Starting phenix.real_space_refine on Fri Aug 22 23:40:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jiq_36324/08_2025/8jiq_36324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jiq_36324/08_2025/8jiq_36324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jiq_36324/08_2025/8jiq_36324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jiq_36324/08_2025/8jiq_36324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jiq_36324/08_2025/8jiq_36324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jiq_36324/08_2025/8jiq_36324.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 55 5.16 5 C 5527 2.51 5 N 1524 2.21 5 O 1601 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8707 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1817 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2510 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 326} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 363 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "E" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2810 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 15, 'TRANS': 363} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 6, 'PHE:plan': 3, 'ASP:plan': 5, 'TYR:plan': 2, 'TRP:plan': 5, 'HIS:plan': 3, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 190 Time building chain proxies: 1.63, per 1000 atoms: 0.19 Number of scatterers: 8707 At special positions: 0 Unit cell: (92.13, 98.77, 161.02, 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 55 16.00 O 1601 8.00 N 1524 7.00 C 5527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 58 " - pdb=" SG CYS R 100 " distance=2.03 Simple disulfide: pdb=" SG CYS R 81 " - pdb=" SG CYS R 121 " distance=2.03 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " 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: 0.51 Conformation dependent library (CDL) restraints added in 372.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 42.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 5.010A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.417A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.770A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.038A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.513A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.796A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.563A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 2 through 29 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.660A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 28 through 50 removed outlier: 4.306A pdb=" N GLN R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 89 removed outlier: 3.514A pdb=" N HIS R 89 " --> pdb=" O PRO R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 131 removed outlier: 4.278A pdb=" N GLU R 129 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 164 removed outlier: 4.256A pdb=" N MET R 137 " --> pdb=" O GLU R 133 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL R 147 " --> pdb=" O VAL R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 203 removed outlier: 3.619A pdb=" N TYR R 202 " --> pdb=" O LEU R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 255 removed outlier: 3.719A pdb=" N VAL R 221 " --> pdb=" O SER R 217 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA R 222 " --> pdb=" O ASP R 218 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY R 223 " --> pdb=" O GLY R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 277 removed outlier: 3.991A pdb=" N ALA R 274 " --> pdb=" O ILE R 270 " (cutoff:3.500A) Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 278 through 290 Processing helix chain 'R' and resid 301 through 335 removed outlier: 3.975A pdb=" N ILE R 306 " --> pdb=" O GLY R 302 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.674A pdb=" N ALA R 331 " --> pdb=" O GLN R 327 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA R 335 " --> pdb=" O ALA R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 353 Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 361 through 368 removed outlier: 3.588A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 402 removed outlier: 4.601A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 418 removed outlier: 4.098A pdb=" N GLU R 410 " --> pdb=" O GLU R 406 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.764A pdb=" N PHE A 222 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.666A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.105A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.222A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.600A 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 151 removed outlier: 3.794A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.758A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.915A 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: 3.680A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.950A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.721A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 57 through 58 removed outlier: 3.675A pdb=" N THR R 71 " --> pdb=" O CYS R 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 77 through 80 449 hydrogen bonds defined for protein. 