Starting phenix.real_space_refine on Wed Sep 17 13:04:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfy_61444/09_2025/9jfy_61444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfy_61444/09_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_61444/09_2025/9jfy_61444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfy_61444/09_2025/9jfy_61444.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfy_61444/09_2025/9jfy_61444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfy_61444/09_2025/9jfy_61444.cif" } resolution = 3.21 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= -0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2, 'TRP: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: 2.24, per 1000 atoms: 0.25 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: 0.76 Conformation dependent library (CDL) restraints added in 480.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.27 Time building geometry restraints manager: 1.01 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.590 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.910 ------------------------------------------------------------------------------- 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 : 5.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG R 207 TYR 0.015 0.001 TYR S 235 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP R 205 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8994) covalent geometry : angle 0.46323 (12202) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.00565 ( 6) hydrogen bonds : bond 0.10903 ( 445) hydrogen bonds : angle 4.95434 ( 1266) 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 : 0.242 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: 0.6690 (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: 0.1076 time to fit residues: 26.7330 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 : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- 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 S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.202346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159375 restraints weight = 9650.818| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 2.57 r_work: 0.3566 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8998 Z= 0.148 Angle : 0.568 10.361 12208 Z= 0.302 Chirality : 0.043 0.205 1393 Planarity : 0.004 0.067 1541 Dihedral : 4.422 67.301 1222 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.08 % Allowed : 19.23 % Favored : 77.68 % 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 aren not related in a simple way. whole: 1.35 (0.26), residues: 1113 helix: 2.55 (0.27), residues: 384 sheet: 0.60 (0.30), residues: 299 loop : -0.39 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.014 0.001 TYR S 235 PHE 0.016 0.002 PHE B 253 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8994) covalent geometry : angle 0.56774 (12202) SS BOND : bond 0.00557 ( 3) SS BOND : angle 0.93990 ( 6) hydrogen bonds : bond 0.03961 ( 445) hydrogen bonds : angle 4.39160 ( 1266) Misc. bond : bond 0.00148 ( 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: 29 poor density : 143 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 191 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7693 (mmt-90) REVERT: A 188 HIS cc_start: 0.7856 (m170) cc_final: 0.7525 (m-70) REVERT: A 197 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8201 (mtpp) REVERT: B 19 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7264 (tpt170) outliers start: 29 outliers final: 15 residues processed: 165 average time/residue: 0.1104 time to fit residues: 24.6095 Evaluate side-chains 133 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 76 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.0170 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4274 r_free = 0.4274 target = 0.200552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156998 restraints weight = 9683.496| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.71 r_work: 0.3535 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8998 Z= 0.123 Angle : 0.525 7.586 12208 Z= 0.278 Chirality : 0.041 0.194 1393 Planarity : 0.004 0.064 1541 Dihedral : 4.310 67.561 1222 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.51 % Allowed : 19.66 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.26), residues: 1113 helix: 2.65 (0.27), residues: 377 sheet: 0.53 (0.29), residues: 297 loop : -0.38 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 