8522 (mmm) cc_final: 0.8130 (mmm) REVERT: S 142 GLN cc_start: 0.6550 (mt0) cc_final: 0.6074 (mt0) REVERT: S 179 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6842 (tp40) outliers start: 34 outliers final: 29 residues processed: 159 average time/residue: 0.2448 time to fit residues: 52.7595 Evaluate side-chains 164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 108 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.198759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155135 restraints weight = 9705.903| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.37 r_work: 0.3584 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8998 Z= 0.118 Angle : 0.520 7.288 12208 Z= 0.276 Chirality : 0.041 0.173 1393 Planarity : 0.004 0.064 1541 Dihedral : 4.274 67.376 1222 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.61 % Allowed : 21.57 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.26), residues: 1113 helix: 2.34 (0.27), residues: 387 sheet: 0.45 (0.29), residues: 295 loop : -0.43 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR S 60 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 445) hydrogen bonds : angle 4.16551 ( 1266) SS BOND : bond 0.00543 ( 3) SS BOND : angle 0.86539 ( 6) covalent geometry : bond 0.00270 ( 8994) covalent geometry : angle 0.51986 (12202) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5801 (t0) cc_final: 0.4908 (m-40) REVERT: R 47 ILE cc_start: 0.7436 (tp) cc_final: 0.7014 (pt) REVERT: R 92 LEU cc_start: 0.8284 (tp) cc_final: 0.7967 (tp) REVERT: A 197 LYS cc_start: 0.8525 (mtpp) cc_final: 0.8324 (mtmm) REVERT: A 243 MET cc_start: 0.6442 (tmm) cc_final: 0.5998 (tmm) REVERT: A 297 GLU cc_start: 0.6724 (tm-30) cc_final: 0.5692 (mt-10) REVERT: A 298 GLU cc_start: 0.6840 (tp30) cc_final: 0.6488 (tp30) REVERT: A 314 LYS cc_start: 0.7703 (mttp) cc_final: 0.7270 (mmmt) REVERT: B 335 PHE cc_start: 0.8134 (m-80) cc_final: 0.7806 (m-80) REVERT: S 38 ARG cc_start: 0.8204 (ptt180) cc_final: 0.7991 (ptt180) REVERT: S 46 GLU cc_start: 0.7625 (tt0) cc_final: 0.7105 (mt-10) REVERT: S 93 MET cc_start: 0.7874 (ttm) cc_final: 0.7487 (ttm) REVERT: S 142 GLN cc_start: 0.6541 (mt0) cc_final: 0.6081 (mt0) REVERT: S 179 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6781 (tp40) outliers start: 34 outliers final: 27 residues processed: 159 average time/residue: 0.2100 time to fit residues: 45.9636 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 2.9990 chunk 92 optimal weight: 0.0060 chunk 106 optimal weight: 0.2980 chunk 20 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 87 optimal weight: 0.0020 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 35 optimal weight: 0.7980 overall best weight: 0.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.203737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.160456 restraints weight = 9763.192| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.38 r_work: 0.3650 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8998 Z= 0.094 Angle : 0.489 6.543 12208 Z= 0.259 Chirality : 0.040 0.150 1393 Planarity : 0.004 0.065 1541 Dihedral : 4.020 63.330 1222 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.59 % Allowed : 23.49 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1113 helix: 2.43 (0.27), residues: 387 sheet: 0.53 (0.29), residues: 295 loop : -0.30 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.004 0.000 HIS A 322 PHE 0.013 0.001 PHE R 56 TYR 0.015 0.001 TYR S 60 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03024 ( 445) hydrogen bonds : angle 4.01567 ( 1266) SS BOND : bond 0.00463 ( 3) SS BOND : angle 0.59571 ( 6) covalent geometry : bond 0.00196 ( 8994) covalent geometry : angle 0.48902 (12202) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5799 (t0) cc_final: 0.4987 (m-40) REVERT: R 47 ILE cc_start: 0.7226 (tp) cc_final: 0.6885 (pt) REVERT: R 92 LEU cc_start: 0.8359 (tp) cc_final: 0.8110 (tp) REVERT: R 191 ARG cc_start: 0.7889 (mmt-90) cc_final: 0.7650 (mmt-90) REVERT: A 197 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8272 (mtmm) REVERT: A 243 MET cc_start: 0.6291 (tmm) cc_final: 0.5896 (tmm) REVERT: A 297 GLU cc_start: 0.6882 (tm-30) cc_final: 0.5878 (mt-10) REVERT: A 298 GLU cc_start: 0.6811 (tp30) cc_final: 0.6494 (tp30) REVERT: A 314 LYS cc_start: 0.7749 (mttp) cc_final: 0.7298 (mmmt) REVERT: B 175 GLN cc_start: 0.8329 (pp30) cc_final: 0.7503 (mp10) REVERT: B 335 PHE cc_start: 0.8028 (m-80) cc_final: 0.7766 (m-80) REVERT: S 46 GLU cc_start: 0.7438 (tt0) cc_final: 0.6979 (mt-10) outliers start: 15 outliers final: 14 residues processed: 154 average time/residue: 0.2337 time to fit residues: 49.5484 Evaluate side-chains 142 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain L residue 5 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 226 ASN A 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.198046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.154948 restraints weight = 9763.746| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.49 r_work: 0.3520 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8998 Z= 0.136 Angle : 0.545 7.226 12208 Z= 0.290 Chirality : 0.042 0.173 1393 Planarity : 0.004 0.066 1541 Dihedral : 4.261 67.581 1222 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.23 % Allowed : 23.38 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1113 helix: 2.46 (0.27), residues: 383 sheet: 0.46 (0.29), residues: 300 loop : -0.31 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.010 0.001 TYR B 59 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 445) hydrogen bonds : angle 4.21493 ( 1266) SS BOND : bond 0.00569 ( 3) SS BOND : angle 0.89824 ( 6) covalent geometry : bond 0.00321 ( 8994) covalent geometry : angle 0.54490 (12202) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5007.83 seconds wall clock time: 87 minutes 31.92 seconds (5251.92 seconds total)