1260 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: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1509 1.32 - 1.44: 2410 1.44 - 1.57: 4897 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8892 Sorted by residual: bond pdb=" C ARG R 199 " pdb=" O ARG R 199 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.53e+00 bond pdb=" C GLY R 101 " pdb=" N PRO R 102 " ideal model delta sigma weight residual 1.335 1.374 -0.039 1.28e-02 6.10e+03 9.33e+00 bond pdb=" CA ARG R 116 " pdb=" C ARG R 116 " ideal model delta sigma weight residual 1.528 1.511 0.017 8.80e-03 1.29e+04 3.59e+00 bond pdb=" CA ASP R 208 " pdb=" C ASP R 208 " ideal model delta sigma weight residual 1.522 1.497 0.026 1.40e-02 5.10e+03 3.32e+00 bond pdb=" C THR R 71 " pdb=" O THR R 71 " ideal model delta sigma weight residual 1.238 1.215 0.023 1.28e-02 6.10e+03 3.30e+00 ... (remaining 8887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11949 2.63 - 5.26: 103 5.26 - 7.88: 5 7.88 - 10.51: 1 10.51 - 13.14: 2 Bond angle restraints: 12060 Sorted by residual: angle pdb=" N ARG R 201 " pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 113.97 100.83 13.14 1.28e+00 6.10e-01 1.05e+02 angle pdb=" N ASP R 208 " pdb=" CA ASP R 208 " pdb=" C ASP R 208 " ideal model delta sigma weight residual 113.17 102.84 10.33 1.26e+00 6.30e-01 6.73e+01 angle pdb=" C THR R 71 " pdb=" N PRO R 72 " pdb=" CA PRO R 72 " ideal model delta sigma weight residual 119.85 113.94 5.91 1.01e+00 9.80e-01 3.43e+01 angle pdb=" C GLY R 101 " pdb=" N PRO R 102 " pdb=" CA PRO R 102 " ideal model delta sigma weight residual 119.28 113.44 5.84 1.10e+00 8.26e-01 2.82e+01 angle pdb=" CA GLN R 113 " pdb=" C GLN R 113 " pdb=" N PRO R 114 " ideal model delta sigma weight residual 120.79 116.76 4.03 9.70e-01 1.06e+00 1.72e+01 ... (remaining 12055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4625 17.44 - 34.87: 496 34.87 - 52.31: 94 52.31 - 69.75: 27 69.75 - 87.18: 10 Dihedral angle restraints: 5252 sinusoidal: 1969 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -37.12 -48.88 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " pdb=" SG CYS R 294 " pdb=" CB CYS R 294 " ideal model delta sinusoidal sigma weight residual 93.00 137.50 -44.50 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS R 81 " pdb=" SG CYS R 81 " pdb=" SG CYS R 121 " pdb=" CB CYS R 121 " ideal model delta sinusoidal sigma weight residual 93.00 53.66 39.34 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 5249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 993 0.044 - 0.088: 271 0.088 - 0.132: 78 0.132 - 0.175: 7 0.175 - 0.219: 4 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA ASN R 74 " pdb=" N ASN R 74 " pdb=" C ASN R 74 " pdb=" CB ASN R 74 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP R 209 " pdb=" N ASP R 209 " pdb=" C ASP R 209 " pdb=" CB ASP R 209 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG R 201 " pdb=" N ARG R 201 " pdb=" C ARG R 201 " pdb=" CB ARG R 201 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.49e-01 ... (remaining 1350 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 241 " -0.021 2.00e-02 2.50e+03 1.96e-02 9.61e+00 pdb=" CG TRP R 241 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP R 241 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP R 241 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 241 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP R 241 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 241 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 241 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 241 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP R 241 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 194 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ILE R 194 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE R 194 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP R 195 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 