241 TYR 0.013 0.001 TYR S 235 PHE 0.014 0.001 PHE R 56 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8994) covalent geometry : angle 0.52460 (12202) SS BOND : bond 0.00620 ( 3) SS BOND : angle 0.79360 ( 6) hydrogen bonds : bond 0.03621 ( 445) hydrogen bonds : angle 4.16035 ( 1266) Misc. bond : bond 0.00053 ( 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 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 117 MET cc_start: 0.5922 (tpp) cc_final: 0.5685 (tpp) REVERT: R 191 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7649 (mmt-90) REVERT: A 188 HIS cc_start: 0.7944 (m170) cc_final: 0.7659 (m-70) REVERT: A 324 THR cc_start: 0.7598 (m) cc_final: 0.7363 (p) REVERT: B 19 ARG cc_start: 0.7487 (mtt90) cc_final: 0.7222 (tpt170) REVERT: S 38 ARG cc_start: 0.8325 (ptt180) cc_final: 0.8054 (ptt180) REVERT: S 142 GLN cc_start: 0.6486 (mm-40) cc_final: 0.5894 (mt0) REVERT: S 179 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7018 (tp40) outliers start: 33 outliers final: 16 residues processed: 161 average time/residue: 0.1056 time to fit residues: 23.0422 Evaluate side-chains 143 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain A residue 28 GLU 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN R 311 ASN G 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.199144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155380 restraints weight = 9875.978| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.75 r_work: 0.3531 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8998 Z= 0.128 Angle : 0.529 6.480 12208 Z= 0.282 Chirality : 0.042 0.198 1393 Planarity : 0.004 0.065 1541 Dihedral : 4.365 68.526 1222 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.83 % Allowed : 20.09 % Favored : 76.09 % 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 aren not related in a simple way. whole: 1.26 (0.26), residues: 1113 helix: 2.60 (0.28), residues: 377 sheet: 0.44 (0.29), residues: 297 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 241 TYR 0.015 0.001 TYR S 235 PHE 0.018 0.002 PHE S 68 TRP 0.010 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8994) covalent geometry : angle 0.52901 (12202) SS BOND : bond 0.00574 ( 3) SS BOND : angle 1.03653 ( 6) hydrogen bonds : bond 0.03668 ( 445) hydrogen bonds : angle 4.15797 ( 1266) Misc. bond : bond 0.00055 ( 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 173 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 117 MET cc_start: 0.5793 (tpp) cc_final: 0.5590 (tpp) REVERT: R 183 HIS cc_start: 0.4902 (OUTLIER) cc_final: 0.4130 (p-80) REVERT: R 191 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7465 (mmt-90) REVERT: R 193 ARG cc_start: 0.6068 (mpt-90) cc_final: 0.5806 (mpt-90) REVERT: L 6 PHE cc_start: 0.7384 (m-80) cc_final: 0.7159 (m-80) REVERT: A 20 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8016 (m-30) REVERT: A 297 GLU cc_start: 0.6570 (tm-30) cc_final: 0.5427 (mt-10) REVERT: A 298 GLU cc_start: 0.6765 (tp30) cc_final: 0.6368 (tp30) REVERT: B 175 GLN cc_start: 0.8305 (pp30) cc_final: 0.7704 (mm-40) REVERT: B 217 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7386 (ptm) REVERT: S 19 LYS cc_start: 0.8164 (tttm) cc_final: 0.7933 (tttt) REVERT: S 38 ARG cc_start: 0.8270 (ptt180) cc_final: 0.7961 (ptt180) REVERT: S 140 MET cc_start: 0.8493 (mmm) cc_final: 0.8073 (mmm) REVERT: S 142 GLN cc_start: 0.6344 (mm-40) cc_final: 0.5856 (mt0) REVERT: S 179 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6989 (tp40) outliers start: 36 outliers final: 26 residues processed: 164 average time/residue: 0.1103 time to fit residues: 24.1291 Evaluate side-chains 158 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 183 HIS Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 332 ILE 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 B residue 138 GLU 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 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 22 CYS Chi-restraints excluded: chain S residue 69 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 62 optimal weight: 0.0170 chunk 108 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN A 195 HIS A 311 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.200752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157456 restraints weight = 9791.874| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.69 r_work: 0.3558 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8998 Z= 0.101 Angle : 0.500 6.300 12208 Z= 0.265 