Starting phenix.real_space_refine on Mon May 12 01:21:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jiq_36324/05_2025/8jiq_36324.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jiq_36324/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jiq_36324/05_2025/8jiq_36324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jiq_36324/05_2025/8jiq_36324.map" model { file = "/net/cci-nas-00/data/ceres_data/8jiq_36324/05_2025/8jiq_36324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jiq_36324/05_2025/8jiq_36324.cif" } resolution = 3.4 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'ASP:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 190 Time building chain proxies: 4.97, per 1000 atoms: 0.57 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: 2.01 Conformation dependent library (CDL) restraints added in 973.8 milliseconds 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: 0.89 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: 2.25 Time building geometry restraints manager: 2.37 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.930 ------------------------------------------------------------------------------- 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 (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: -0.03 (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 TRP 0.052 0.002 TRP R 241 HIS 0.005 0.001 HIS R 45 PHE 0.009 0.001 PHE A 212 TYR 0.016 0.001 TYR R 145 ARG 0.004 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.11562 ( 449) hydrogen bonds : angle 4.98411 ( 1260) SS BOND : bond 0.00387 ( 5) SS BOND : angle 1.97508 ( 10) covalent geometry : bond 0.00327 ( 8892) covalent geometry : angle 0.63668 (12060) *********************** 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 : 1.025 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: 0.2114 time to fit residues: 49.5061 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 : 1.004 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 55 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.0870 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.126890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.089354 restraints weight = 17112.129| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.41 r_work: 0.3280 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8897 Z= 0.108 Angle : 0.533 6.760 12070 Z= 0.278 Chirality : 0.041 0.158 1353 Planarity : 0.003 0.033 1546 Dihedral : 4.124 51.066 1226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer: Outliers : 1.01 % Allowed : 11.22 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1112 helix: 1.63 (0.26), residues: 406 sheet: -0.60 (0.35), residues: 218 loop : -0.68 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 241 HIS 0.003 0.000 HIS B 183 PHE 0.025 0.001 PHE E 22 TYR 0.017 0.001 TYR B 111 ARG 0.002 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 449) hydrogen bonds : angle 4.16715 ( 1260) SS BOND : bond 0.00294 ( 5) SS BOND : angle 1.72568 ( 10) covalent geometry : bond 0.00232 ( 8892) covalent geometry : angle 0.53040 (12060) *********************** 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 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 130 GLU cc_start: 0.7642 (mp0) cc_final: 0.7344 (mp0) REVERT: C 42 GLU cc_start: 0.8607 (tt0) cc_final: 0.8323 (pp20) REVERT: E 11 SER cc_start: 0.8829 (t) cc_final: 0.8586 (p) REVERT: E 27 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8502 (tpt) REVERT: N 73 ASP cc_start: 0.8830 (t0) cc_final: 0.8513 (t0) REVERT: R 355 ILE cc_start: 0.9103 (mt) cc_final: 0.8738 (mt) outliers start: 9 outliers final: 4 residues processed: 142 average time/residue: 0.2015 time to fit residues: 39.9053 Evaluate side-chains 127 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 27 MET 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 50 optimal weight: 0.0570 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.125800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088394 restraints weight = 17268.074| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.36 r_work: 0.3260 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8897 Z= 0.117 Angle : 0.516 6.241 12070 Z= 0.268 Chirality : 0.041 0.153 1353 Planarity : 0.003 0.033 1546 Dihedral : 4.039 57.628 1225 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.23 % Allowed : 14.03 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1112 