Starting phenix.real_space_refine on Mon May 12 06:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jfy_61444/05_2025/9jfy_61444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jfy_61444/05_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_61444/05_2025/9jfy_61444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jfy_61444/05_2025/9jfy_61444.map" model { file = "/net/cci-nas-00/data/ceres_data/9jfy_61444/05_2025/9jfy_61444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jfy_61444/05_2025/9jfy_61444.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5635 2.51 5 N 1482 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8805 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2323 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "L" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 97 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1631 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2568 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 414 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 5.03, per 1000 atoms: 0.57 Number of scatterers: 8805 At special positions: 0 Unit cell: (92.4, 119.7, 133.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1622 8.00 N 1482 7.00 C 5635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 206 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 955.3 milliseconds 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: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 41 through 73 removed outlier: 3.782A pdb=" N ILE R 55 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 98 Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 114 through 149 removed outlier: 3.667A pdb=" N GLY R 126 " --> pdb=" O GLY R 122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU R 136 " --> pdb=" O SER R 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 181 Proline residue: R 177 - end of helix Processing helix chain 'R' and resid 212 through 228 Processing helix chain 'R' and resid 228 through 248 removed outlier: 3.571A pdb=" N LEU R 232 " --> pdb=" O TYR R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 300 removed outlier: 3.647A pdb=" N TRP R 287 " --> pdb=" O PHE R 283 " (cutoff:3.500A) Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 303 through 313 Processing helix chain 'R' and resid 314 through 336 removed outlier: 3.566A pdb=" N SER R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN R 329 " --> pdb=" O ASN R 325 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 337 through 342 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.642A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.616A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.110A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.091A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.863A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.936A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.825A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.802A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 33 through 35 removed outlier: 6.284A pdb=" N THR R 33 " --> pdb=" O ARG R 191 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ARG R 193 " --> pdb=" O THR R 33 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL R 35 " --> pdb=" O ARG R 193 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL R 203 " --> pdb=" O GLU R 187 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N TYR R 189 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N SER R 201 " --> pdb=" O TYR R 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.882A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.332A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.833A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.957A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.139A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.961A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.604A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.760A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.793A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.400A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.592A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 2.39 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8998 Z= 0.131 Angle : 0.464 5.790 12208 Z= 0.254 Chirality : 0.041 0.188 1393 Planarity : 0.004 0.059 1541 