Starting phenix.real_space_refine on Sun Apr 5 01:06:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9odf_70357/04_2026/9odf_70357.cif Found real_map, /net/cci-nas-00/data/ceres_data/9odf_70357/04_2026/9odf_70357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9odf_70357/04_2026/9odf_70357.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9odf_70357/04_2026/9odf_70357.map" model { file = "/net/cci-nas-00/data/ceres_data/9odf_70357/04_2026/9odf_70357.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9odf_70357/04_2026/9odf_70357.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.046 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 4243 2.51 5 N 1103 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6614 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2455 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 4, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 365 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2110 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "A" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1621 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'EID': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.37, per 1000 atoms: 0.21 Number of scatterers: 6614 At special positions: 0 Unit cell: (72, 101.76, 132.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 3 15.00 Mg 1 11.99 O 1212 8.00 N 1103 7.00 C 4243 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 227.2 milliseconds 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 45.5% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 7 through 26 removed outlier: 3.656A pdb=" N ASN B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.608A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 48 removed outlier: 3.698A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 96 removed outlier: 3.591A pdb=" N TYR D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 86 " --> pdb=" O GLY D 82 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 130 removed outlier: 3.554A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 128 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 171 removed outlier: 3.509A pdb=" N ASN D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.805A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 195 Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.768A pdb=" N GLY D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 225 through 241 removed outlier: 3.883A pdb=" N ASN D 230 " --> pdb=" O TRP D 226 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 232 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 259 removed outlier: 3.647A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 266 removed outlier: 5.852A pdb=" N ARG D 263 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET D 264 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 280 removed outlier: 3.652A pdb=" N LEU D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 306 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 3.626A pdb=" N THR D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N CYS D 330 " --> pdb=" O TYR D 326 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.557A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.677A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.660A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.707A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.058A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.514A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.759A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.887A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.716A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.628A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.881A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.821A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.967A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 206 through 209 Processing sheet with id=AA9, first strand: chain 'A' and resid 56 through 57 removed outlier: 4.536A pdb=" N HIS A 188 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 972 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1057 1.31 - 1.44: 1849 1.44 - 1.57: 3765 1.57 - 1.70: 5 1.70 - 1.83: 74 Bond restraints: 6750 Sorted by residual: bond pdb=" C03 EID D 501 " pdb=" N05 EID D 501 " ideal model delta sigma weight residual 1.363 1.459 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C27 EID D 501 " pdb=" O29 EID D 501 " ideal model delta sigma weight residual 1.318 1.397 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" N LEU B 117 " pdb=" CA LEU B 117 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" N ILE B 120 " pdb=" CA ILE B 120 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.72e+00 bond pdb=" N ILE D 198 " pdb=" CA ILE D 198 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.11e+00 ... (remaining 6745 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 8497 1.31 - 2.62: 588 2.62 - 3.94: 96 3.94 - 5.25: 24 5.25 - 6.56: 7 Bond angle restraints: 9212 Sorted by residual: angle pdb=" CA MET D 99 " pdb=" C MET D 99 " pdb=" O MET D 99 " ideal model delta sigma weight residual 122.03 118.05 3.98 1.25e+00 6.40e-01 1.01e+01 angle pdb=" N VAL D 126 " pdb=" CA VAL D 126 " pdb=" C VAL D 126 " ideal model delta sigma weight residual 113.16 108.43 4.73 1.49e+00 4.50e-01 1.01e+01 angle pdb=" CA GLU A 43 " pdb=" C GLU A 43 " pdb=" O GLU A 43 " ideal model delta sigma weight residual 120.81 116.90 3.91 1.24e+00 6.50e-01 9.94e+00 angle pdb=" N PRO B 236 " pdb=" CA PRO B 236 " pdb=" C PRO B 236 " ideal model delta sigma weight residual 113.75 118.04 -4.29 1.49e+00 4.50e-01 8.27e+00 angle pdb=" N ASP B 118 " pdb=" CA ASP B 118 " pdb=" C ASP B 118 " ideal model delta sigma weight residual 113.18 109.81 3.37 1.21e+00 6.83e-01 7.74e+00 ... (remaining 9207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.10: 3843 32.10 - 64.21: 106 64.21 - 96.31: 9 96.31 - 128.41: 1 128.41 - 160.52: 2 Dihedral angle restraints: 3961 sinusoidal: 1377 harmonic: 2584 Sorted by residual: dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -55.92 160.52 1 2.00e+01 2.50e-03 4.66e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 274.12 137.87 136.25 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 133.91 126.96 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 3958 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 721 0.040 - 0.080: 285 0.080 - 0.120: 79 0.120 - 0.160: 18 0.160 - 0.200: 3 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA ILE D 198 " pdb=" N ILE D 198 " pdb=" C ILE D 198 " pdb=" CB ILE D 198 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA GLU A 216 " pdb=" N GLU A 216 " pdb=" C GLU A 216 " pdb=" CB GLU A 216 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA PRO B 236 " pdb=" N PRO B 236 " pdb=" C PRO B 236 " pdb=" CB PRO B 236 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 1103 not shown) Planarity restraints: 1145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO B 236 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 99 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C MET D 99 " 0.032 2.00e-02 2.50e+03 pdb=" O MET D 99 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS D 100 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 20 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" CG ASP A 20 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP A 20 " 0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP A 20 " 0.011 2.00e-02 2.50e+03 ... (remaining 1142 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 57 2.66 - 3.22: 5794 3.22 - 3.78: 9546 3.78 - 4.34: 13840 4.34 - 4.90: 22371 Nonbonded interactions: 51608 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.096 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.247 3.040 nonbonded pdb=" O ILE D 290 " pdb=" OG1 THR D 294 " model vdw 2.249 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.257 3.040 nonbonded pdb=" OD1 ASN D 109 " pdb=" NE1 TRP D 192 " model vdw 2.303 3.120 ... (remaining 51603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.310 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.005 0.096 6751 Z= 0.251 Angle : 0.762 6.562 9214 Z= 0.449 Chirality : 0.047 0.200 1106 Planarity : 0.005 0.053 1145 Dihedral : 15.757 160.515 2278 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.26 % Favored : 95.63 % Rotamer: Outliers : 0.61 % Allowed : 13.44 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 869 helix: 0.00 (0.27), residues: 362 sheet: 1.15 (0.40), residues: 168 loop : -1.82 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.012 0.002 TYR B 111 PHE 0.016 0.002 PHE B 278 TRP 0.016 0.002 TRP B 99 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 6750) covalent geometry : angle 0.76110 ( 9212) SS BOND : bond 0.00160 ( 1) SS BOND : angle 2.18328 ( 2) hydrogen bonds : bond 0.21960 ( 339) hydrogen bonds : angle 6.36980 ( 972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.243 Fit side-chains REVERT: D 90 MET cc_start: 0.6734 (mtm) cc_final: 0.6270 (mtt) REVERT: A 32 ARG cc_start: 0.7851 (mtm110) cc_final: 0.7604 (mtm180) outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.6160 time to fit residues: 62.4771 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 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: B 91 HIS ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138677 restraints weight = 6139.850| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.69 r_work: 0.3365 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6751 Z= 0.149 Angle : 0.622 8.209 9214 Z= 0.334 Chirality : 0.045 0.150 1106 Planarity : 0.004 0.067 1145 Dihedral : 9.877 155.228 986 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.57 % Favored : 96.32 % Rotamer: Outliers : 2.14 % Allowed : 12.52 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.27), residues: 869 helix: 1.11 (0.27), residues: 363 sheet: 1.26 (0.39), residues: 168 loop : -1.55 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.022 0.001 TYR D 149 PHE 0.015 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6750) covalent geometry : angle 0.62187 ( 9212) SS BOND : bond 0.00098 ( 1) SS BOND : angle 1.29676 ( 2) hydrogen