Starting phenix.real_space_refine on Thu Mar 13 16:39:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d7m_30608/03_2025/7d7m_30608_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d7m_30608/03_2025/7d7m_30608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d7m_30608/03_2025/7d7m_30608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d7m_30608/03_2025/7d7m_30608.map" model { file = "/net/cci-nas-00/data/ceres_data/7d7m_30608/03_2025/7d7m_30608_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d7m_30608/03_2025/7d7m_30608_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1953 atoms to isotropic. 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 40 5.16 5 C 4707 2.51 5 N 1226 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7326 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2097 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 272} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 2276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2276 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 377 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 19, 'ASN:plan1': 8, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 328 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1713 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 11, 'ARG:plan': 9, 'ASN:plan1': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 129 Chain: "E" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 887 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.87, per 1000 atoms: 0.66 Number of scatterers: 7326 At special positions: 0 Unit cell: (100.362, 91.026, 119.034, 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 40 16.00 O 1353 8.00 N 1226 7.00 C 4707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 170 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.02 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: 1.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 40.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.222A pdb=" N ALA A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 83 Proline residue: A 74 - end of helix removed outlier: 3.731A pdb=" N THR A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 123 removed outlier: 3.615A pdb=" N LEU A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 132 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 178 through 217 removed outlier: 3.681A pdb=" N GLN A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 298 removed outlier: 4.011A pdb=" N MET A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 273 " --> pdb=" O GLN A 269 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.558A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 330 Proline residue: A 322 - end of helix Proline residue: A 326 - end of helix removed outlier: 3.710A pdb=" N TYR A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.652A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.520A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.721A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'D' and resid 13 through 40 Processing helix chain 'D' and resid 252 through 279 removed outlier: 3.834A pdb=" N GLN D 267 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 268 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.975A pdb=" N TYR D 311 " --> pdb=" O LYS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 316 Processing helix chain 'D' and resid 331 through 353 removed outlier: 3.577A pdb=" N ARG D 342 " --> pdb=" O LYS D 338 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY D 353 " --> pdb=" O SER D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 392 removed outlier: 3.972A pdb=" N ASP D 381 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 382 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 390 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D 391 " --> pdb=" O HIS D 387 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.764A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.228A 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: 3.777A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 7.075A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.648A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.257A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.663A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 41 through 43 removed