Starting phenix.real_space_refine on Thu Jul 2 05:17:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t2g_25612/07_2026/7t2g_25612.cif" } resolution = 2.5 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= 0.028 sd= 0.242 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 59 5.16 5 C 4461 2.51 5 N 1154 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6922 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1690 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2481 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 2, 'ARG:plan': 8, 'GLU:plan': 5, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 348 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 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: "R" Number of atoms: 2279 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 288, 2270 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 288, 2270 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 2317 Chain: "R" Number of atoms: 124 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 11, 94 Unusual residues: {'CLR': 2, 'EIG': 1} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} Conformer: "B" Number of residues, atoms: 11, 94 Unusual residues: {'CLR': 2, 'EIG': 1} Classifications: {'undetermined': 3, 'water': 8} Link IDs: {None: 10} bond proxies already assigned to first conformer: 62 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AEIG R 501 " occ=0.50 ... (58 atoms not shown) pdb=" O05BEIG R 501 " occ=0.50 Time building chain proxies: 1.49, per 1000 atoms: 0.22 Number of scatterers: 6922 At special positions: 0 Unit cell: (91.84, 98.4, 114.8, 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 59 16.00 O 1248 8.00 N 1154 7.00 C 4461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 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: 0.48 Conformation dependent library (CDL) restraints added in 431.4 milliseconds 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1706 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 47.8% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.630A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.061A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 Processing helix chain 'A' and resid 228 through 232 removed outlier: 3.722A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.691A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 46 removed outlier: 4.638A pdb=" N LYS C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 Processing helix chain 'R' and resid 101 through 120 removed outlier: 3.630A pdb=" N THR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 130 Processing helix chain 'R' and resid 135 through 171 removed outlier: 4.173A pdb=" N LEU R 139 " --> pdb=" O PHE R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 179 removed outlier: 4.142A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 195 Processing helix chain 'R' and resid 195 through 206 Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 224 through 241 removed outlier: 3.598A pdb=" N TRP R 228 " --> pdb=" O PRO R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 260 Processing helix chain 'R' and resid 268 through 306 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 337 removed outlier: 3.852A pdb=" N VAL R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 340 through 348 removed outlier: 3.610A pdb=" N ARG R 345 " --> pdb=" O GLU R 341 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 346 " --> pdb=" O ASN R 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.189A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.524A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.826A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.987A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.524A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.696A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.526A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 5.826A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 208 through 211 398 hydrogen bonds defined for protein. 1158 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: 0.89 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1094 1.30 - 1.43: 1855 1.43 - 1.56: 4029 1.56 - 1.69: 6 1.69 - 1.82: 83 Bond restraints: 7067 Sorted by residual: bond pdb=" C08BEIG R 501 " pdb=" N01BEIG R 501 " ideal model delta sigma weight residual 1.448 1.271 0.177 2.00e-02 2.50e+03 7.83e+01 bond pdb=" C17BEIG R 501 " pdb=" C19BEIG R 501 " ideal model delta sigma weight residual 1.470 1.611 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C08BEIG R 501 " pdb=" C09BEIG R 501 " ideal model delta sigma weight residual 1.529 1.404 0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C LEU B 252 " pdb=" O LEU B 252 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.22e-02 6.72e+03 2.97e+01 bond pdb=" C17AEIG R 501 " pdb=" C20AEIG R 501 " ideal model delta sigma weight residual 1.348 1.445 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 7062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 9565 4.04 - 8.08: 60 8.08 - 12.12: 6 12.12 - 16.16: 0 16.16 - 20.20: 1 Bond angle restraints: 9632 Sorted by residual: angle pdb=" C09BEIG R 501 " pdb=" C08BEIG R 501 " pdb=" C12BEIG R 501 " ideal model delta sigma weight residual 114.95 94.75 20.20 3.00e+00 1.11e-01 4.53e+01 angle pdb=" N GLY B 64 " pdb=" CA GLY B 64 " pdb=" C GLY B 64 " ideal model delta sigma weight residual 112.82 105.38 7.44 1.38e+00 5.25e-01 2.90e+01 angle pdb=" N ASN R 328 " pdb=" CA ASN R 328 " pdb=" C ASN R 328 " ideal model delta sigma weight residual 112.54 106.25 6.29 1.22e+00 6.72e-01 2.66e+01 angle pdb=" N SER R 329 " pdb=" CA SER R 329 " pdb=" C SER R 329 " ideal model delta sigma weight residual 112.23 105.84 6.39 1.26e+00 6.30e-01 2.57e+01 angle pdb=" N LYS C 32 " pdb=" CA LYS C 32 " pdb=" C LYS C 32 " ideal model delta sigma weight residual 112.90 106.27 6.63 1.31e+00 5.83e-01 2.56e+01 ... (remaining 9627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 3934 17.02 - 34.03: 236 34.03 - 51.05: 35 51.05 - 68.07: 18 68.07 - 85.09: 4 Dihedral angle restraints: 4227 sinusoidal: 1598 harmonic: 2629 Sorted by residual: dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 293 " pdb=" C ASN B 293 " pdb=" N CYS B 294 " pdb=" CA CYS B 294 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1069 0.096 - 0.192: 68 0.192 - 0.288: 1 0.288 - 0.383: 1 0.383 - 0.479: 1 Chirality restraints: 1140 Sorted by residual: chirality pdb=" C08BEIG R 501 " pdb=" C09BEIG R 501 " pdb=" C10BEIG R 501 " pdb=" C12BEIG R 501 " both_signs ideal model delta sigma weight residual False -2.77 -2.29 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C14BEIG R 501 " pdb=" C13BEIG R 501 " pdb=" C15BEIG R 501 " pdb=" C17BEIG R 501 " both_signs ideal model delta sigma weight residual False -2.26 -2.58 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C10AEIG R 501 " pdb=" C08AEIG R 501 " pdb=" C13AEIG R 501 " pdb=" N02AEIG R 501 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1137 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C14BEIG R 501 " -0.022 2.00e-02 2.50e+03 4.86e-02 2.95e+01 pdb=" C17BEIG R 501 " 0.016 2.00e-02 2.50e+03 pdb=" C19BEIG R 501 " 0.029 2.00e-02 2.50e+03 pdb=" C20BEIG R 501 " -0.082 2.00e-02 2.50e+03 pdb=" O03BEIG R 501 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 251 " 0.413 9.50e-02 1.11e+02 1.85e-01 2.10e+01 pdb=" NE ARG B 251 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG B 251 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG B 251 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 251 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 252 " -0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C LEU B 252 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU B 252 " -0.027 2.00e-02 2.50e+03 pdb=" N PHE B 253 " -0.024 2.00e-02 2.50e+03 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1007 2.75 - 3.29: 7286 3.29 - 3.83: 12842 3.83 - 4.36: 16022 4.36 - 4.90: 25912 Nonbonded interactions: 63069 Sorted by model distance: nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASN B 110 " pdb=" NZ LYS B 127 " model vdw 2.284 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.300 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.308 3.120 nonbonded pdb=" OD2 ASP R 147 " pdb=" OH TYR R 326 " model vdw 2.314 3.040 ... (remaining 63064 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=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.270 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 : 0.007 0.177 7068 Z= 0.421 Angle : 0.880 20.195 9634 Z= 0.534 Chirality : 0.049 0.479 1140 Planarity : 0.008 0.185 1190 Dihedral : 12.261 85.085 2518 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.00 % Allowed : 7.30 % Favored : 91.70 % 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: 0.61 (0.28), residues: 890 helix: 1.29 (0.27), residues: 376 sheet: 0.19 (0.37), residues: 175 loop : -0.38 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 251 TYR 0.019 0.002 TYR R 326 PHE 0.015 0.002 PHE B 151 TRP 0.024 0.002 TRP R 192 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.42 ( 7067) covalent geometry : angle 0.87975 / 0.53 ( 9632) SS BOND : bond 0.00223 / 0.12 ( 1) SS BOND : angle 0.54843 / 0.31 ( 2) hydrogen bonds : bond 0.20224 / 13.89 ( 398) hydrogen bonds : angle 8.00504 / 5.83 ( 1158) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.172 Fit side-chains REVERT: B 75 GLN cc_start: 0.7678 (mm110) cc_final: 0.7038 (mm110) REVERT: B 83 ASP cc_start: 0.8110 (t0) cc_final: 0.7830 (t0) outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 0.4699 time to fit residues: 83.1241 Evaluate side-chains 155 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain R residue 160 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 269 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 259 GLN B 293 ASN B 340 ASN R 109 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.111119 restraints weight = 19750.172| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.58 r_work: 0.3299 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7068 