helix: 1.74 (0.26), residues: 406 sheet: -0.73 (0.34), residues: 222 loop : -0.62 (0.30), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 241 HIS 0.002 0.000 HIS B 183 PHE 0.013 0.001 PHE N 108 TYR 0.019 0.001 TYR A 318 ARG 0.002 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 449) hydrogen bonds : angle 4.02714 ( 1260) SS BOND : bond 0.00284 ( 5) SS BOND : angle 1.80389 ( 10) covalent geometry : bond 0.00262 ( 8892) covalent geometry : angle 0.51335 (12060) *********************** 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 140 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.964 Fit side-chains REVERT: B 130 GLU cc_start: 0.7635 (mp0) cc_final: 0.7343 (mp0) REVERT: C 42 GLU cc_start: 0.8630 (tt0) cc_final: 0.8341 (pp20) REVERT: E 11 SER cc_start: 0.8887 (t) cc_final: 0.8590 (p) REVERT: N 73 ASP cc_start: 0.8886 (t0) cc_final: 0.8562 (t0) REVERT: R 355 ILE cc_start: 0.9105 (mt) cc_final: 0.8736 (mt) REVERT: R 378 ARG cc_start: 0.6018 (OUTLIER) cc_final: 0.4282 (ppt170) outliers start: 11 outliers final: 5 residues processed: 137 average time/residue: 0.2006 time to fit residues: 38.8511 Evaluate side-chains 124 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 PHE Chi-restraints excluded: chain R residue 244 VAL 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 50 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 15 optimal weight: 0.0970 chunk 103 optimal weight: 0.1980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.123865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.088104 restraints weight = 17393.539| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.27 r_work: 0.3271 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 8897 Z= 0.098 Angle : 0.489 6.318 12070 Z= 0.255 Chirality : 0.040 0.151 1353 Planarity : 0.003 0.033 1546 Dihedral : 3.868 54.390 1225 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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 (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: 0.44 (0.26), residues: 1112 helix: 1.86 (0.26), residues: 405 sheet: -0.59 (0.35), residues: 218 loop : -0.56 (0.30), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 241 HIS 0.002 0.000 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR A 360 ARG 0.002 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 449) hydrogen bonds : angle 3.89457 ( 1260) SS BOND : bond 0.00254 ( 5) SS BOND : angle 1.58603 ( 10) covalent geometry : bond 0.00219 ( 8892) covalent geometry : angle 0.48722 (12060) *********************** 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 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.098 Fit side-chains REVERT: B 130 GLU cc_start: 0.7658 (mp0) cc_final: 0.7375 (mp0) REVERT: C 42 GLU cc_start: 0.8549 (tt0) cc_final: 0.8259 (pp20) REVERT: E 11 SER cc_start: 0.8831 (t) cc_final: 0.8566 (p) REVERT: N 73 ASP cc_start: 0.8911 (t0) cc_final: 0.8569 (t0) REVERT: R 291 ASN cc_start: 0.8178 (t0) cc_final: 0.7729 (t0) REVERT: R 355 ILE cc_start: 0.9004 (mt) cc_final: 0.8646 (mt) REVERT: R 378 ARG cc_start: 0.6026 (OUTLIER) cc_final: 0.4227 (ppt170) outliers start: 16 outliers final: 9 residues processed: 140 average time/residue: 0.1913 time to fit residues: 37.9179 Evaluate side-chains 132 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 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 378 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.0060 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.126850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.089595 restraints weight = 16946.198| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.37 r_work: 0.3294 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8897 Z= 0.097 Angle : 0.490 6.586 12070 Z= 0.255 Chirality : 0.040 0.154 1353 Planarity : 0.003 0.033 1546 Dihedral : 3.721 48.408 1225 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.02 % Allowed : 16.72 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1112 helix: 1.89 (0.26), residues: 406 sheet: -0.55 (0.35), residues: 218 loop : -0.53 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 241 HIS 0.002 0.000 HIS R 44 PHE 0.010 0.001 PHE R 312 TYR 0.019 0.001 TYR A 360 ARG 0.002 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.03007 ( 449) hydrogen bonds : angle 3.85658 ( 1260) SS BOND : bond 0.00227 ( 5) SS BOND : angle 1.52355 ( 10) covalent geometry : bond 0.00216 ( 