outlier: 6.360A pdb=" N HIS D 41 " --> pdb=" O HIS D 220 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE D 222 " --> pdb=" O HIS D 41 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 43 " --> pdb=" O PHE D 222 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP D 223 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.222A pdb=" N PHE D 246 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN D 292 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 248 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.867A pdb=" N GLY E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL E 124 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1074 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1521 1.33 - 1.45: 1792 1.45 - 1.57: 4122 1.57 - 1.69: 1 1.69 - 1.81: 50 Bond restraints: 7486 Sorted by residual: bond pdb=" C15 P2E A 401 " pdb=" C16 P2E A 401 " ideal model delta sigma weight residual 1.530 1.574 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C14 P2E A 401 " pdb=" C15 P2E A 401 " ideal model delta sigma weight residual 1.503 1.540 -0.037 2.00e-02 2.50e+03 3.37e+00 bond pdb=" C12 P2E A 401 " pdb=" C13 P2E A 401 " ideal model delta sigma weight residual 1.491 1.525 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" C11 P2E A 401 " pdb=" C12 P2E A 401 " ideal model delta sigma weight residual 1.529 1.563 -0.034 2.00e-02 2.50e+03 2.88e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.84e+00 ... (remaining 7481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 10101 1.96 - 3.91: 138 3.91 - 5.87: 24 5.87 - 7.82: 1 7.82 - 9.78: 4 Bond angle restraints: 10268 Sorted by residual: angle pdb=" CB LEU B 95 " pdb=" CG LEU B 95 " pdb=" CD2 LEU B 95 " ideal model delta sigma weight residual 110.70 120.48 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C7 P2E A 401 " pdb=" C8 P2E A 401 " pdb=" C9 P2E A 401 " ideal model delta sigma weight residual 115.46 106.47 8.99 3.00e+00 1.11e-01 8.97e+00 angle pdb=" C14 P2E A 401 " pdb=" C15 P2E A 401 " pdb=" O5 P2E A 401 " ideal model delta sigma weight residual 113.16 104.24 8.92 3.00e+00 1.11e-01 8.84e+00 angle pdb=" CA GLY B 144 " pdb=" C GLY B 144 " pdb=" N TYR B 145 " ideal model delta sigma weight residual 114.84 117.91 -3.07 1.06e+00 8.90e-01 8.40e+00 angle pdb=" CB LEU B 95 " pdb=" CG LEU B 95 " pdb=" CD1 LEU B 95 " ideal model delta sigma weight residual 110.70 119.25 -8.55 3.00e+00 1.11e-01 8.12e+00 ... (remaining 10263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3896 18.00 - 36.00: 350 36.00 - 53.99: 69 53.99 - 71.99: 18 71.99 - 89.99: 5 Dihedral angle restraints: 4338 sinusoidal: 1339 harmonic: 2999 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 170 " pdb=" CB CYS A 170 " ideal model delta sinusoidal sigma weight residual -86.00 -124.46 38.46 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.35 35.65 1 1.00e+01 1.00e-02 1.80e+01 dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual 93.00 122.66 -29.66 1 1.00e+01 1.00e-02 1.26e+01 ... (remaining 4335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.299: 1252 0.299 - 0.599: 1 0.599 - 0.898: 0 0.898 - 1.198: 0 1.198 - 1.497: 1 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CG LEU B 95 " pdb=" CB LEU B 95 " pdb=" CD1 LEU B 95 " pdb=" CD2 LEU B 95 " both_signs ideal model delta sigma weight residual False -2.59 -1.09 -1.50 2.00e-01 2.50e+01 5.60e+01 chirality pdb=" C15 P2E A 401 " pdb=" C14 P2E A 401 " pdb=" C16 P2E A 401 " pdb=" O5 P2E A 401 " both_signs ideal model delta sigma weight residual False 2.23 2.57 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C8 P2E A 401 " pdb=" C12 P2E A 401 " pdb=" C7 P2E A 401 " pdb=" C9 P2E A 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.81 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 1251 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 333 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ARG A 333 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG A 333 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS A 334 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 321 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.82e+00 pdb=" N PRO A 322 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 236 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 915 2.75 - 3.28: 7758 3.28 - 3.82: 12033 3.82 - 4.36: 13491 4.36 - 4.90: 23927 Nonbonded