Chirality : 0.041 0.174 1393 Planarity : 0.004 0.062 1541 Dihedral : 4.212 66.406 1222 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.08 % Allowed : 21.15 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.26), residues: 1113 helix: 2.56 (0.27), residues: 382 sheet: 0.49 (0.29), residues: 292 loop : -0.43 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 241 TYR 0.016 0.001 TYR S 60 PHE 0.017 0.001 PHE S 68 TRP 0.009 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 8994) covalent geometry : angle 0.49950 (12202) SS BOND : bond 0.00531 ( 3) SS BOND : angle 0.72670 ( 6) hydrogen bonds : bond 0.03330 ( 445) hydrogen bonds : angle 4.05391 ( 1266) Misc. bond : bond 0.00029 ( 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 174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 99 MET cc_start: 0.7052 (mtp) cc_final: 0.6774 (mtp) REVERT: R 193 ARG cc_start: 0.6084 (mpt-90) cc_final: 0.5820 (mpt-90) REVERT: R 315 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7309 (t80) REVERT: A 20 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.8006 (m-30) REVERT: A 243 MET cc_start: 0.6202 (tmm) cc_final: 0.5862 (tmm) REVERT: A 260 THR cc_start: 0.8119 (t) cc_final: 0.7743 (p) REVERT: A 297 GLU cc_start: 0.6432 (tm-30) cc_final: 0.5284 (mt-10) REVERT: A 298 GLU cc_start: 0.6713 (tp30) cc_final: 0.6384 (tp30) REVERT: A 322 HIS cc_start: 0.5745 (OUTLIER) cc_final: 0.4468 (m-70) REVERT: B 175 GLN cc_start: 0.8329 (pp30) cc_final: 0.7683 (mm-40) REVERT: S 19 LYS cc_start: 0.8116 (tttm) cc_final: 0.7820 (tttt) REVERT: S 38 ARG cc_start: 0.8233 (ptt180) cc_final: 0.8030 (ptt180) REVERT: S 46 GLU cc_start: 0.7673 (tt0) cc_final: 0.7131 (mt-10) REVERT: S 142 GLN cc_start: 0.6290 (mm-40) cc_final: 0.5777 (mt0) outliers start: 29 outliers final: 21 residues processed: 164 average time/residue: 0.1126 time to fit residues: 24.6122 Evaluate side-chains 152 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 157 ILE Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain R residue 328 VAL 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 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 183 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 75 GLN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154466 restraints weight = 9809.493| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.67 r_work: 0.3527 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8998 Z= 0.134 Angle : 0.533 7.846 12208 Z= 0.285 Chirality : 0.042 0.195 1393 Planarity : 0.004 0.066 1541 Dihedral : 4.398 68.320 1222 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.04 % Allowed : 21.68 % Favored : 74.28 % 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 aren not related in a simple way. whole: 1.15 (0.26), residues: 1113 helix: 2.41 (0.27), residues: 382 sheet: 0.45 (0.29), residues: 295 loop : -0.47 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 241 TYR 0.016 0.001 TYR S 60 PHE 0.028 0.002 PHE S 68 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8994) covalent geometry : angle 0.53308 (12202) SS BOND : bond 0.00588 ( 3) SS BOND : angle 0.86071 ( 6) hydrogen bonds : bond 0.03734 ( 445) hydrogen bonds : angle 4.19522 ( 1266) Misc. bond : bond 0.00061 ( 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 180 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 191 ARG cc_start: 0.7888 (mmt-90) cc_final: 0.7571 (mmt-90) REVERT: R 193 ARG cc_start: 0.6214 (mpt-90) cc_final: 0.5962 (mpt-90) REVERT: A 20 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: A 197 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8113 (mtmm) REVERT: A 243 MET cc_start: 0.6346 (tmm) cc_final: 0.5959 (tmm) REVERT: A 260 THR cc_start: 0.8109 (t) cc_final: 0.7763 (p) REVERT: A 297 GLU cc_start: 0.6623 (tm-30) cc_final: 0.5514 (mt-10) REVERT: A 298 GLU cc_start: 0.6834 (tp30) cc_final: 0.6573 (tp30) REVERT: A 322 HIS cc_start: 0.5750 (OUTLIER) cc_final: 0.4421 (m-70) REVERT: B 172 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7269 (pm20) REVERT: B 175 GLN cc_start: 0.8342 (pp30) cc_final: 0.7491 (mp10) REVERT: B 335 PHE cc_start: 0.8100 (m-80) cc_final: 0.7705 (m-80) REVERT: S 19 LYS cc_start: 0.8127 (tttm) cc_final: 0.7815 (tttt) REVERT: S 38 ARG cc_start: 0.8240 (ptt180) cc_final: 0.7975 (ptt180) REVERT: S 76 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7655 (mtmm) REVERT: S 140 MET cc_start: 0.8524 (mmm) cc_final: 0.8149 (mmm) REVERT: S 142 GLN cc_start: 0.6630 (mm-40) cc_final: 