Z= 0.157 Angle : 0.574 5.568 9634 Z= 0.311 Chirality : 0.042 0.159 1140 Planarity : 0.004 0.037 1190 Dihedral : 6.240 55.283 1096 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.43 % Allowed : 12.02 % Favored : 85.55 % 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: 0.94 (0.28), residues: 890 helix: 1.91 (0.26), residues: 390 sheet: 0.22 (0.38), residues: 167 loop : -0.69 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 251 TYR 0.009 0.001 TYR R 326 PHE 0.015 0.002 PHE R 237 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 7067) covalent geometry : angle 0.57439 / 0.31 ( 9632) SS BOND : bond 0.00300 / 0.16 ( 1) SS BOND : angle 0.62583 / 0.36 ( 2) hydrogen bonds : bond 0.05017 / 3.53 ( 398) hydrogen bonds : angle 5.51871 / 3.92 ( 1158) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.263 Fit side-chains REVERT: A 285 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7147 (mt) REVERT: A 308 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6996 (mm-30) REVERT: B 32 GLN cc_start: 0.7707 (mt0) cc_final: 0.7489 (mt0) REVERT: B 75 GLN cc_start: 0.7704 (mm110) cc_final: 0.7128 (mm110) REVERT: B 83 ASP cc_start: 0.8240 (t0) cc_final: 0.7972 (t0) REVERT: R 230 ASN cc_start: 0.7870 (m-40) cc_final: 0.7579 (m-40) REVERT: R 280 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (mtt-85) outliers start: 17 outliers final: 6 residues processed: 173 average time/residue: 0.5464 time to fit residues: 99.3524 Evaluate side-chains 159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain R residue 160 THR Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 280 ARG Chi-restraints excluded: chain R residue 316 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 195 HIS A 269 ASN ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN R 150 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110880 restraints weight = 27920.416| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.26 r_work: 0.3248 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7068 Z= 0.143 Angle : 0.534 5.588 9634 Z= 0.287 Chirality : 0.041 0.160 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.824 57.647 1096 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.00 % Allowed : 15.59 % Favored : 82.40 % 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: 0.89 (0.28), residues: 890 helix: 1.94 (0.26), residues: 392 sheet: 0.04 (0.37), residues: 167 loop : -0.73 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.011 0.001 TYR R 149 PHE 0.012 0.001 PHE R 237 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7067) covalent geometry : angle 0.53430 / 0.29 ( 9632) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 0.24869 / 0.14 ( 2) hydrogen bonds : bond 0.04570 / 3.23 ( 398) hydrogen bonds : angle 5.26850 / 3.75 ( 1158) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.260 Fit side-chains REVERT: A 19 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7254 (pt) REVERT: A 53 MET cc_start: 0.4875 (mtt) cc_final: 0.4169 (tpp) REVERT: A 207 GLU cc_start: 0.7195 (tp30) cc_final: 0.6757 (mm-30) REVERT: A 285 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7104 (mt) REVERT: A 308 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6985 (mm-30) REVERT: B 75 GLN cc_start: 0.7644 (mm110) cc_final: 0.6758 (mm-40) REVERT: B 83 ASP cc_start: 0.8108 (t0) cc_final: 0.7907 (t0) REVERT: R 276 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7568 (ttp80) outliers start: 14 outliers final: 3 residues processed: 162 average time/residue: 0.5315 time to fit residues: 90.7236 Evaluate side-chains 154 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 195 HIS A 269 ASN A 311 ASN B 220 GLN B 259 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110051 restraints weight = 31017.339| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.59 r_work: 0.3204 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7068 Z= 0.160 Angle : 0.551 5.909 9634 Z= 0.293 Chirality : 0.042 0.159 1140 Planarity : 0.004 0.035 1190 Dihedral : 5.760 54.210 1096 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.43 % Allowed : 15.59 % Favored : 81.97 % 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: 0.69 (0.27), residues: 890 helix: 1.78 (0.25), residues: 398 sheet: -0.04 (0.37), residues: 167 loop : -0.91 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 280 TYR 0.012 0.001 TYR R 326 PHE 0.013 0.002 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 7067) covalent geometry : angle 0.55058 / 0.29 ( 9632) SS BOND : bond 0.00188 / 0.10 ( 1) SS BOND : angle 0.05227 / 0.03 ( 2) hydrogen bonds : bond 0.04583 / 3.23 ( 398) hydrogen bonds : angle 5.22695 / 3.73 ( 1158) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.273 Fit side-chains REVERT: A 19 ILE cc_start: 0.7496 (OUTLIER) cc_final: 0.7269 (pt) REVERT: A 53 MET cc_start: 0.4833 (mtt) cc_final: 0.4077 (tpp) REVERT: A 207 GLU cc_start: 0.7362 (tp30) cc_final: 0.6909 (mm-30) REVERT: A 285 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7043 (mt) REVERT: B 44 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: B 75 GLN cc_start: 0.7729 (mm110) cc_final: 0.6843 (mm-40) REVERT: B 83 ASP cc_start: 0.8131 (t0) cc_final: 0.7911 (t0) outliers start: 17 outliers final: 5 residues processed: 161 average time/residue: 0.5025 time to fit residues: 85.3506 Evaluate side-chains 158 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 150 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 264 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 20 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 84 optimal weight: 0.0040 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 269 ASN B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 ASN R 109 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.127297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111336 restraints weight = 27195.474| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.25 r_work: 0.3259 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7068 Z= 0.143 Angle : 0.538 6.132 9634 Z= 0.287 Chirality : 0.041 0.159 1140 Planarity : 0.004 0.036 1190 Dihedral : 5.595 54.060 1095 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.29 % Allowed : 16.60 % Favored : 81.12 % 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: 0.69 (0.28), residues: 890 helix: 1.79 (0.25), residues: 402 sheet: -0.15 (0.37), residues: 174 loop : -0.90 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 280 TYR 0.015 0.001 TYR R 149 PHE 0.012 0.001 PHE R 237 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 7067) covalent geometry : angle 0.53855 / 0.29 ( 9632) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.04505 / 0.03 ( 2) hydrogen bonds : bond 0.04332 / 3.06 ( 398) hydrogen bonds : angle 5.13339 / 3.67 ( 1158) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.262 Fit side-chains REVERT: A 14 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7445 (tp30) REVERT: A 19 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7249 (pt) REVERT: A 52 GLN cc_start: 0.7226 (mm-40) cc_final: 0.6926 (mm110) REVERT: A 53 MET cc_start: 0.4849 (mtt) cc_final: 0.3962 (tpp) REVERT: A 207 GLU cc_start: 0.7335 (tp30) cc_final: 0.6938 (mm-30) REVERT: A 285 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7033 (mt) REVERT: A 308 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6877 (mm-30) REVERT: B 44 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: B 75 GLN cc_start: 0.7655 (mm110) cc_final: 0.6775 (mm-40) REVERT: R 243 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7445 (mpm) REVERT: R 276 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7481 (ttp80) outliers start: 16 outliers final: 6 residues processed: 158 average time/residue: 0.5268 time to fit residues: 87.6666 Evaluate side-chains 159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 243 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 0.0670 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 269 ASN B 220 GLN B 259 GLN B 340 ASN ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.128920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.112484 restraints weight = 28890.389| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.05 r_work: 0.3326 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7068 Z= 0.126 Angle : 0.518 6.197 9634 Z= 0.276 Chirality : 0.041 0.159 1140 Planarity : 0.003 0.038 1190 Dihedral : 5.401 53.652 1095 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.43 % Allowed : 17.17 % Favored : 80.40 % 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: 0.81 (0.28), residues: 890 helix: 1.87 (0.25), residues: 402 sheet: 0.04 (0.37), residues: 173 loop : -0.90 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 280 TYR 0.009 0.001 TYR R 128 PHE 0.012 0.001 PHE R 237 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7067) covalent geometry : angle 0.51814 / 0.28 ( 9632) SS BOND : bond 0.00144 / 0.08 ( 1) SS BOND : angle 0.09936 / 0.06 ( 2) hydrogen bonds : bond 0.04087 / 2.89 ( 398) hydrogen bonds : angle 5.03032 / 3.59 ( 1158) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.214 Fit side-chains REVERT: A 14 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7685 (tp30) REVERT: A 19 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7240 (pt) REVERT: A 52 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6993 (mm110) REVERT: A 53 MET cc_start: 0.4655 (mtt) cc_final: 0.3917 (mpp) REVERT: A 285 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7065 (mt) REVERT: A 308 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6957 (mm-30) REVERT: B 75 GLN cc_start: 0.7815 (mm110) cc_final: 0.6928 (mm-40) REVERT: B 83 ASP cc_start: 0.8229 (t0) cc_final: 0.7883 (t0) REVERT: B 220 GLN cc_start: 0.8397 (mt0) cc_final: 0.8162 (mt0) REVERT: R 243 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7528 (mpm) REVERT: R 276 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7603 (ttp80) REVERT: R 343 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7084 (m-80) outliers start: 17 outliers final: 6 residues processed: 166 average time/residue: 0.5265 time to fit residues: 92.0766 Evaluate