interactions: 58124 Sorted by model distance: nonbonded pdb=" O ASP D 223 " pdb=" OD1 ASP D 223 " model vdw 2.208 3.040 nonbonded pdb=" O VAL E 48 " pdb=" OG1 THR E 61 " model vdw 2.237 3.040 nonbonded pdb=" O ASP A 167 " pdb=" OD1 ASP A 167 " model vdw 2.295 3.040 nonbonded pdb=" O THR D 325 " pdb=" OG1 THR D 325 " model vdw 2.319 3.040 nonbonded pdb=" O ALA D 48 " pdb=" OG SER D 51 " model vdw 2.333 3.040 ... (remaining 58119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 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 : 0.004 0.044 7486 Z= 0.266 Angle : 0.637 9.779 10268 Z= 0.342 Chirality : 0.059 1.497 1254 Planarity : 0.004 0.074 1298 Dihedral : 15.090 89.988 2393 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1019 helix: 1.79 (0.26), residues: 390 sheet: -1.00 (0.36), residues: 197 loop : -0.92 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 234 HIS 0.010 0.002 HIS B 142 PHE 0.016 0.002 PHE B 241 TYR 0.014 0.002 TYR A 127 ARG 0.008 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.723 Fit side-chains REVERT: A 133 LYS cc_start: 0.7671 (tmmt) cc_final: 0.7332 (tmtt) REVERT: A 261 ARG cc_start: 0.6012 (mtt-85) cc_final: 0.5677 (mmt90) REVERT: B 59 TYR cc_start: 0.8657 (t80) cc_final: 0.8396 (t80) REVERT: D 253 TYR cc_start: 0.8249 (m-10) cc_final: 0.8020 (m-80) REVERT: D 344 GLU cc_start: 0.8373 (tp30) cc_final: 0.8138 (tp30) REVERT: D 377 ASN cc_start: 0.7824 (t0) cc_final: 0.7414 (t0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1592 time to fit residues: 39.0350 Evaluate side-chains 157 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN B 311 HIS D 267 GLN D 271 ASN E 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.191048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149823 restraints weight = 8112.310| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.59 r_work: 0.3363 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7486 Z= 0.243 Angle : 0.639 8.851 10268 Z= 0.326 Chirality : 0.042 0.158 1254 Planarity : 0.004 0.061 1298 Dihedral : 7.657 84.531 1121 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.06 % Allowed : 15.00 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1019 helix: 2.24 (0.26), residues: 399 sheet: -1.04 (0.34), residues: 209 loop : -0.60 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 234 HIS 0.006 0.001 HIS B 311 PHE 0.016 0.002 PHE A 28 TYR 0.012 0.001 TYR E 95 ARG 0.003 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.737 Fit side-chains REVERT: A 23 ILE cc_start: 0.6263 (mt) cc_final: 0.5923 (mm) REVERT: A 30 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6339 (t80) REVERT: A 261 ARG cc_start: 0.6673 (mtt-85) cc_final: 0.6312 (mmt90) REVERT: D 252 ASP cc_start: 0.7487 (t0) cc_final: 0.7192 (t0) REVERT: D 347 ARG cc_start: 0.7758 (tmm-80) cc_final: 0.7522 (ttp80) REVERT: D 377 ASN cc_start: 0.8180 (t0) cc_final: 0.7681 (t0) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.1534 time to fit residues: 35.6569 Evaluate side-chains 153 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 PHE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 74 optimal weight: 0.0970 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN D 23 ASN D 271 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.187395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146301 restraints weight = 8319.720| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.65 r_work: 0.3329 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7486 Z= 0.232 Angle : 0.586 8.243 10268 Z= 0.299 Chirality : 0.041 0.138 1254 Planarity : 0.004 0.052 1298 Dihedral : 6.817 80.473 1121 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.94 % Allowed : 19.71 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1019 helix: 2.31 (0.26), residues: 399 sheet: -1.11 (0.33), residues: 217 loop : -0.49 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 234 HIS 0.004 0.001 HIS D 357 PHE 0.016 0.001 PHE A 28 TYR 0.012 0.001 TYR E 95 ARG 0.003 0.000 ARG D 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.962 Fit side-chains REVERT: A 23 ILE cc_start: 0.6389 (mt) cc_final: 0.6055 (mm) REVERT: A 169 TRP cc_start: 0.7227 (p-90) cc_final: 0.6940 (p-90) REVERT: B 101 MET cc_start: 0.8848 (mtp) cc_final: 0.8504 (mtp) REVERT: B 146 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8259 (tp) REVERT: B 264 TYR cc_start: 0.8877 (m-80) cc_final: 0.8640 (m-80) REVERT: D 252 ASP cc_start: 0.7549 (t0) cc_final: 0.7167 (t0) REVERT: D 253 TYR cc_start: 0.7770 (m-80) cc_final: 0.7353 (m-80) REVERT: D 377 ASN cc_start: 0.7991 (t0) cc_final: 0.7474 (t0) REVERT: E 94 TYR cc_start: 0.8428 (m-10) cc_final: 0.8124 (m-80) REVERT: E 104 THR cc_start: 0.7586 (m) cc_final: 0.7347 (p) outliers start: 20 outliers final: 14 residues processed: 162 average time/residue: 0.1901 time to fit residues: 43.6612 Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN D 239 ASN D 271 ASN E 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141934 restraints weight = 8284.151| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.59 r_work: 0.3266 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7486 Z= 0.310 Angle : 0.620 9.306 10268 Z= 0.316 Chirality : 0.042 0.139 1254 Planarity : 0.004 0.052 1298 Dihedral : 6.579 80.485 1121 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.26 % Allowed : 21.47 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 1019 helix: 2.25 (0.26), residues: 398 sheet: -1.18 (0.33), residues: 227 loop : -0.53 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 234 HIS 0.013 0.002 HIS B 54 PHE 0.019 0.002 PHE E 68 TYR 0.018 0.002 TYR E 95 ARG 0.003 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.749 Fit side-chains REVERT: A 23 ILE cc_start: 0.6458 (mt) cc_final: 0.6120 (mm) REVERT: B 101 MET cc_start: 0.8900 (mtp) cc_final: 0.8569 (mtp) REVERT: B 146 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8204 (tp) REVERT: D 25 LYS cc_start: 0.7566 (ttmm) cc_final: 0.7081 (mttp) REVERT: D 252 ASP cc_start: 0.7662 (t0) cc_final: 0.7232 (t0) REVERT: D 253 TYR cc_start: 0.7912 (m-80) cc_final: 0.7679 (m-80) REVERT: D 271 ASN cc_start: 0.7453 (m-40) cc_final: 0.7165 (m110) REVERT: E 104 THR cc_start: 0.7740 (m) cc_final: 0.7516 (p) outliers start: 29 outliers final: 25 residues processed: 156 average time/residue: 0.1676 time to fit residues: 37.5480 Evaluate side-chains 158 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN D 239 ASN E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144327 restraints weight = 8154.169| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.53 r_work: 0.3295 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7486 Z= 0.226 Angle : 0.557 9.020 10268 Z= 0.287 Chirality : 0.041 0.134 1254 Planarity : 0.004 0.049 1298 Dihedral : 6.263 83.345 1121 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.00 % Allowed : 21.62 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 1019 helix: 2.35 (0.26), residues: 397 sheet: -1.28 (0.33), residues: 225 loop : -0.57 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 234 HIS 0.011 0.001 HIS B 54 PHE 0.020 0.001 PHE A 28 TYR 0.013 0.001 TYR E 95 ARG 0.002 0.000 ARG E 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.842 Fit side-chains REVERT: A 23 ILE cc_start: 0.6468 (mt) cc_final: 0.6128 (mm) REVERT: B 101 MET cc_start: 0.8911 (mtp) cc_final: 0.8656 (mtp) REVERT: B 146 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8093 (tp) REVERT: B 264 TYR cc_start: 0.9118 (m-80) cc_final: 0.8757 (m-80) REVERT: B 339 TRP cc_start: 0.8825 (m100) cc_final: 0.8573 (m100) REVERT: D 25 LYS cc_start: 0.7565 (ttmm) cc_final: 0.7090 (mttp) REVERT: D 252 ASP cc_start: 0.7583 (t0) cc_final: 0.7115 (t0) REVERT: D 253 TYR cc_start: 0.7870 (m-80) cc_final: 0.7661 (m-80) REVERT: E 104 THR cc_start: 0.7688 (m) cc_final: 0.7460 (p) outliers start: 34 outliers final: 23 residues processed: 160 average time/residue: 0.1821 time to fit residues: 40.9476 Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN E 31 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141909 restraints weight = 8241.255| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.42 r_work: 0.3325 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7486 Z= 0.184 Angle : 0.547 8.983 10268 Z= 0.279 Chirality : 0.040 0.135 1254 Planarity : 0.004 0.046 1298 Dihedral : 6.000 84.650 1121 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.82 % Allowed : 22.94 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1019 helix: 2.47 (0.26), residues: 397 sheet: -1.31 (0.32), residues: 227 loop : -0.51 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 169 HIS 0.010 0.001 HIS B 54 PHE 0.020 0.001 PHE A 28 TYR 0.013 0.001 TYR E 95 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.731 