bonds : bond 0.06455 ( 339) hydrogen bonds : angle 4.42848 ( 972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.242 Fit side-chains REVERT: B 234 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7126 (t80) REVERT: D 90 MET cc_start: 0.6847 (mtm) cc_final: 0.6331 (mtm) outliers start: 14 outliers final: 3 residues processed: 93 average time/residue: 0.5639 time to fit residues: 55.0050 Evaluate side-chains 87 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN B 340 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139746 restraints weight = 6076.568| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.56 r_work: 0.3372 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6751 Z= 0.141 Angle : 0.583 7.040 9214 Z= 0.311 Chirality : 0.044 0.147 1106 Planarity : 0.004 0.069 1145 Dihedral : 9.326 153.132 982 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 2.14 % Allowed : 12.37 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.28), residues: 869 helix: 1.65 (0.27), residues: 364 sheet: 1.36 (0.39), residues: 168 loop : -1.46 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.010 0.001 TYR D 128 PHE 0.016 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6750) covalent geometry : angle 0.58305 ( 9212) SS BOND : bond 0.00032 ( 1) SS BOND : angle 1.26068 ( 2) hydrogen bonds : bond 0.05802 ( 339) hydrogen bonds : angle 4.12934 ( 972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.227 Fit side-chains REVERT: B 217 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7988 (pmt) REVERT: B 234 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.7187 (t80) REVERT: C 21 MET cc_start: 0.6789 (mtp) cc_final: 0.6158 (ttt) REVERT: D 90 MET cc_start: 0.6977 (mtm) cc_final: 0.6414 (mtm) REVERT: D 128 TYR cc_start: 0.6853 (t80) cc_final: 0.6430 (t80) outliers start: 14 outliers final: 4 residues processed: 92 average time/residue: 0.5908 time to fit residues: 57.0454 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 34 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 124 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.176642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.140191 restraints weight = 6137.542| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.57 r_work: 0.3371 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6751 Z= 0.137 Angle : 0.571 6.486 9214 Z= 0.305 Chirality : 0.044 0.145 1106 Planarity : 0.004 0.070 1145 Dihedral : 9.194 152.261 982 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.22 % Favored : 96.66 % Rotamer: Outliers : 2.14 % Allowed : 12.98 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.28), residues: 869 helix: 1.95 (0.27), residues: 364 sheet: 1.44 (0.39), residues: 168 loop : -1.38 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.017 0.001 TYR D 149 PHE 0.017 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 6750) covalent geometry : angle 0.57090 ( 9212) SS BOND : bond 0.00006 ( 1) SS BOND : angle 0.97571 ( 2) hydrogen bonds : bond 0.05625 ( 339) hydrogen bonds : angle 4.08580 ( 972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.239 Fit side-chains REVERT: B 75 GLN cc_start: 0.8273 (mt0) cc_final: 0.8061 (mt0) REVERT: B 217 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7968 (pmt) REVERT: B 234 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7214 (t80) REVERT: D 90 MET cc_start: 0.6895 (mtm) cc_final: 0.6308 (mtt) REVERT: D 128 TYR cc_start: 0.6725 (t80) cc_final: 0.6412 (t80) outliers start: 14 outliers final: 6 residues processed: 89 average time/residue: 0.5908 time to fit residues: 55.0231 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.176655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140297 restraints weight = 6191.536| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.67 r_work: 0.3366 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6751 Z= 0.139 Angle : 0.571 6.413 9214 Z= 0.306 Chirality : 0.044 0.146 1106 Planarity : 0.004 0.069 1145 Dihedral : 9.130 151.944 982 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.78 % Rotamer: Outliers : 2.60 % Allowed : 13.28 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.28), residues: 869 helix: 2.12 (0.27), residues: 364 sheet: 1.45 (0.38), residues: 168 loop : -1.31 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.017 0.001 TYR D 149 PHE 0.017 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6750) covalent geometry : angle 0.57097 ( 9212) SS BOND : bond 0.00054 ( 1) SS BOND : angle 0.87731 ( 2) hydrogen bonds : bond 0.05631 ( 339) hydrogen bonds : angle 4.07798 ( 972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.303 Fit side-chains REVERT: B 75 GLN cc_start: 0.8277 (mt0) cc_final: 0.8065 (mt0) REVERT: B 217 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7950 (pmt) REVERT: B 234 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.7198 (t80) REVERT: D 90 MET cc_start: 0.6929 (mtm) cc_final: 0.6642 (ttp) REVERT: D 128 TYR cc_start: 0.6681 (t80) cc_final: 0.6360 (t80) outliers start: 17 outliers final: 8 residues processed: 92 average time/residue: 0.6324 time to fit residues: 60.8903 Evaluate side-chains 82 