8892) covalent geometry : angle 0.48788 (12060) *********************** 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 150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.903 Fit side-chains REVERT: B 42 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6858 (tpp-160) REVERT: B 130 GLU cc_start: 0.7618 (mp0) cc_final: 0.7346 (mp0) REVERT: C 42 GLU cc_start: 0.8581 (tt0) cc_final: 0.8222 (pp20) REVERT: E 11 SER cc_start: 0.8822 (t) cc_final: 0.8562 (p) REVERT: N 73 ASP cc_start: 0.8910 (t0) cc_final: 0.8602 (t70) REVERT: R 142 GLN cc_start: 0.8475 (tp40) cc_final: 0.8274 (tp40) REVERT: R 355 ILE cc_start: 0.8921 (mt) cc_final: 0.8561 (mt) REVERT: R 378 ARG cc_start: 0.5934 (OUTLIER) cc_final: 0.4184 (ppt170) outliers start: 18 outliers final: 10 residues processed: 145 average time/residue: 0.1923 time to fit residues: 39.0417 Evaluate side-chains 131 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 N residue 69 THR Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 54 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.122348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086819 restraints weight = 17361.779| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 3.22 r_work: 0.3245 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8897 Z= 0.122 Angle : 0.516 8.647 12070 Z= 0.268 Chirality : 0.041 0.197 1353 Planarity : 0.003 0.033 1546 Dihedral : 3.784 42.212 1225 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.24 % Allowed : 17.73 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1112 helix: 1.89 (0.26), residues: 407 sheet: -0.64 (0.35), residues: 220 loop : -0.56 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 295 HIS 0.002 0.001 HIS B 183 PHE 0.012 0.001 PHE N 108 TYR 0.018 0.001 TYR A 360 ARG 0.006 0.000 ARG R 201 Details of bonding type rmsd hydrogen bonds : bond 0.03113 ( 449) hydrogen bonds : angle 3.89283 ( 1260) SS BOND : bond 0.00282 ( 5) SS BOND : angle 1.83026 ( 10) covalent geometry : bond 0.00276 ( 8892) covalent geometry : angle 0.51360 (12060) *********************** 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 145 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.919 Fit side-chains REVERT: B 130 GLU cc_start: 0.7652 (mp0) cc_final: 0.7336 (mp0) REVERT: C 42 GLU cc_start: 0.8563 (tt0) cc_final: 0.8252 (pp20) REVERT: E 11 SER cc_start: 0.8841 (t) cc_final: 0.8575 (p) REVERT: R 291 ASN cc_start: 0.8047 (t0) cc_final: 0.7691 (t0) REVERT: R 355 ILE cc_start: 0.8974 (mt) cc_final: 0.8613 (mt) REVERT: R 378 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.4187 (ppt170) outliers start: 20 outliers final: 16 residues processed: 138 average time/residue: 0.1918 time to fit residues: 37.3465 Evaluate side-chains 134 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.040 ------------------------------------------------------------------------------- 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 255 LEU 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 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 185 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 395 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 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 = 0.4034 r_free = 0.4034 target = 0.126091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.088580 restraints weight = 17465.974| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.44 r_work: 0.3270 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8897 Z= 0.105 Angle : 0.515 8.814 12070 Z= 0.266 Chirality : 0.041 0.166 1353 Planarity : 0.003 0.033 1546 Dihedral : 3.699 37.396 1225 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 18.29 % 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 (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: 0.50 (0.26), residues: 1112 helix: 1.92 (0.26), residues: 407 sheet: -0.60 (0.35), residues: 220 loop : -0.53 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP R 295 HIS 0.002 0.000 HIS R 44 PHE 0.010 0.001 PHE N 108 TYR 0.019 0.001 TYR A 360 ARG 0.005 0.000 ARG R 201 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 449) hydrogen bonds : angle 3.86399 ( 1260) SS BOND : bond 0.00244 ( 5) SS BOND : angle 1.63933 ( 10) covalent geometry : bond 0.00238 ( 8892) covalent geometry : angle 0.51347 (12060) *********************** 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 146 