0.6211 (mt0) REVERT: S 179 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.6902 (tp40) outliers start: 38 outliers final: 29 residues processed: 165 average time/residue: 0.1018 time to fit residues: 22.7786 Evaluate side-chains 167 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 246 LEU Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 315 TYR 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 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 172 GLU 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 22 CYS 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 10 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.200355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157206 restraints weight = 9854.779| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.68 r_work: 0.3558 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4108 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= 0.104 Angle : 0.511 8.592 12208 Z= 0.271 Chirality : 0.041 0.170 1393 Planarity : 0.004 0.063 1541 Dihedral : 4.241 65.903 1222 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.29 % Allowed : 22.42 % Favored : 74.28 % 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 aren not related in a simple way. whole: 1.21 (0.26), residues: 1113 helix: 2.39 (0.27), residues: 388 sheet: 0.45 (0.29), residues: 300 loop : -0.40 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 241 TYR 0.015 0.001 TYR S 60 PHE 0.021 0.001 PHE S 68 TRP 0.010 0.001 TRP R 205 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8994) covalent geometry : angle 0.51093 (12202) SS BOND : bond 0.00515 ( 3) SS BOND : angle 0.95260 ( 6) hydrogen bonds : bond 0.03303 ( 445) hydrogen bonds : angle 4.07885 ( 1266) Misc. bond : bond 0.00036 ( 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 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.6045 (t0) cc_final: 0.5002 (m-40) REVERT: R 47 ILE cc_start: 0.7511 (tp) cc_final: 0.7031 (pt) REVERT: A 243 MET cc_start: 0.6315 (tmm) cc_final: 0.5922 (tmm) REVERT: A 260 THR cc_start: 0.8076 (t) cc_final: 0.7771 (p) REVERT: A 297 GLU cc_start: 0.6732 (tm-30) cc_final: 0.5651 (mt-10) REVERT: A 322 HIS cc_start: 0.5738 (OUTLIER) cc_final: 0.4378 (m-70) REVERT: B 170 ASP cc_start: 0.8029 (t0) cc_final: 0.7624 (t0) REVERT: B 172 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: B 175 GLN cc_start: 0.8387 (pp30) cc_final: 0.7560 (mp10) REVERT: B 335 PHE cc_start: 0.8106 (m-80) cc_final: 0.7754 (m-80) REVERT: S 19 LYS cc_start: 0.8105 (tttm) cc_final: 0.7790 (tttt) REVERT: S 46 GLU cc_start: 0.7639 (tt0) cc_final: 0.7116 (mt-10) REVERT: S 140 MET cc_start: 0.8534 (mmm) cc_final: 0.8114 (mmm) REVERT: S 142 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6133 (mt0) REVERT: S 179 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6861 (tp40) outliers start: 31 outliers final: 22 residues processed: 159 average time/residue: 0.1085 time to fit residues: 23.2535 Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR 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 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 196 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 100 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 51 optimal weight: 6.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.200634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155572 restraints weight = 9707.453| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.65 r_work: 0.3574 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8998 Z= 0.106 Angle : 0.509 7.259 12208 Z= 0.270 Chirality : 0.041 0.158 1393 Planarity : 0.004 0.066 1541 Dihedral : 4.211 65.664 1222 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.72 % Allowed : 21.79 % Favored : 74.50 % 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 aren not related in a simple way. whole: 1.19 (0.26), residues: 1113 helix: 2.38 (0.27), residues: 388 sheet: 0.49 (0.29), residues: 295 loop : -0.44 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 241 TYR 0.013 0.001 TYR S 60 PHE 0.014 0.001 PHE A 336 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8994) covalent geometry : angle 0.50917 (12202) SS BOND : bond 0.00502 ( 3) SS BOND : angle 0.85893 ( 6) hydrogen bonds : bond 0.03303 ( 445) hydrogen bonds : angle 4.05921 ( 1266) Misc. bond : bond 0.00035 ( 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 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5916 (t0) cc_final: 0.4935 (m-40) REVERT: R 