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140872 restraints weight = 6163.689| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.57 r_work: 0.3383 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6751 Z= 0.128 Angle : 0.548 6.466 9214 Z= 0.293 Chirality : 0.043 0.144 1106 Planarity : 0.004 0.068 1145 Dihedral : 8.963 151.339 982 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.44 % Allowed : 13.13 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.28), residues: 869 helix: 2.26 (0.27), residues: 364 sheet: 1.42 (0.38), residues: 170 loop : -1.23 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 314 TYR 0.017 0.001 TYR D 149 PHE 0.017 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 6750) covalent geometry : angle 0.54751 ( 9212) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.87440 ( 2) hydrogen bonds : bond 0.05230 ( 339) hydrogen bonds : angle 4.01941 ( 972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.289 Fit side-chains REVERT: B 217 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7957 (pmt) REVERT: B 234 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.7221 (t80) REVERT: B 273 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8378 (mt) REVERT: C 18 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.5083 (tm-30) REVERT: D 90 MET cc_start: 0.6937 (mtm) cc_final: 0.6707 (ttp) REVERT: D 128 TYR cc_start: 0.6716 (t80) cc_final: 0.6397 (t80) outliers start: 16 outliers final: 6 residues processed: 90 average time/residue: 0.6383 time to fit residues: 60.0429 Evaluate side-chains 85 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 80 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 0.0570 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140201 restraints weight = 6072.200| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.50 r_work: 0.3388 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6751 Z= 0.123 Angle : 0.537 6.488 9214 Z= 0.287 Chirality : 0.043 0.143 1106 Planarity : 0.004 0.068 1145 Dihedral : 8.862 150.833 982 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.29 % Allowed : 13.44 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.28), residues: 869 helix: 2.37 (0.27), residues: 364 sheet: 1.45 (0.38), residues: 170 loop : -1.20 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.018 0.001 TYR D 149 PHE 0.016 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6750) covalent geometry : angle 0.53664 ( 9212) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.82957 ( 2) hydrogen bonds : bond 0.05028 ( 339) hydrogen bonds : angle 3.98713 ( 972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.239 Fit side-chains REVERT: B 75 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7658 (mm110) REVERT: B 217 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7964 (pmt) REVERT: B 234 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7234 (t80) REVERT: B 273 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8355 (mt) REVERT: D 90 MET cc_start: 0.6888 (mtm) cc_final: 0.6667 (ttp) REVERT: D 128 TYR cc_start: 0.6761 (t80) cc_final: 0.6461 (t80) REVERT: D 243 MET cc_start: 0.7748 (ttp) cc_final: 0.7108 (mmt) REVERT: A 15 ARG cc_start: 0.7637 (ttt90) cc_final: 0.6262 (ttp-170) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 0.5863 time to fit residues: 55.9699 Evaluate side-chains 84 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 7 optimal weight: 0.0270 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN A 22 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139486 restraints weight = 6133.653| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.65 r_work: 0.3368 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6751 Z= 0.139 Angle : 0.566 6.455 9214 Z= 0.304 Chirality : 0.044 0.146 1106 Planarity : 0.004 0.068 1145 Dihedral : 8.992 151.450 982 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.29 % Allowed : 14.05 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.28), residues: 869 helix: 2.33 (0.27), residues: 364 sheet: 1.52 (0.39), residues: 168 loop : -1.23 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.018 0.001 TYR D 149 PHE 0.017 0.001 PHE B 151 TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6750) covalent geometry : angle 0.56630 ( 9212) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.90645 ( 2) hydrogen bonds : bond 0.05545 ( 339) hydrogen bonds : angle 4.09111 ( 972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.310 Fit side-chains REVERT: B 75 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7712 (mm110) REVERT: B 217 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7962 (pmt) REVERT: B 234 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.7206 (t80) REVERT: B 273 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 18 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.5173 (tm-30) REVERT: D 90 MET cc_start: 0.6883 (mtm) cc_final: 0.6659 (ttp) REVERT: D 128 TYR cc_start: 0.6772 (t80) cc_final: 0.6474 (t80) outliers start: 15 outliers final: 7 residues processed: 84 average time/residue: 0.6217 time to fit residues: 54.7248 