Dihedral : 15.557 87.735 3182 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 20.30 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1113 helix: 2.51 (0.27), residues: 388 sheet: 0.71 (0.30), residues: 297 loop : -0.37 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 205 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR S 235 ARG 0.003 0.000 ARG R 207 Details of bonding type rmsd hydrogen bonds : bond 0.10903 ( 445) hydrogen bonds : angle 4.95434 ( 1266) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.00565 ( 6) covalent geometry : bond 0.00251 ( 8994) covalent geometry : angle 0.46323 (12202) Misc. bond : bond 0.06228 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 GLN cc_start: 0.7668 (mt0) cc_final: 0.7375 (mt0) REVERT: B 258 ASP cc_start: 0.7014 (t0) cc_final: 0.6691 (t70) REVERT: S 93 MET cc_start: 0.7019 (tpp) cc_final: 0.6797 (ttm) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2334 time to fit residues: 57.4199 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 : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN B 88 ASN B 259 GLN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.201935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158701 restraints weight = 9656.167| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.65 r_work: 0.3540 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8998 Z= 0.141 Angle : 0.566 11.407 12208 Z= 0.299 Chirality : 0.043 0.198 1393 Planarity : 0.004 0.067 1541 Dihedral : 4.406 67.541 1222 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 19.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1113 helix: 2.55 (0.27), residues: 386 sheet: 0.60 (0.30), residues: 299 loop : -0.35 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS S 232 PHE 0.015 0.002 PHE B 253 TYR 0.014 0.001 TYR S 190 ARG 0.005 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 445) hydrogen bonds : angle 4.36227 ( 1266) SS BOND : bond 0.00561 ( 3) SS BOND : angle 0.92796 ( 6) covalent geometry : bond 0.00323 ( 8994) covalent geometry : angle 0.56550 (12202) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7861 (m170) cc_final: 0.7489 (m-70) REVERT: A 197 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8196 (mtpp) REVERT: B 19 ARG cc_start: 0.7464 (mtt90) cc_final: 0.7208 (tpt170) REVERT: S 46 GLU cc_start: 0.7596 (tt0) cc_final: 0.7161 (mt-10) REVERT: S 142 GLN cc_start: 0.6386 (mm-40) cc_final: 0.6009 (mt0) outliers start: 27 outliers final: 15 residues processed: 165 average time/residue: 0.2269 time to fit residues: 50.9091 Evaluate side-chains 139 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.195889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.151603 restraints weight = 9827.009| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.75 r_work: 0.3497 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8998 Z= 0.183 Angle : 0.597 8.147 12208 Z= 0.317 Chirality : 0.044 0.258 1393 Planarity : 0.004 0.061 1541 Dihedral : 4.704 73.036 1222 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.46 % Allowed : 18.92 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1113 helix: 2.33 (0.27), residues: 386 sheet: 0.35 (0.29), residues: 303 loop : -0.50 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 47 HIS 0.006 0.001 HIS S 35 PHE 0.017 0.002 PHE B 199 TYR 0.022 0.002 TYR S 235 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 445) hydrogen bonds : angle 4.44218 ( 1266) SS BOND : bond 0.00728 ( 3) SS BOND : angle 1.15332 ( 6) covalent geometry : bond 0.00437 ( 8994) covalent geometry : angle 0.59637 (12202) Misc. bond : bond 0.00096 ( 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 191 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 191 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7573 (mmt-90) REVERT: R 193 ARG cc_start: 0.6109 (mpt-90) cc_final: 0.5902 (mpt-90) REVERT: R 241 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7563 (mtt-85) REVERT: R 311 ASN cc_start: 0.8061 (m110) cc_final: 0.7839 (m-40) REVERT: A 188 HIS cc_start: 0.8031 (m170) cc_final: 0.7787 (m-70) REVERT: A 197 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8383 (mtpp) REVERT: A 297 GLU cc_start: 0.6532 (tm-30) cc_final: 0.5365 (mt-10) REVERT: A 298 GLU cc_start: 0.6505 (tp30) cc_final: 0.6223 (tp30) REVERT: B 175 GLN cc_start: 0.8415 (pp30) cc_final: 0.7757 (mm-40) REVERT: S 18 