side-chains 161 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 151 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** 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 = 0.3651 r_free = 0.3651 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109030 restraints weight = 25336.579| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.22 r_work: 0.3225 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7068 Z= 0.197 Angle : 0.595 6.284 9634 Z= 0.317 Chirality : 0.043 0.167 1140 Planarity : 0.004 0.036 1190 Dihedral : 5.824 55.980 1095 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.86 % Allowed : 18.60 % Favored : 78.54 % 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: 0.58 (0.27), residues: 890 helix: 1.67 (0.25), residues: 400 sheet: -0.11 (0.37), residues: 172 loop : -0.96 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 280 TYR 0.017 0.002 TYR R 149 PHE 0.015 0.002 PHE A 189 TRP 0.012 0.002 TRP B 99 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 ( 7067) covalent geometry : angle 0.59540 / 0.32 ( 9632) SS BOND : bond 0.00189 / 0.10 ( 1) SS BOND : angle 0.22538 / 0.13 ( 2) hydrogen bonds : bond 0.04769 / 3.33 ( 398) hydrogen bonds : angle 5.26634 / 3.76 ( 1158) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.248 Fit side-chains REVERT: A 19 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7244 (pt) REVERT: A 52 GLN cc_start: 0.7216 (mm-40) cc_final: 0.6929 (mm110) REVERT: A 53 MET cc_start: 0.4897 (mtt) cc_final: 0.4005 (mpp) REVERT: A 257 LYS cc_start: 0.7340 (pmtt) cc_final: 0.7140 (pptt) REVERT: A 285 ILE cc_start: 0.7614 (OUTLIER) cc_final: 0.7043 (mt) REVERT: A 308 GLU cc_start: 0.7433 (mt-10) cc_final: 0.6899 (mm-30) REVERT: B 44 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: B 75 GLN cc_start: 0.7651 (mm110) cc_final: 0.6735 (mm-40) REVERT: B 83 ASP cc_start: 0.8126 (t0) cc_final: 0.7922 (t0) REVERT: R 243 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7577 (mpm) REVERT: R 276 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7466 (ttp80) REVERT: R 343 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6814 (m-80) outliers start: 20 outliers final: 7 residues processed: 160 average time/residue: 0.4940 time to fit residues: 83.4532 Evaluate side-chains 157 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 269 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 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 = 0.3695 r_free = 0.3695 target = 0.128248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112475 restraints weight = 24592.791| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.11 r_work: 0.3278 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3277 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3277 r_free = 0.3277 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3277 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7068 Z= 0.133 Angle : 0.533 6.490 9634 Z= 0.284 Chirality : 0.041 0.157 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.467 54.066 1095 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.15 % Allowed : 19.03 % Favored : 78.83 % 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: 0.59 (0.27), residues: 890 helix: 1.63 (0.25), residues: 402 sheet: -0.03 (0.37), residues: 173 loop : -0.94 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 280 TYR 0.008 0.001 TYR R 326 PHE 0.012 0.001 PHE R 237 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7067) covalent geometry : angle 0.53279 / 0.28 ( 9632) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 0.06211 / 0.04 ( 2) hydrogen bonds : bond 0.04200 / 2.98 ( 398) hydrogen bonds : angle 5.08375 / 3.62 ( 1158) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.278 Fit side-chains REVERT: A 19 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7221 (pt) REVERT: A 52 GLN cc_start: 0.7216 (mm-40) cc_final: 0.7013 (mm110) REVERT: A 285 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7023 (mt) REVERT: B 44 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: B 75 GLN cc_start: 0.7648 (mm110) cc_final: 0.6675 (mm-40) REVERT: R 243 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7442 (mpm) REVERT: R 276 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7506 (ttp80) REVERT: R 343 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6885 (m-80) outliers start: 15 outliers final: 5 residues processed: 155 average time/residue: 0.5135 time to fit residues: 83.9011 Evaluate side-chains 159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 0.0020 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 269 ASN B 17 GLN B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.127840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111945 restraints weight = 27699.750| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.41 r_work: 0.3259 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7068 Z= 0.145 Angle : 0.550 6.921 9634 Z= 0.292 Chirality : 0.042 0.181 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.522 54.796 1095 