199 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C ARG R 199 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG R 199 " -0.012 2.00e-02 2.50e+03 pdb=" N THR R 200 " -0.011 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 836 2.74 - 3.28: 8826 3.28 - 3.82: 14736 3.82 - 4.36: 16765 4.36 - 4.90: 29215 Nonbonded interactions: 70378 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP A 240 " pdb=" NZ LYS B 57 " model vdw 2.247 3.120 nonbonded pdb=" OG1 THR R 172 " pdb=" OH TYR R 248 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.292 3.040 ... (remaining 70373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.280 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8897 Z= 0.189 Angle : 0.639 13.140 12070 Z= 0.389 Chirality : 0.044 0.219 1353 Planarity : 0.003 0.035 1546 Dihedral : 15.174 87.182 3113 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.14 % Favored : 95.50 % Rotamer: Outliers : 2.47 % Allowed : 1.35 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.26), residues: 1112 helix: 1.46 (0.27), residues: 402 sheet: -0.75 (0.35), residues: 224 loop : -0.87 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.016 0.001 TYR R 145 PHE 0.009 0.001 PHE A 212 TRP 0.052 0.002 TRP R 241 HIS 0.005 0.001 HIS R 45 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8892) covalent geometry : angle 0.63668 (12060) SS BOND : bond 0.00387 ( 5) SS BOND : angle 1.97508 ( 10) hydrogen bonds : bond 0.11562 ( 449) hydrogen bonds : angle 4.98411 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.207 Fit side-chains REVERT: R 376 THR cc_start: 0.4124 (OUTLIER) cc_final: 0.3439 (p) REVERT: R 378 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.4137 (ptt90) outliers start: 22 outliers final: 0 residues processed: 171 average time/residue: 0.0770 time to fit residues: 18.2574 Evaluate side-chains 125 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** B 295 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 = 0.3997 r_free = 0.3997 target = 0.123836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.085577 restraints weight = 17452.816| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.43 r_work: 0.3205 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8897 Z= 0.167 Angle : 0.565 6.596 12070 Z= 0.296 Chirality : 0.042 0.157 1353 Planarity : 0.003 0.034 1546 Dihedral : 4.320 51.940 1226 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.87 % Favored : 95.95 % Rotamer: Outliers : 1.35 % Allowed : 11.90 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 1112 helix: 1.58 (0.26), residues: 406 sheet: -0.76 (0.34), residues: 226 loop : -0.73 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.018 0.001 TYR A 358 PHE 0.026 0.001 PHE E 22 TRP 0.032 0.001 TRP R 241 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8892) covalent geometry : angle 0.56172 (12060) SS BOND : bond 0.00401 ( 5) SS BOND : angle 2.27548 ( 10) hydrogen bonds : bond 0.03614 ( 449) hydrogen bonds : angle 4.29162 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: C 42 GLU cc_start: 0.8649 (tt0) cc_final: 0.8362 (pp20) REVERT: E 11 SER cc_start: 0.8876 (t) cc_final: 0.8614 (p) REVERT: N 73 ASP cc_start: 0.8816 (t0) cc_final: 0.8501 (t0) REVERT: R 355 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8942 (mt) outliers start: 12 outliers final: 9 residues processed: 134 average time/residue: 0.0758 time to fit residues: 14.1989 Evaluate side-chains 125 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 355 ILE Chi-restraints excluded: chain R residue 376 THR Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 50 optimal weight: 0.0770 chunk 40 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 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 = 0.4033 r_free = 0.4033 target = 0.126243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088641 restraints weight = 17078.057| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.41 r_work: 0.3265 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8897 Z= 0.102 Angle : 0.503 6.659 12070 Z= 0.263 Chirality : 0.040 0.158 1353 Planarity : 0.003 0.033 1546 Dihedral : 4.084 58.117 1226 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.01 % Allowed : 13.69 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.26), residues: 1112 helix: 1.77 (0.26), residues: 406 sheet: -0.70 (0.35), residues: 218 loop : -0.64 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.020 0.001 TYR A 318 PHE 0.011 0.001 PHE A 212 TRP 0.025 0.001 TRP R 241 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 8892) covalent