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7800 (tpt170) REVERT: S 19 LYS cc_start: 0.8174 (tttm) cc_final: 0.7968 (tttt) REVERT: S 38 ARG cc_start: 0.8324 (ptt180) cc_final: 0.8065 (ptt180) REVERT: S 76 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7598 (mtmm) REVERT: S 93 MET cc_start: 0.7993 (ttm) cc_final: 0.7506 (ttm) REVERT: S 140 MET cc_start: 0.8496 (mmm) cc_final: 0.8051 (mmm) REVERT: S 142 GLN cc_start: 0.6565 (mm-40) cc_final: 0.6227 (mt0) REVERT: S 179 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6851 (tp40) outliers start: 42 outliers final: 26 residues processed: 179 average time/residue: 0.2281 time to fit residues: 55.2707 Evaluate side-chains 164 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 278 ILE Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL 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 88 SER Chi-restraints excluded: chain S residue 159 CYS Chi-restraints excluded: chain S residue 179 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 63 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN R 308 GLN R 311 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.197426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153128 restraints weight = 9662.939| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.51 r_work: 0.3525 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8998 Z= 0.123 Angle : 0.534 7.216 12208 Z= 0.282 Chirality : 0.042 0.208 1393 Planarity : 0.004 0.063 1541 Dihedral : 4.450 70.041 1222 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.83 % Allowed : 19.55 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1113 helix: 2.50 (0.28), residues: 377 sheet: 0.27 (0.28), residues: 307 loop : -0.51 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 205 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE R 56 TYR 0.016 0.001 TYR S 235 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 445) hydrogen bonds : angle 4.23722 ( 1266) SS BOND : bond 0.00557 ( 3) SS BOND : angle 1.28017 ( 6) covalent geometry : bond 0.00282 ( 8994) covalent geometry : angle 0.53329 (12202) Misc. bond : bond 0.00050 ( 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 177 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 191 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7465 (mmt-90) REVERT: R 193 ARG cc_start: 0.6136 (mpt-90) cc_final: 0.5914 (mpt-90) REVERT: A 188 HIS cc_start: 0.8078 (m170) cc_final: 0.7851 (m-70) REVERT: A 260 THR cc_start: 0.8125 (t) cc_final: 0.7764 (p) REVERT: A 297 GLU cc_start: 0.6533 (tm-30) cc_final: 0.5290 (mt-10) REVERT: A 298 GLU cc_start: 0.6734 (tp30) cc_final: 0.6502 (tp30) REVERT: A 322 HIS cc_start: 0.5708 (OUTLIER) cc_final: 0.4423 (m-70) REVERT: B 175 GLN cc_start: 0.8323 (pp30) cc_final: 0.7709 (mm-40) REVERT: S 38 ARG cc_start: 0.8303 (ptt180) cc_final: 0.7985 (ptt180) REVERT: S 93 MET cc_start: 0.7968 (ttm) cc_final: 0.7535 (ttm) REVERT: S 142 GLN cc_start: 0.6474 (mm-40) cc_final: 0.6095 (mt0) REVERT: S 179 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.6870 (tp40) outliers start: 36 outliers final: 18 residues processed: 165 average time/residue: 0.2208 time to fit residues: 49.1229 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 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 230 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.193563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.149850 restraints weight = 9730.575| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.47 r_work: 0.3494 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8998 Z= 0.190 Angle : 0.599 8.415 12208 Z= 0.318 Chirality : 0.044 0.262 1393 Planarity : 0.004 0.062 1541 Dihedral : 4.769 75.246 1222 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.36 % Allowed : 20.51 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1113 helix: 2.19 (0.27), residues: 386 sheet: 0.16 (0.29), residues: 306 loop : -0.52 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS S 35 PHE 0.038 0.002 PHE S 68 TYR 0.024 0.002 TYR S 235 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 445) hydrogen bonds : angle 4.47746 ( 1266) SS BOND : bond 0.00706 ( 3) SS BOND : angle 1.31624 ( 6) covalent geometry : bond 0.00460 ( 8994) covalent geometry : angle 0.59826 (12202) Misc. bond : bond 0.00108 ( 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 188 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.7469 (m-40) cc_final: 0.7212 (m110) REVERT: A 243 MET cc_start: 0.6303 (tmm) cc_final: 0.5933 (tmm) REVERT: A 260 THR cc_start: 0.8055 (t) cc_final: 0.7747 (p) REVERT: A 322 HIS cc_start: 0.5839 (OUTLIER) cc_final: 0.4510 (m-70) REVERT: B 178 THR cc_start: 0.8467 (OUTLIER) cc_final: 0.8173 (p) REVERT: S 38 ARG cc_start: 0.8331 (ptt180) cc_final: 0.8076 (ptt180) REVERT: S 76 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7711 (mtmm) REVERT: S 93 MET cc_start: 0.7948 (ttm) cc_final: 0.7580 (ttm) REVERT: S 140 MET cc_start: 0.8561 (mmm) cc_final: 0.8135 (mmm) REVERT: S 142 GLN cc_start: 0.6722 (mt0) cc_final: 0.6471 (mt0) REVERT: S 179 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6791 (tp40) outliers start: 41 outliers final: 31 residues processed: 176 average time/residue: 0.2232 time to fit residues: 52.8916 Evaluate side-chains 170 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 183 HIS Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain 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 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 307 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS B 239 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 = 0.4240 r_free = 0.4240 target = 0.196641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.153217 restraints weight = 9703.518| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.66 r_work: 0.3511 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4200 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= 0.134 Angle : 0.553 8.004 12208 Z= 0.292 Chirality : 0.042 0.221 1393 Planarity : 0.004 0.059 1541 Dihedral : 4.557 71.200 1222 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.14 % Allowed : 21.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1113 helix: 2.25 (0.27), residues: 383 sheet: 0.24 (0.28), residues: 305 loop : -0.51 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.024 0.002 PHE S 68 TYR 0.017 0.001 TYR S 235 ARG 0.009 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 445) hydrogen bonds : angle 4.33959 ( 1266) SS BOND : bond 0.00612 ( 3) SS BOND : angle 1.00011 ( 6) covalent geometry : bond 0.00313 ( 8994) covalent geometry : angle 0.55239 (12202) Misc. bond : bond 0.00059 ( 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 183 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.6232 (t0) cc_final: 0.4956 (m-40) REVERT: R 63 ASN cc_start: 0.5489 (m-40) cc_final: 0.5238 (t0) REVERT: R 193 ARG cc_start: 0.6410 (OUTLIER) cc_final: 0.6144 (mpt-90) REVERT: A 20 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: A 243 MET cc_start: 0.6320 (tmm) cc_final: 0.5902 (tmm) REVERT: A 260 THR cc_start: 0.8085 (t) cc_final: 0.7861 (p) REVERT: A 297 GLU cc_start: 0.6722 (tm-30) cc_final: 0.5536 (mt-10) REVERT: A 298 GLU cc_start: 0.6799 (tp30) cc_final: 0.4657 (pt0) REVERT: A 314 LYS cc_start: 0.7561 (mttp) cc_final: 0.7186 (mmmt) REVERT: A 322 HIS cc_start: 0.5731 (OUTLIER) cc_final: 0.4356 (m-70) REVERT: B 19 ARG cc_start: 0.7665 (ttm-80) cc_final: 0.7357 (tpt170) REVERT: B 217 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7450 (ptt) REVERT: B 335 PHE cc_start: 0.8205 (m-80) cc_final: 0.7854 (m-80) REVERT: G 27 ARG cc_start: 0.8668 (mtt90) cc_final: 0.8399 (mtt-85) REVERT: S 19 LYS cc_start: 0.8202 (tttm) cc_final: 0.7967 (tttt) REVERT: S 38 ARG cc_start: 0.8332 (ptt180) cc_final: 0.8083 (ptt180) REVERT: S 93 MET cc_start: 0.7975 (ttm) cc_final: 0.7597 (ttm) REVERT: S 142 GLN cc_start: 0.6653 (mt0) cc_final: 0.6363 (mt0) REVERT: S 179 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6860 (tp40) REVERT: S 235 TYR cc_start: 0.6015 (OUTLIER) cc_final: 0.5708 (t80) outliers start: 39 outliers final: 26 residues processed: 172 average time/residue: 0.2199 time to fit residues: 50.7972 Evaluate side-chains 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 183 HIS Chi-restraints excluded: chain R residue 193 ARG Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain R residue 328 VAL Chi-restraints excluded: chain R residue 332 ILE Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 182 THR 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 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR 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 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 Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.0980 chunk 48 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.197109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.154110 restraints weight = 9732.346| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.40 r_work: 0.3543 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.4345 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= 0.127 Angle : 0.543 7.391 12208 Z= 0.288 Chirality : 0.042 0.201 1393 Planarity : 0.004 0.062 1541 Dihedral : 4.470 69.351 1222 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.46 % Allowed : 21.