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.981 Fit side-chains REVERT: B 130 GLU cc_start: 0.7674 (mp0) cc_final: 0.7371 (mp0) REVERT: C 42 GLU cc_start: 0.8593 (tt0) cc_final: 0.8264 (pp20) REVERT: E 11 SER cc_start: 0.8793 (t) cc_final: 0.8524 (p) REVERT: N 73 ASP cc_start: 0.9018 (t70) cc_final: 0.8650 (t0) REVERT: R 290 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7847 (mm-30) REVERT: R 291 ASN cc_start: 0.8057 (t0) cc_final: 0.7651 (t0) REVERT: R 355 ILE cc_start: 0.8937 (mt) cc_final: 0.8556 (mt) REVERT: R 378 ARG cc_start: 0.5829 (OUTLIER) cc_final: 0.4195 (ppt170) outliers start: 19 outliers final: 11 residues processed: 139 average time/residue: 0.1963 time to fit residues: 38.2857 Evaluate side-chains 133 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 273 ILE Chi-restraints excluded: chain B residue 317 CYS 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 185 VAL Chi-restraints excluded: chain R residue 230 PHE Chi-restraints excluded: chain R residue 378 ARG Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 47 optimal weight: 0.3980 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 74 optimal weight: 0.0060 chunk 86 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 68 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.088811 restraints weight = 17462.803| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.44 r_work: 0.3276 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8897 Z= 0.103 Angle : 0.522 9.720 12070 Z= 0.268 Chirality : 0.041 0.280 1353 Planarity : 0.003 0.047 1546 Dihedral : 3.623 32.194 1225 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.36 % Allowed : 18.18 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1112 helix: 1.95 (0.26), residues: 407 sheet: -0.59 (0.35), residues: 222 loop : -0.49 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 295 HIS 0.002 0.000 HIS R 44 PHE 0.012 0.001 PHE R 312 TYR 0.017 0.001 TYR A 360 ARG 0.012 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 449) hydrogen bonds : angle 3.82212 ( 1260) SS BOND : bond 0.00238 ( 5) SS BOND : angle 1.57239 ( 10) covalent geometry : bond 0.00231 ( 8892) covalent geometry : angle 0.52010 (12060) *********************** 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 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.913 Fit side-chains REVERT: B 42 ARG cc_start: 0.7244 (mmt-90) cc_final: 0.6860 (tpp-160) REVERT: B 130 GLU cc_start: 0.7601 (mp0) cc_final: 0.7336 (mp0) REVERT: C 42 GLU cc_start: 0.8587 (tt0) cc_final: 0.8264 (pp20) REVERT: E 11 SER cc_start: 0.8783 (t) cc_final: 0.8508 (p) REVERT: N 73 ASP cc_start: 0.9036 (t70) cc_final: 0.8638 (t0) REVERT: R 290 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7872 (mm-30) REVERT: R 291 ASN cc_start: 0.8115 (t0) cc_final: 0.7673 (t0) REVERT: R 355 ILE cc_start: 0.8941 (mt) cc_final: 0.8563 (mt) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.1832 time to fit residues: 37.5363 Evaluate side-chains 136 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 E residue 9 ASP Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 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 = 0.3978 r_free = 0.3978 target = 0.122111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.086397 restraints weight = 17629.480| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.26 r_work: 0.3237 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8897 Z= 0.124 Angle : 0.569 12.085 12070 Z= 0.284 Chirality : 0.042 0.274 1353 Planarity : 0.003 0.050 1546 Dihedral : 3.593 19.698 1221 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.24 % Allowed : 19.08 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1112 helix: 1.90 (0.26), residues: 407 sheet: -0.60 (0.35), residues: 222 loop : -0.51 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 295 HIS 0.002 0.000 HIS B 183 PHE 0.012 0.001 PHE N 108 TYR 0.017 0.001 TYR A 360 ARG 0.012 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 449) hydrogen bonds : angle 3.88802 ( 1260) SS BOND : bond 0.00289 ( 5) SS BOND : angle 1.81084 ( 10) covalent geometry : bond 0.00284 ( 8892) covalent geometry : angle 0.56670 (12060) *********************** 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 142 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.972 Fit side-chains REVERT: A 343 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7956 (p0) REVERT: B 130 GLU cc_start: 0.7617 (mp0) cc_final: 