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.00 % Allowed : 20.17 % Favored : 77.83 % 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: 0.59 (0.27), residues: 890 helix: 1.62 (0.25), residues: 402 sheet: -0.04 (0.37), residues: 175 loop : -0.94 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 280 TYR 0.016 0.001 TYR R 149 PHE 0.012 0.002 PHE A 189 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 7067) covalent geometry : angle 0.54961 / 0.29 ( 9632) SS BOND : bond 0.00184 / 0.10 ( 1) SS BOND : angle 0.01867 / 0.01 ( 2) hydrogen bonds : bond 0.04300 / 3.03 ( 398) hydrogen bonds : angle 5.09545 / 3.63 ( 1158) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.225 Fit side-chains REVERT: A 14 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7475 (tp30) REVERT: A 52 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6950 (mm110) REVERT: A 53 MET cc_start: 0.4868 (mtt) cc_final: 0.3877 (mpp) REVERT: A 285 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.6988 (mt) REVERT: A 308 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6788 (mm-30) REVERT: B 44 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: B 75 GLN cc_start: 0.7664 (mm110) cc_final: 0.6687 (mm-40) REVERT: B 83 ASP cc_start: 0.8134 (t0) cc_final: 0.7906 (t0) REVERT: R 243 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7472 (mpm) REVERT: R 276 ARG cc_start: 0.7754 (mtm-85) cc_final: 0.7512 (ttp80) REVERT: R 343 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6798 (m-80) outliers start: 14 outliers final: 6 residues processed: 158 average time/residue: 0.5163 time to fit residues: 85.9663 Evaluate side-chains 159 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 255 MET Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111499 restraints weight = 20453.052| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.69 r_work: 0.3314 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7068 Z= 0.160 Angle : 0.568 6.944 9634 Z= 0.303 Chirality : 0.042 0.177 1140 Planarity : 0.004 0.037 1190 Dihedral : 5.582 55.141 1093 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.72 % Allowed : 20.17 % Favored : 78.11 % 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: 0.49 (0.27), residues: 890 helix: 1.52 (0.25), residues: 402 sheet: -0.07 (0.37), residues: 177 loop : -0.96 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 280 TYR 0.010 0.001 TYR R 326 PHE 0.012 0.002 PHE A 189 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7067) covalent geometry : angle 0.56833 / 0.30 ( 9632) SS BOND : bond 0.00173 / 0.09 ( 1) SS BOND : angle 0.09018 / 0.05 ( 2) hydrogen bonds : bond 0.04442 / 3.12 ( 398) hydrogen bonds : angle 5.15727 / 3.67 ( 1158) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1780 Ramachandran restraints generated. 890 Oldfield, 0 Emsley, 890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.178 Fit side-chains REVERT: A 53 MET cc_start: 0.4964 (mtt) cc_final: 0.3878 (mpp) REVERT: A 285 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7025 (mt) REVERT: A 308 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6882 (mm-30) REVERT: B 32 GLN cc_start: 0.7809 (mt0) cc_final: 0.7599 (mt0) REVERT: B 44 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: B 75 GLN cc_start: 0.7767 (mm110) cc_final: 0.6839 (mm-40) REVERT: B 83 ASP cc_start: 0.8234 (t0) cc_final: 0.7931 (t0) REVERT: B 220 GLN cc_start: 0.8352 (mt0) cc_final: 0.8139 (mt0) REVERT: R 243 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7619 (mpm) REVERT: R 276 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7569 (ttp80) REVERT: R 343 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.6837 (m-80) outliers start: 12 outliers final: 5 residues processed: 157 average time/residue: 0.5019 time to fit residues: 82.9888 Evaluate side-chains 160 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 343 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 195 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108293 restraints weight = 29771.001| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.13 r_work: 0.3247 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7068 Z= 0.204 Angle : 0.623 6.881 9634 Z= 0.330 Chirality : 0.044 0.193 1140 Planarity : 0.004 0.036 1190 Dihedral : 5.878 56.462 1093 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.43 % Allowed : 20.46 % Favored : 78.11 % 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: 0.35 (0.27), residues: 890 helix: 1.36 (0.25), residues: 403 sheet: -0.15 (0.37), residues: 177 loop : -0.98 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 280 TYR 0.016 0.002 TYR R 149 PHE 0.015 0.002 PHE A 189 TRP 0.017 0.002 TRP R 192 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 ( 7067) covalent geometry : angle 0.62258 / 0.33 ( 9632) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.26454 / 0.16 ( 2) hydrogen bonds : bond 0.04875 / 3.41 ( 398) hydrogen bonds : angle 5.31020 / 3.78 ( 1158) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2960.43 seconds wall clock time: 51 minutes 17.67 seconds (3077.67 seconds total)