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1113 helix: 2.29 (0.28), residues: 384 sheet: 0.26 (0.29), residues: 295 loop : -0.46 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.030 0.002 PHE A 336 TYR 0.015 0.001 TYR S 235 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 445) hydrogen bonds : angle 4.29705 ( 1266) SS BOND : bond 0.00568 ( 3) SS BOND : angle 0.94281 ( 6) covalent geometry : bond 0.00294 ( 8994) covalent geometry : angle 0.54311 (12202) Misc. bond : bond 0.00052 ( 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 182 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.6053 (t0) cc_final: 0.4905 (m-40) REVERT: R 47 ILE cc_start: 0.7598 (tp) cc_final: 0.7121 (pt) REVERT: R 193 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.6180 (mpt-90) REVERT: A 20 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: A 243 MET cc_start: 0.6380 (tmm) cc_final: 0.5952 (tmm) REVERT: A 297 GLU cc_start: 0.6787 (tm-30) cc_final: 0.5641 (mt-10) REVERT: A 298 GLU cc_start: 0.6850 (tp30) cc_final: 0.6486 (tp30) REVERT: A 314 LYS cc_start: 0.7781 (mttp) cc_final: 0.7342 (mmmt) REVERT: B 19 ARG cc_start: 0.7670 (ttm-80) cc_final: 0.7399 (tpt170) REVERT: B 178 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.8199 (p) REVERT: B 217 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7514 (ptt) REVERT: B 335 PHE cc_start: 0.8154 (m-80) cc_final: 0.7821 (m-80) REVERT: S 19 LYS cc_start: 0.8193 (tttm) cc_final: 0.7887 (tttt) REVERT: S 38 ARG cc_start: 0.8305 (ptt180) cc_final: 0.8068 (ptt180) REVERT: S 93 MET cc_start: 0.7887 (ttm) cc_final: 0.7503 (ttm) REVERT: S 142 GLN cc_start: 0.6620 (mt0) cc_final: 0.6303 (mt0) outliers start: 42 outliers final: 31 residues processed: 170 average time/residue: 0.2219 time to fit residues: 50.5991 Evaluate side-chains 171 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 183 HIS Chi-restraints excluded: chain R residue 193 ARG Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain 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 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 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 301 LYS 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 183 GLN Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 81 ASN R 226 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.197298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.153404 restraints weight = 9829.543| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.58 r_work: 0.3518 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8998 Z= 0.124 Angle : 0.544 7.283 12208 Z= 0.288 Chirality : 0.042 0.192 1393 Planarity : 0.004 0.061 1541 Dihedral : 4.430 69.023 1222 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.57 % Allowed : 21.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1113 helix: 2.32 (0.27), residues: 384 sheet: 0.23 (0.28), residues: 300 loop : -0.44 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS A 322 PHE 0.028 0.002 PHE S 68 TYR 0.015 0.001 TYR S 60 ARG 0.006 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 445) hydrogen bonds : angle 4.26954 ( 1266) SS BOND : bond 0.00560 ( 3) SS BOND : angle 1.82501 ( 6) covalent geometry : bond 0.00284 ( 8994) covalent geometry : angle 0.54240 (12202) Misc. bond : bond 0.00050 ( 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 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5850 (t0) cc_final: 0.4800 (m-40) REVERT: R 47 ILE cc_start: 0.7378 (tp) cc_final: 0.6965 (pt) REVERT: R 193 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.6188 (mpt-90) REVERT: A 20 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: A 297 GLU cc_start: 0.6843 (tm-30) cc_final: 0.5735 (mt-10) REVERT: A 298 GLU cc_start: 0.6789 (tp30) cc_final: 0.6411 (tp30) REVERT: A 314 LYS cc_start: 0.7769 (mttp) cc_final: 0.7276 (mmmt) REVERT: A 322 HIS cc_start: 