geometry : angle 0.50044 (12060) SS BOND : bond 0.00273 ( 5) SS BOND : angle 1.73425 ( 10) hydrogen bonds : bond 0.03212 ( 449) hydrogen bonds : angle 4.04054 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.206 Fit side-chains REVERT: B 130 GLU cc_start: 0.7674 (mp0) cc_final: 0.7334 (mp0) REVERT: C 42 GLU cc_start: 0.8605 (tt0) cc_final: 0.8323 (pp20) REVERT: E 11 SER cc_start: 0.8879 (t) cc_final: 0.8580 (p) REVERT: N 73 ASP cc_start: 0.8867 (t0) cc_final: 0.8554 (t0) REVERT: R 355 ILE cc_start: 0.9137 (mt) cc_final: 0.8746 (mt) REVERT: R 378 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.4303 (ppt170) outliers start: 9 outliers final: 3 residues processed: 139 average time/residue: 0.0716 time to fit residues: 14.1066 Evaluate side-chains 124 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 71 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.122721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086700 restraints weight = 17651.683| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.28 r_work: 0.3243 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8897 Z= 0.110 Angle : 0.505 6.624 12070 Z= 0.262 Chirality : 0.041 0.155 1353 Planarity : 0.003 0.033 1546 Dihedral : 3.951 54.373 1225 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.80 % Allowed : 15.38 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.26), residues: 1112 helix: 1.81 (0.26), residues: 406 sheet: -0.70 (0.34), residues: 220 loop : -0.58 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 228 TYR 0.016 0.001 TYR R 145 PHE 0.011 0.001 PHE A 212 TRP 0.040 0.001 TRP R 241 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8892) covalent geometry : angle 0.50272 (12060) SS BOND : bond 0.00291 ( 5) SS BOND : angle 1.77750 ( 10) hydrogen bonds : bond 0.03150 ( 449) hydrogen bonds : angle 3.98960 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.349 Fit side-chains REVERT: B 130 GLU cc_start: 0.7707 (mp0) cc_final: 0.7380 (mp0) REVERT: C 42 GLU cc_start: 0.8589 (tt0) cc_final: 0.8316 (pp20) REVERT: E 11 SER cc_start: 0.8850 (t) cc_final: 0.8578 (p) REVERT: N 73 ASP cc_start: 0.8907 (t0) cc_final: 0.8548 (t0) REVERT: R 355 ILE cc_start: 0.9094 (mt) cc_final: 0.8709 (mt) REVERT: R 378 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.4204 (ppt170) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.0675 time to fit residues: 13.6474 Evaluate side-chains 134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 378 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.4031 r_free = 0.4031 target = 0.126034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.088421 restraints weight = 17323.378| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 3.38 r_work: 0.3263 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8897 Z= 0.108 Angle : 0.497 6.887 12070 Z= 0.260 Chirality : 0.041 0.156 1353 Planarity : 0.003 0.033 1546 Dihedral : 3.822 47.771 1225 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.24 % Allowed : 16.16 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.26), residues: 1112 helix: 1.84 (0.26), residues: 406 sheet: -0.67 (0.34), residues: 220 loop : -0.55 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 173 TYR 0.016 0.001 TYR R 145 PHE 0.011 0.001 PHE N 108 TRP 0.031 0.001 TRP R 241 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8892) covalent geometry : angle 0.49527 (12060) SS BOND : bond 0.00255 ( 5) SS BOND : angle 1.70664 ( 10) hydrogen bonds : bond 0.03078 ( 449) hydrogen bonds : angle 3.94888 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.199 Fit side-chains REVERT: B 130 GLU cc_start: 0.7665 (mp0) cc_final: 0.7348 (mp0) REVERT: C 42 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8302 (pp20) REVERT: E 11 SER cc_start: 0.8817 (t) cc_final: 0.8545 (p) REVERT: N 73 ASP cc_start: 0.8921 (t0) cc_final: 0.8593 (t70) REVERT: R 355 ILE cc_start: 0.9015 (mt) cc_final: 0.8646 (mt) REVERT: R 378 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.4132 (ppt170) outliers start: 20 outliers final: 12 residues processed: 139 average time/residue: 0.0730 time to fit residues: 14.1004 Evaluate side-chains 132 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN R 232 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083711 restraints weight = 17733.036| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.25 r_work: 0.3181 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8897 Z= 0.181 Angle : 0.558 8.789 12070 Z= 0.291 Chirality : 0.042 0.186 1353 Planarity : 0.003 0.041 1546 Dihedral : 4.002 40.722 1225 