47 ILE cc_start: 0.7436 (tp) cc_final: 0.6891 (pt) REVERT: R 191 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7496 (mmt-90) REVERT: A 197 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8096 (mtmm) REVERT: A 243 MET cc_start: 0.6378 (tmm) cc_final: 0.5985 (tmm) REVERT: A 260 THR cc_start: 0.8018 (t) cc_final: 0.7718 (p) REVERT: A 297 GLU cc_start: 0.6701 (tm-30) cc_final: 0.5663 (mt-10) REVERT: A 298 GLU cc_start: 0.6765 (tp30) cc_final: 0.6386 (tp30) REVERT: A 314 LYS cc_start: 0.7600 (mttp) cc_final: 0.7286 (mmmt) REVERT: A 322 HIS cc_start: 0.5690 (OUTLIER) cc_final: 0.4360 (m-70) REVERT: B 19 ARG cc_start: 0.7537 (ttm-80) cc_final: 0.7223 (tpt170) REVERT: B 170 ASP cc_start: 0.7921 (t0) cc_final: 0.7528 (t0) REVERT: B 175 GLN cc_start: 0.8344 (pp30) cc_final: 0.7436 (mp10) REVERT: B 335 PHE cc_start: 0.8072 (m-80) cc_final: 0.7736 (m-80) REVERT: G 27 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8309 (mtt-85) REVERT: S 19 LYS cc_start: 0.8081 (tttm) cc_final: 0.7792 (tttt) REVERT: S 46 GLU cc_start: 0.7647 (tt0) cc_final: 0.7100 (mt-10) REVERT: S 93 MET cc_start: 0.7953 (ttm) cc_final: 0.7554 (ttm) REVERT: S 142 GLN cc_start: 0.6518 (mm-40) cc_final: 0.6026 (mt0) REVERT: S 179 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.6872 (tp40) REVERT: S 183 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.5931 (tm-30) outliers start: 35 outliers final: 27 residues processed: 160 average time/residue: 0.1007 time to fit residues: 22.1036 Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 MET 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 281 LEU Chi-restraints excluded: chain R residue 315 TYR 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 196 THR 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 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 183 GLN Chi-restraints excluded: chain S residue 214 LEU 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 37 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.0970 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.198422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154390 restraints weight = 9710.404| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.47 r_work: 0.3569 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8998 Z= 0.124 Angle : 0.539 7.179 12208 Z= 0.288 Chirality : 0.042 0.179 1393 Planarity : 0.004 0.064 1541 Dihedral : 4.301 66.741 1222 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.72 % Allowed : 22.21 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.26), residues: 1113 helix: 2.40 (0.27), residues: 382 sheet: 0.38 (0.29), residues: 300 loop : -0.41 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 241 TYR 0.013 0.001 TYR S 235 PHE 0.018 0.001 PHE S 68 TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8994) covalent geometry : angle 0.53850 (12202) SS BOND : bond 0.00516 ( 3) SS BOND : angle 0.88650 ( 6) hydrogen bonds : bond 0.03498 ( 445) hydrogen bonds : angle 4.20585 ( 1266) Misc. bond : bond 0.00047 ( 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 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5684 (t0) cc_final: 0.4974 (m-40) REVERT: R 47 ILE cc_start: 0.7235 (tp) cc_final: 0.6910 (pt) REVERT: R 175 MET cc_start: 0.6277 (mtp) cc_final: 0.6033 (mtm) REVERT: R 193 ARG cc_start: 0.6257 (mpt-90) cc_final: 0.6014 (mpt-90) REVERT: A 197 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8081 (mtmm) REVERT: A 243 MET cc_start: 0.6453 (tmm) cc_final: 0.6024 (tmm) REVERT: A 260 THR cc_start: 0.7999 (t) cc_final: 0.7732 (p) REVERT: A 297 GLU cc_start: 0.6702 (tm-30) cc_final: 0.5636 (mt-10) REVERT: A 298 GLU cc_start: 0.6846 (tp30) cc_final: 0.6490 (tp30) REVERT: A 314 LYS cc_start: 0.7685 (mttp) cc_final: 0.7261 (mmmt) REVERT: B 19 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7340 (tpt170) REVERT: B 175 GLN cc_start: 0.8235 (pp30) cc_final: 0.7400 (mp10) REVERT: B 335 PHE cc_start: 0.8073 (m-80) cc_final: 0.7769 (m-80) REVERT: G 27 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8353 (mtt-85) REVERT: S 19 LYS cc_start: 0.8081 (tttm) cc_final: 0.7783 (tttt) REVERT: S 46 GLU cc_start: 0.7641 (tt0) cc_final: 0.7119 (mt-10) REVERT: S 93 MET cc_start: 0.7923 (ttm) cc_final: 0.7530 (ttm) REVERT: S 142 GLN cc_start: 0.6537 (mm-40) cc_final: 0.6092 (mt0) REVERT: S 179 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6787 (tp40) outliers start: 35 outliers final: 30 residues processed: 157 average time/residue: 0.1051 