0.5532 (OUTLIER) cc_final: 0.5101 (t-90) REVERT: B 19 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.7237 (tpt170) REVERT: B 178 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8185 (p) REVERT: B 217 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7498 (ptt) REVERT: B 335 PHE cc_start: 0.8125 (m-80) cc_final: 0.7816 (m-80) REVERT: S 46 GLU cc_start: 0.7752 (tt0) cc_final: 0.7157 (mt-10) REVERT: S 93 MET cc_start: 0.7954 (ttm) cc_final: 0.7603 (ttm) REVERT: S 140 MET cc_start: 0.8532 (mmm) cc_final: 0.8265 (mmm) REVERT: S 142 GLN cc_start: 0.6584 (mt0) cc_final: 0.6260 (mt0) REVERT: S 179 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6877 (tp40) REVERT: S 235 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.5484 (t80) outliers start: 43 outliers final: 32 residues processed: 168 average time/residue: 0.2208 time to fit residues: 49.9168 Evaluate side-chains 172 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 193 ARG Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain 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 182 THR 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 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 301 LYS 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 Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 226 ASN B 156 GLN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.194873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.150807 restraints weight = 9811.350| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.54 r_work: 0.3522 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8998 Z= 0.152 Angle : 0.569 7.384 12208 Z= 0.302 Chirality : 0.043 0.219 1393 Planarity : 0.004 0.062 1541 Dihedral : 4.584 71.005 1222 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.68 % Allowed : 21.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1113 helix: 2.23 (0.27), residues: 382 sheet: 0.15 (0.28), residues: 311 loop : -0.49 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.034 0.002 PHE S 68 TYR 0.017 0.001 TYR S 235 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 445) hydrogen bonds : angle 4.37866 ( 1266) SS BOND : bond 0.00607 ( 3) SS BOND : angle 1.83312 ( 6) covalent geometry : bond 0.00363 ( 8994) covalent geometry : angle 0.56802 (12202) Misc. bond : bond 0.00075 ( 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: 44 poor density : 128 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5890 (t0) cc_final: 0.5000 (m-40) REVERT: R 47 ILE cc_start: 0.7418 (tp) cc_final: 0.7017 (pt) REVERT: A 297 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6017 (mt-10) REVERT: A 298 GLU cc_start: 0.6876 (tp30) cc_final: 0.6405 (tp30) REVERT: A 314 LYS cc_start: 0.7794 (mttp) cc_final: 0.7320 (mmmt) REVERT: A 322 HIS cc_start: 0.5469 (OUTLIER) cc_final: 0.5099 (t-90) REVERT: B 19 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7370 (tpt170) REVERT: B 178 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 217 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7513 (ptt) REVERT: B 335 PHE cc_start: 0.8138 (m-80) cc_final: 0.7836 (m-80) REVERT: S 19 LYS cc_start: 0.8296 (tttm) cc_final: 0.8043 (tttt) REVERT: S 93 MET cc_start: 0.7968 (ttm) cc_final: 0.7637 (ttm) REVERT: S 140 MET cc_start: 0.8523 (mmm) cc_final: 0.8138 (mmm) REVERT: S 142 GLN cc_start: 0.6665 (mt0) cc_final: 0.6388 (mt0) REVERT: S 179 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6790 (tp40) REVERT: S 235 TYR cc_start: 0.5998 (OUTLIER) cc_final: 0.5719 (t80) outliers start: 44 outliers final: 36 residues processed: 161 average time/residue: 0.2133 time to fit residues: 47.3386 Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 76 MET Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 157 ILE Chi-restraints excluded: chain R residue 183 HIS Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 242 ILE Chi-restraints excluded: chain R residue 245 SER Chi-restraints excluded: chain R residue 246 LEU Chi-restraints excluded: chain R residue 286 SER Chi-restraints excluded: chain R residue 299 TYR Chi-restraints excluded: chain R residue 315 TYR 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 182 THR 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 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR 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 Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 142 GLN ** 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 = 0.4244 r_free = 0.4244 target = 0.196687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.153100 restraints weight = 9822.494| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.43 r_work: 0.3539 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8998 Z= 0.123 Angle : 0.544 7.072 12208 Z= 0.288 Chirality : 0.042 0.193 1393 Planarity : 0.004 0.060 1541 Dihedral : 4.439 68.553 1222 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.14 % Allowed : 21.