Fit side-chains REVERT: A 23 ILE cc_start: 0.6426 (mt) cc_final: 0.6043 (mm) REVERT: B 101 MET cc_start: 0.8837 (mtp) cc_final: 0.8579 (mtp) REVERT: B 146 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8026 (tp) REVERT: B 156 GLN cc_start: 0.7823 (mm-40) cc_final: 0.6752 (mt0) REVERT: B 264 TYR cc_start: 0.8964 (m-80) cc_final: 0.8576 (m-80) REVERT: B 327 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8517 (p) REVERT: B 339 TRP cc_start: 0.8818 (m100) cc_final: 0.8550 (m100) REVERT: D 25 LYS cc_start: 0.7550 (ttmm) cc_final: 0.7196 (mttp) REVERT: D 252 ASP cc_start: 0.7523 (t0) cc_final: 0.7011 (t0) REVERT: E 104 THR cc_start: 0.7610 (m) cc_final: 0.7342 (p) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 0.1573 time to fit residues: 34.5338 Evaluate side-chains 154 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141310 restraints weight = 8225.817| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.51 r_work: 0.3261 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7486 Z= 0.311 Angle : 0.602 9.197 10268 Z= 0.310 Chirality : 0.042 0.142 1254 Planarity : 0.004 0.047 1298 Dihedral : 6.184 82.953 1121 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.71 % Allowed : 22.50 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1019 helix: 2.17 (0.26), residues: 403 sheet: -1.22 (0.33), residues: 214 loop : -0.55 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.016 0.001 HIS B 54 PHE 0.020 0.002 PHE A 28 TYR 0.017 0.002 TYR E 95 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.847 Fit side-chains REVERT: A 23 ILE cc_start: 0.6582 (mt) cc_final: 0.6216 (mm) REVERT: B 101 MET cc_start: 0.8847 (mtp) cc_final: 0.8563 (mtp) REVERT: B 146 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8137 (tp) REVERT: B 156 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7024 (mt0) REVERT: B 339 TRP cc_start: 0.8866 (m100) cc_final: 0.8625 (m100) REVERT: D 25 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7254 (mttp) REVERT: D 252 ASP cc_start: 0.7642 (t0) cc_final: 0.7158 (t0) REVERT: E 104 THR cc_start: 0.7657 (m) cc_final: 0.7395 (p) outliers start: 32 outliers final: 24 residues processed: 161 average time/residue: 0.1541 time to fit residues: 35.5126 Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 0.0270 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 88 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145884 restraints weight = 8239.350| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.55 r_work: 0.3306 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7486 Z= 0.188 Angle : 0.555 8.958 10268 Z= 0.281 Chirality : 0.040 0.136 1254 Planarity : 0.003 0.044 1298 Dihedral : 5.913 84.014 1121 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.82 % Allowed : 22.94 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.27), residues: 1019 helix: 2.35 (0.26), residues: 403 sheet: -1.15 (0.34), residues: 215 loop : -0.50 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.012 0.001 HIS B 54 PHE 0.025 0.001 PHE A 28 TYR 0.013 0.001 TYR E 95 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.739 Fit side-chains REVERT: A 23 ILE cc_start: 0.6525 (mt) cc_final: 0.5871 (mm) REVERT: A 316 ARG cc_start: 0.6033 (ttm110) cc_final: 0.5284 (ttp-170) REVERT: B 101 MET cc_start: 0.8844 (mtt) cc_final: 0.8595 (mtp) REVERT: B 146 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7977 (tp) REVERT: B 156 GLN cc_start: 0.7743 (mm-40) cc_final: 0.6903 (mt0) REVERT: B 264 TYR cc_start: 0.9029 (m-80) cc_final: 0.8602 (m-80) REVERT: B 327 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 339 TRP cc_start: 0.8848 (m100) cc_final: 0.8586 (m100) REVERT: D 25 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7228 (mttp) REVERT: D 252 ASP cc_start: 0.7569 (t0) cc_final: 0.7058 (t0) REVERT: E 104 THR cc_start: 0.7519 (m) cc_final: 0.7309 (p) outliers start: 26 outliers final: 20 residues processed: 156 average time/residue: 0.1550 time to fit residues: 34.1399 Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain E residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 6 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 0.0570 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 80 optimal weight: 0.0770 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.190831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.149895 