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.24 % Allowed : 17.28 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1112 helix: 1.73 (0.26), residues: 407 sheet: -0.82 (0.34), residues: 228 loop : -0.60 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 201 TYR 0.016 0.001 TYR B 111 PHE 0.019 0.001 PHE N 108 TRP 0.027 0.001 TRP R 241 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8892) covalent geometry : angle 0.55416 (12060) SS BOND : bond 0.00391 ( 5) SS BOND : angle 2.31911 ( 10) hydrogen bonds : bond 0.03342 ( 449) hydrogen bonds : angle 4.10216 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.318 Fit side-chains REVERT: B 130 GLU cc_start: 0.7783 (mp0) cc_final: 0.7422 (mp0) REVERT: C 42 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8320 (pp20) REVERT: E 11 SER cc_start: 0.8825 (t) cc_final: 0.8563 (p) REVERT: R 355 ILE cc_start: 0.9019 (mt) cc_final: 0.8624 (mt) REVERT: R 378 ARG cc_start: 0.5879 (OUTLIER) cc_final: 0.4157 (ppt170) outliers start: 20 outliers final: 15 residues processed: 137 average time/residue: 0.0649 time to fit residues: 12.6197 Evaluate side-chains 130 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 46 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 78 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.4018 r_free = 0.4018 target = 0.125172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087288 restraints weight = 17522.396| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.44 r_work: 0.3247 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8897 Z= 0.107 Angle : 0.525 9.838 12070 Z= 0.271 Chirality : 0.041 0.163 1353 Planarity : 0.003 0.048 1546 Dihedral : 3.769 35.135 1225 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.02 % Allowed : 18.41 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.26), residues: 1112 helix: 1.77 (0.26), residues: 407 sheet: -0.67 (0.34), residues: 220 loop : -0.54 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 96 TYR 0.015 0.001 TYR R 145 PHE 0.011 0.001 PHE A 212 TRP 0.029 0.001 TRP R 241 HIS 0.002 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8892) covalent geometry : angle 0.52260 (12060) SS BOND : bond 0.00262 ( 5) SS BOND : angle 1.82973 ( 10) hydrogen bonds : bond 0.03065 ( 449) hydrogen bonds : angle 3.96512 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.230 Fit side-chains REVERT: C 42 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8284 (pp20) REVERT: E 11 SER cc_start: 0.8790 (t) cc_final: 0.8514 (p) REVERT: N 73 ASP cc_start: 0.9048 (t70) cc_final: 0.8669 (t0) REVERT: R 295 TRP cc_start: 0.8129 (m-10) cc_final: 0.7696 (m-10) REVERT: R 355 ILE cc_start: 0.8935 (mt) cc_final: 0.8502 (mt) REVERT: R 378 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.4190 (ppt170) outliers start: 18 outliers final: 12 residues processed: 137 average time/residue: 0.0627 time to fit residues: 12.2177 Evaluate side-chains 133 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.4019 r_free = 0.4019 target = 0.125212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087545 restraints weight = 17297.631| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.43 r_work: 0.3249 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8897 Z= 0.109 Angle : 0.536 10.609 12070 Z= 0.274 Chirality : 0.041 0.162 1353 Planarity : 0.003 0.045 1546 Dihedral : 3.672 30.429 1225 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.13 % Allowed : 18.97 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1112 helix: 1.80 (0.26), residues: 407 sheet: -0.61 (0.34), residues: 220 loop : -0.53 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 96 TYR 0.015 0.001 TYR B 111 PHE 0.011 0.001 PHE R 312 TRP 0.027 0.001 TRP R 241 HIS 0.002 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 8892) covalent geometry : angle 0.53406 (12060) SS BOND : bond 0.00247 ( 5) SS BOND : angle 1.70475 ( 10) hydrogen bonds : bond 0.03069 ( 449) hydrogen bonds : angle 3.94254 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.240 Fit side-chains REVERT: B 130 GLU cc_start: 0.7711 (mp0) cc_final: 0.7366 (mp0) REVERT: C 42 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8272 (pp20) REVERT: E 11 SER cc_start: 0.8808 (t) cc_final: 0.8543 (p) REVERT: N 73 ASP cc_start: 0.9036 (t70) cc_final: 0.8615 (t0) REVERT: R 295 TRP cc_start: 0.8179 (m-10) cc_final: 0.7720 (m-10) REVERT: R 355 ILE cc_start: 0.8888 (mt) cc_final: 0.8517 (mt) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.0611 time to fit residues: 11.7921 Evaluate side-chains 134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 