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1113 helix: 2.33 (0.27), residues: 383 sheet: 0.13 (0.28), residues: 310 loop : -0.45 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.024 0.001 PHE S 68 TYR 0.016 0.001 TYR S 60 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 445) hydrogen bonds : angle 4.29523 ( 1266) SS BOND : bond 0.00557 ( 3) SS BOND : angle 1.57477 ( 6) covalent geometry : bond 0.00285 ( 8994) covalent geometry : angle 0.54327 (12202) Misc. bond : bond 0.00051 ( 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: 39 poor density : 132 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 ASN cc_start: 0.5919 (t0) cc_final: 0.4967 (m-40) REVERT: R 47 ILE cc_start: 0.7390 (tp) cc_final: 0.7050 (pt) REVERT: A 20 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 28 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: A 297 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6070 (mt-10) REVERT: A 298 GLU cc_start: 0.6845 (tp30) cc_final: 0.6256 (tp30) REVERT: A 314 LYS cc_start: 0.7895 (mttp) cc_final: 0.7370 (mmmt) REVERT: A 322 HIS cc_start: 0.5397 (OUTLIER) cc_final: 0.5046 (t-90) REVERT: B 19 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7379 (tpt170) REVERT: B 178 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 217 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7468 (ptt) REVERT: B 335 PHE cc_start: 0.8138 (m-80) cc_final: 0.7850 (m-80) REVERT: S 46 GLU cc_start: 0.7741 (tt0) cc_final: 0.7189 (mt-10) REVERT: S 93 MET cc_start: 0.7947 (ttm) cc_final: 0.7589 (ttm) REVERT: S 140 MET cc_start: 0.8544 (mmm) cc_final: 0.8186 (mmm) REVERT: S 142 GLN cc_start: 0.6592 (mt0) cc_final: 0.6308 (mt0) REVERT: S 179 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.6915 (tp40) REVERT: S 235 TYR cc_start: 0.5694 (OUTLIER) cc_final: 0.5445 (t80) outliers start: 39 outliers final: 31 residues processed: 161 average time/residue: 0.2089 time to fit residues: 46.2661 Evaluate side-chains 167 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 77 HIS Chi-restraints excluded: chain R residue 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 286 SER Chi-restraints excluded: chain R residue 299 TYR Chi-restraints excluded: chain R residue 315 TYR Chi-restraints excluded: chain A residue 20 ASP 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 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 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR 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 Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 32 optimal weight: 0.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 142 GLN ** 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 = 0.4214 r_free = 0.4214 target = 0.193508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.149477 restraints weight = 9897.580| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.59 r_work: 0.3488 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8998 Z= 0.187 Angle : 0.608 7.743 12208 Z= 0.322 Chirality : 0.044 0.247 1393 Planarity : 0.004 0.063 1541 Dihedral : 4.731 71.909 1222 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.14 % Allowed : 22.10 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1113 helix: 2.19 (0.27), residues: 383 sheet: 0.03 (0.29), residues: 305 loop : -0.49 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 47 HIS 0.006 0.001 HIS B 91 PHE 0.047 0.002 PHE S 68 TYR 0.020 0.001 TYR S 235 ARG 0.007 0.000 ARG R 241 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 445) hydrogen bonds : angle 4.50177 ( 1266) SS BOND : bond 0.00666 ( 3) SS BOND : angle 1.79316 ( 6) covalent geometry : bond 0.00452 ( 8994) covalent geometry : angle 0.60732 (12202) Misc. bond : bond 0.00104 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4436.67 seconds wall clock time: 77 minutes 37.81 seconds (4657.81 seconds total)