0.7322 (mp0) REVERT: C 42 GLU cc_start: 0.8569 (tt0) cc_final: 0.8265 (pp20) REVERT: E 11 SER cc_start: 0.8775 (t) cc_final: 0.8502 (p) REVERT: N 73 ASP cc_start: 0.9021 (t70) cc_final: 0.8612 (t0) REVERT: R 290 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7897 (mm-30) REVERT: R 291 ASN cc_start: 0.8151 (t0) cc_final: 0.7926 (t0) REVERT: R 355 ILE cc_start: 0.8980 (mt) cc_final: 0.8605 (mt) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.1838 time to fit residues: 36.3723 Evaluate side-chains 136 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASP 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 E residue 9 ASP Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 82 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.0170 chunk 4 optimal weight: 0.0970 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.127415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090676 restraints weight = 17198.477| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.39 r_work: 0.3301 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8897 Z= 0.101 Angle : 0.562 11.621 12070 Z= 0.279 Chirality : 0.042 0.270 1353 Planarity : 0.003 0.046 1546 Dihedral : 3.480 18.975 1221 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.57 % Allowed : 19.75 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1112 helix: 1.91 (0.26), residues: 407 sheet: -0.48 (0.35), residues: 220 loop : -0.49 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 241 HIS 0.002 0.000 HIS B 311 PHE 0.011 0.001 PHE R 312 TYR 0.017 0.001 TYR A 360 ARG 0.011 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 449) hydrogen bonds : angle 3.86284 ( 1260) SS BOND : bond 0.00179 ( 5) SS BOND : angle 1.33898 ( 10) covalent geometry : bond 0.00228 ( 8892) covalent geometry : angle 0.56110 (12060) ********************** 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 144 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.065 Fit side-chains REVERT: A 343 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7841 (p0) REVERT: B 42 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.6818 (tpp-160) REVERT: B 130 GLU cc_start: 0.7562 (mp0) cc_final: 0.7300 (mp0) REVERT: C 42 GLU cc_start: 0.8582 (tt0) cc_final: 0.8265 (pp20) REVERT: C 62 ARG cc_start: 0.6372 (ptp90) cc_final: 0.5905 (ptp90) REVERT: E 11 SER cc_start: 0.8769 (t) cc_final: 0.8507 (p) REVERT: N 73 ASP cc_start: 0.9010 (t70) cc_final: 0.8592 (t0) REVERT: R 290 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7896 (mm-30) REVERT: R 291 ASN cc_start: 0.8041 (t0) cc_final: 0.7786 (t0) REVERT: R 355 ILE cc_start: 0.8925 (mt) cc_final: 0.8557 (mt) REVERT: R 362 GLU cc_start: 0.7765 (mp0) cc_final: 0.7374 (mm-30) outliers start: 14 outliers final: 11 residues processed: 139 average time/residue: 0.1817 time to fit residues: 36.1132 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 : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ASP 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 E residue 9 ASP Chi-restraints excluded: chain E residue 25 TRP Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 185 VAL Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 19 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 94 optimal weight: 0.0370 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.124895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.088792 restraints weight = 17350.261| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.33 r_work: 0.3280 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8897 Z= 0.102 Angle : 0.584 14.342 12070 Z= 0.285 Chirality : 0.042 0.265 1353 Planarity : 0.003 0.046 1546 Dihedral : 3.475 18.949 1221 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.46 % Allowed : 20.31 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1112 helix: 1.88 (0.26), residues: 407 sheet: -0.48 (0.35), residues: 220 loop : -0.45 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 295 HIS 0.002 0.000 HIS B 183 PHE 0.018 0.001 PHE E 22 TYR 0.022 0.001 TYR R 145 ARG 0.011 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03035 ( 449) hydrogen bonds : angle 3.89186 ( 1260) SS BOND : bond 0.00220 ( 5) SS BOND : angle 1.36692 ( 10) covalent geometry : bond 0.00233 ( 8892) covalent geometry : angle 0.58290 (12060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4671.01 seconds wall clock time: 81 minutes 24.23 seconds (4884.23 seconds total)