time to fit residues: 22.4884 Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.324 ------------------------------------------------------------------------------- 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 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 281 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain A residue 28 GLU 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 196 THR 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 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 ASN A 322 HIS B 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.197156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153119 restraints weight = 9714.457| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.63 r_work: 0.3516 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8998 Z= 0.140 Angle : 0.561 7.289 12208 Z= 0.301 Chirality : 0.042 0.199 1393 Planarity : 0.004 0.065 1541 Dihedral : 4.425 68.143 1222 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.61 % Allowed : 22.42 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1113 helix: 2.33 (0.27), residues: 382 sheet: 0.25 (0.29), residues: 302 loop : -0.44 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 241 TYR 0.015 0.001 TYR S 60 PHE 0.025 0.002 PHE S 68 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8994) covalent geometry : angle 0.56037 (12202) SS BOND : bond 0.00541 ( 3) SS BOND : angle 0.90769 ( 6) hydrogen bonds : bond 0.03715 ( 445) hydrogen bonds : angle 4.29893 ( 1266) Misc. bond : bond 0.00059 ( 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 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5752 (t0) cc_final: 0.4994 (m-40) REVERT: R 47 ILE cc_start: 0.7165 (tp) cc_final: 0.6887 (pt) REVERT: R 63 ASN cc_start: 0.5432 (m-40) cc_final: 0.5108 (t0) REVERT: R 191 ARG cc_start: 0.7907 (mmt-90) cc_final: 0.7700 (mmt-90) REVERT: R 193 ARG cc_start: 0.6350 (mpt-90) cc_final: 0.6102 (mpt-90) REVERT: A 197 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8123 (mtmm) REVERT: A 243 MET cc_start: 0.6481 (tmm) cc_final: 0.6022 (tmm) REVERT: A 297 GLU cc_start: 0.6870 (tm-30) cc_final: 0.5832 (mt-10) REVERT: A 298 GLU cc_start: 0.6873 (tp30) cc_final: 0.6513 (tp30) REVERT: A 314 LYS cc_start: 0.7720 (mttp) cc_final: 0.7280 (mmmt) REVERT: B 19 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.7354 (tpt170) REVERT: B 175 GLN cc_start: 0.8316 (pp30) cc_final: 0.7504 (mp10) REVERT: B 335 PHE cc_start: 0.8075 (m-80) cc_final: 0.7781 (m-80) REVERT: G 27 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8341 (mtt-85) REVERT: S 19 LYS cc_start: 0.8126 (tttm) cc_final: 0.7815 (tttt) REVERT: S 46 GLU cc_start: 0.7751 (tt0) cc_final: 0.7229 (mt-10) REVERT: S 93 MET cc_start: 0.8001 (ttm) cc_final: 0.7631 (ttm) REVERT: S 142 GLN cc_start: 0.6617 (mm-40) cc_final: 0.6168 (mt0) REVERT: S 179 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.6825 (tp40) outliers start: 34 outliers final: 32 residues processed: 159 average time/residue: 0.0950 time to fit residues: 20.7703 Evaluate side-chains 165 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 182 THR 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 196 THR 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 88 SER 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 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 48 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN R 311 ASN A 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155485 restraints weight = 9655.887| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.40 r_work: 0.3583 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8998 Z= 0.115 Angle : 0.534 7.063 12208 Z= 0.285 Chirality : 0.041 0.179 1393 Planarity : 0.004 0.063 1541 Dihedral : 4.331 65.816 1222 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.40 % Allowed : 22.53 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.26), residues: 1113 helix: 2.42 (0.27), residues: 382 sheet: 0.33 (0.29), residues: 297 loop : -0.43 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 241 TYR 0.014 0.001 TYR S 60 PHE 0.018 0.001 PHE S 68 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8994) covalent geometry : angle 0.53393 (12202) SS BOND : bond 0.00481 ( 3) SS BOND : angle 0.76498 ( 6) hydrogen bonds : bond 0.03456 ( 445) hydrogen bonds : angle 4.20936 ( 1266) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.01 seconds wall clock time: 41 minutes 25.24 seconds (2485.24 seconds total)