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.175514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138869 restraints weight = 6130.265| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.56 r_work: 0.3354 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6751 Z= 0.155 Angle : 0.598 6.686 9214 Z= 0.321 Chirality : 0.045 0.147 1106 Planarity : 0.004 0.068 1145 Dihedral : 9.180 152.509 982 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.60 % Allowed : 13.89 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.28), residues: 869 helix: 2.22 (0.27), residues: 365 sheet: 1.50 (0.39), residues: 168 loop : -1.26 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.018 0.002 TYR D 149 PHE 0.019 0.002 PHE B 151 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6750) covalent geometry : angle 0.59830 ( 9212) SS BOND : bond 0.00075 ( 1) SS BOND : angle 0.84845 ( 2) hydrogen bonds : bond 0.06034 ( 339) hydrogen bonds : angle 4.16922 ( 972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.249 Fit side-chains REVERT: B 75 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7751 (mm110) REVERT: B 217 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7955 (pmt) REVERT: B 234 PHE cc_start: 0.8755 (OUTLIER) cc_final: 0.7122 (t80) REVERT: C 18 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.5046 (tm-30) REVERT: C 36 ASP cc_start: 0.7995 (t0) cc_final: 0.7215 (m-30) REVERT: D 90 MET cc_start: 0.6875 (mtm) cc_final: 0.6297 (mtm) REVERT: D 128 TYR cc_start: 0.6758 (t80) cc_final: 0.6450 (t80) outliers start: 17 outliers final: 9 residues processed: 85 average time/residue: 0.6292 time to fit residues: 56.0504 Evaluate side-chains 83 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 17 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140403 restraints weight = 6139.446| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.63 r_work: 0.3387 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6751 Z= 0.123 Angle : 0.545 7.077 9214 Z= 0.289 Chirality : 0.043 0.144 1106 Planarity : 0.004 0.068 1145 Dihedral : 8.858 151.222 982 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.98 % Allowed : 14.66 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.28), residues: 869 helix: 2.42 (0.27), residues: 364 sheet: 1.50 (0.39), residues: 170 loop : -1.20 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.018 0.001 TYR D 149 PHE 0.016 0.001 PHE B 151 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6750) covalent geometry : angle 0.54528 ( 9212) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.83511 ( 2) hydrogen bonds : bond 0.04980 ( 339) hydrogen bonds : angle 4.00617 ( 972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1738 Ramachandran restraints generated. 869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.324 Fit side-chains REVERT: B 75 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7684 (mm110) REVERT: B 217 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7982 (pmt) REVERT: B 234 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7226 (t80) REVERT: B 273 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8334 (mt) REVERT: C 18 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.5199 (tm-30) REVERT: C 21 MET cc_start: 0.6714 (mtp) cc_final: 0.6126 (ttt) REVERT: C 36 ASP cc_start: 0.7985 (t0) cc_final: 0.7198 (m-30) REVERT: D 90 MET cc_start: 0.6823 (mtm) cc_final: 0.6617 (ttp) REVERT: D 128 TYR cc_start: 0.6762 (t80) cc_final: 0.6403 (t80) REVERT: D 243 MET cc_start: 0.7683 (ttp) cc_final: 0.7029 (mmt) REVERT: D 327 THR cc_start: 0.7963 (m) cc_final: 0.7759 (t) outliers start: 13 outliers final: 7 residues processed: 87 average time/residue: 0.6188 time to fit residues: 56.4736 Evaluate side-chains 87 residues out of total 770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 18 GLN Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 324 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.0370 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN A 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.175103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138263 restraints weight = 6097.612| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.56 r_work: 0.3353 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6751 Z= 0.165 Angle : 0.615 6.812 9214 Z= 0.329 Chirality : 0.045 0.148 1106 Planarity : 0.004 0.068 1145 Dihedral : 9.226 152.856 982 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.75 % Allowed : 14.05 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.28), residues: 869 helix: 2.21 (0.27), residues: 365 sheet: 1.51 (0.39), residues: 168 loop : -1.25 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.019 0.002 TYR D 149 PHE 0.020 0.002 PHE B 151 TRP 0.008 0.002 TRP B 82 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6750) covalent geometry : angle 0.61534 ( 9212) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.81585 ( 2) hydrogen bonds : bond 0.06226 ( 339) hydrogen bonds : angle 4.19589 ( 972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3208.69 seconds wall clock time: 55 minutes 17.08 seconds (3317.08 seconds total)