restraints weight = 8220.197| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.61 r_work: 0.3328 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7486 Z= 0.161 Angle : 0.533 8.946 10268 Z= 0.272 Chirality : 0.040 0.141 1254 Planarity : 0.003 0.043 1298 Dihedral : 5.719 85.479 1121 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.09 % Allowed : 23.97 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.27), residues: 1019 helix: 2.36 (0.26), residues: 404 sheet: -1.09 (0.34), residues: 215 loop : -0.46 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 234 HIS 0.007 0.001 HIS B 54 PHE 0.028 0.001 PHE A 28 TYR 0.012 0.001 TYR A 94 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.758 Fit side-chains REVERT: A 23 ILE cc_start: 0.6472 (mt) cc_final: 0.5877 (mm) REVERT: A 91 LEU cc_start: 0.5205 (tt) cc_final: 0.4996 (tt) REVERT: A 291 ARG cc_start: 0.5049 (tpm170) cc_final: 0.4752 (tpm170) REVERT: A 316 ARG cc_start: 0.6075 (ttm110) cc_final: 0.5411 (ttp-170) REVERT: B 101 MET cc_start: 0.8819 (mtt) cc_final: 0.8585 (mtp) REVERT: B 146 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7982 (tp) REVERT: B 156 GLN cc_start: 0.7786 (mm-40) cc_final: 0.6982 (mt0) REVERT: B 327 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8543 (p) REVERT: B 339 TRP cc_start: 0.8851 (m100) cc_final: 0.8605 (m100) REVERT: D 25 LYS cc_start: 0.7568 (ttmm) cc_final: 0.7229 (mttp) REVERT: D 252 ASP cc_start: 0.7543 (t0) cc_final: 0.7043 (t0) REVERT: E 104 THR cc_start: 0.7531 (m) cc_final: 0.7307 (p) outliers start: 21 outliers final: 15 residues processed: 156 average time/residue: 0.1646 time to fit residues: 35.8608 Evaluate side-chains 150 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 61 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.187296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146253 restraints weight = 8290.279| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.59 r_work: 0.3327 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.191 Angle : 0.552 8.625 10268 Z= 0.280 Chirality : 0.040 0.137 1254 Planarity : 0.003 0.045 1298 Dihedral : 5.769 87.154 1121 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.38 % Allowed : 24.12 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.27), residues: 1019 helix: 2.37 (0.26), residues: 403 sheet: -1.02 (0.34), residues: 209 loop : -0.47 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS B 54 PHE 0.030 0.001 PHE A 28 TYR 0.012 0.001 TYR E 95 ARG 0.006 0.000 ARG E 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.791 Fit side-chains REVERT: A 23 ILE cc_start: 0.6508 (mt) cc_final: 0.5890 (mm) REVERT: A 91 LEU cc_start: 0.5142 (tt) cc_final: 0.4932 (tt) REVERT: A 291 ARG cc_start: 0.5165 (tpm170) cc_final: 0.4890 (tpm170) REVERT: A 316 ARG cc_start: 0.6021 (ttm110) cc_final: 0.5315 (ttp-170) REVERT: B 101 MET cc_start: 0.8807 (mtt) cc_final: 0.8587 (mtp) REVERT: B 146 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7867 (tp) REVERT: B 156 GLN cc_start: 0.7780 (mm-40) cc_final: 0.6999 (mt0) REVERT: B 192 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7894 (mp) REVERT: B 327 VAL cc_start: 0.8866 (OUTLIER) cc_final: 0.8541 (p) REVERT: B 339 TRP cc_start: 0.8858 (m100) cc_final: 0.8613 (m100) REVERT: D 25 LYS cc_start: 0.7575 (ttmm) cc_final: 0.7139 (mttp) REVERT: D 252 ASP cc_start: 0.7531 (t0) cc_final: 0.7015 (t0) outliers start: 23 outliers final: 17 residues processed: 150 average time/residue: 0.1618 time to fit residues: 34.2590 Evaluate side-chains 152 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143024 restraints weight = 8184.330| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.68 r_work: 0.3318 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7486 Z= 0.187 Angle : 0.553 8.705 10268 Z= 0.279 Chirality : 0.040 0.135 1254 Planarity : 0.003 0.045 1298 Dihedral : 5.729 86.485 1121 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.09 % Allowed : 24.71 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 1019 helix: 2.39 (0.26), residues: 403 sheet: -0.97 (0.34), residues: 209 loop : -0.46 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.008 0.001 HIS B 54 PHE 0.031 0.001 PHE A 28 TYR 0.012 0.001 TYR E 95 ARG 0.005 0.000 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.86 seconds wall clock time: 80 minutes 48.51 seconds (4848.51 seconds total)