76 optimal weight: 8.9990 chunk 108 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.3965 r_free = 0.3965 target = 0.121493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.085641 restraints weight = 17546.356| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.27 r_work: 0.3220 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8897 Z= 0.122 Angle : 0.542 9.577 12070 Z= 0.277 Chirality : 0.041 0.162 1353 Planarity : 0.003 0.039 1546 Dihedral : 3.624 19.969 1221 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.80 % Allowed : 19.64 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1112 helix: 1.81 (0.26), residues: 407 sheet: -0.56 (0.34), residues: 219 loop : -0.56 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.015 0.001 TYR B 111 PHE 0.011 0.001 PHE N 108 TRP 0.028 0.001 TRP R 241 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8892) covalent geometry : angle 0.53935 (12060) SS BOND : bond 0.00259 ( 5) SS BOND : angle 1.84386 ( 10) hydrogen bonds : bond 0.03115 ( 449) hydrogen bonds : angle 3.97199 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.346 Fit side-chains REVERT: B 130 GLU cc_start: 0.7725 (mp0) cc_final: 0.7388 (mp0) REVERT: C 42 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8278 (pp20) REVERT: E 11 SER cc_start: 0.8821 (t) cc_final: 0.8556 (p) REVERT: N 73 ASP cc_start: 0.9040 (t70) cc_final: 0.8631 (t0) REVERT: R 295 TRP cc_start: 0.8158 (m-10) cc_final: 0.7724 (m-10) REVERT: R 355 ILE cc_start: 0.8930 (mt) cc_final: 0.8556 (mt) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.0667 time to fit residues: 12.4755 Evaluate side-chains 131 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.4008 r_free = 0.4008 target = 0.124530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.086733 restraints weight = 17429.289| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.43 r_work: 0.3234 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8897 Z= 0.122 Angle : 0.568 12.540 12070 Z= 0.284 Chirality : 0.041 0.162 1353 Planarity : 0.003 0.038 1546 Dihedral : 3.616 19.972 1221 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.57 % Allowed : 20.09 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1112 helix: 1.82 (0.26), residues: 407 sheet: -0.55 (0.34), residues: 219 loop : -0.55 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 96 TYR 0.014 0.001 TYR B 111 PHE 0.012 0.001 PHE N 108 TRP 0.030 0.001 TRP R 241 HIS 0.002 0.000 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8892) covalent geometry : angle 0.56602 (12060) SS BOND : bond 0.00251 ( 5) SS BOND : angle 1.79972 ( 10) hydrogen bonds : bond 0.03108 ( 449) hydrogen bonds : angle 3.96967 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.342 Fit side-chains REVERT: B 130 GLU cc_start: 0.7747 (mp0) cc_final: 0.7426 (mp0) REVERT: C 42 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8275 (pp20) REVERT: C 62 ARG cc_start: 0.6449 (ptp90) cc_final: 0.6215 (ptp90) REVERT: E 11 SER cc_start: 0.8818 (t) cc_final: 0.8540 (p) REVERT: N 73 ASP cc_start: 0.9036 (t70) cc_final: 0.8622 (t0) REVERT: R 295 TRP cc_start: 0.8179 (m-10) cc_final: 0.7765 (m-10) REVERT: R 355 ILE cc_start: 0.8906 (mt) cc_final: 0.8531 (mt) outliers start: 14 outliers final: 12 residues processed: 128 average time/residue: 0.0623 time to fit residues: 11.7943 Evaluate side-chains 132 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 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 = 0.3941 r_free = 0.3941 target = 0.120067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083097 restraints weight = 17457.504| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.32 r_work: 0.3172 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8897 Z= 0.169 Angle : 0.599 11.997 12070 Z= 0.304 Chirality : 0.042 0.161 1353 Planarity : 0.003 0.036 1546 Dihedral : 3.839 25.326 1221 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 20.20 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.26), residues: 1112 helix: 1.74 (0.26), residues: 408 sheet: -0.73 (0.34), residues: 224 loop : -0.61 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 96 TYR 0.014 0.001 TYR B 111 PHE 0.018 0.001 PHE N 108 TRP 0.033 0.001 TRP R 241 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8892) covalent geometry : angle 0.59610 (12060) SS BOND : bond 0.00301 ( 5) SS BOND : angle 2.22224 ( 10) hydrogen bonds : bond 0.03310 ( 449) hydrogen bonds : angle 4.10308 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1814.30 seconds wall clock time: 31 minutes 43.48 seconds (1903.48 seconds total)