Starting phenix.real_space_refine on Thu Mar 13 06:59:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flu_29287/03_2025/8flu_29287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flu_29287/03_2025/8flu_29287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8flu_29287/03_2025/8flu_29287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flu_29287/03_2025/8flu_29287.map" model { file = "/net/cci-nas-00/data/ceres_data/8flu_29287/03_2025/8flu_29287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flu_29287/03_2025/8flu_29287_neut.cif" } resolution = 2.76 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= -0.002 sd= 0.078 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 54 5.16 5 C 5577 2.51 5 N 1518 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2528 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 382 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "P" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2790 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 5.63, per 1000 atoms: 0.65 Number of scatterers: 8725 At special positions: 0 Unit cell: (74.62, 95.12, 168.92, 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 54 16.00 O 1576 8.00 N 1518 7.00 C 5577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 44.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.534A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.548A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.103A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.810A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.573A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.578A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 removed outlier: 3.717A pdb=" N ASP P 17 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 169 through 174 removed outlier: 3.743A pdb=" N LYS R 172 " --> pdb=" O GLU R 169 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE R 173 " --> pdb=" O CYS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.840A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.841A pdb=" N SER R 246 " --> pdb=" O ALA R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.503A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.585A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.809A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.531A pdb=" N ASN R 380 " --> pdb=" O ILE R 376 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL R 384 " --> pdb=" O ASN R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 434 through 460 removed outlier: 3.971A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.407A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.388A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.557A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.447A 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: 6.606A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.205A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.520A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A 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: 6.556A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.287A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.125A 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 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 489 hydrogen bonds defined for protein. 1380 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: 2.73 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2836 1.34 - 1.46: 1836 1.46 - 1.58: 4173 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 8920 Sorted by residual: bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.536 1.483 0.053 1.42e-02 4.96e+03 1.37e+01 bond pdb=" CA SER B 275 " pdb=" CB SER B 275 " ideal model delta sigma weight residual 1.534 1.483 0.051 1.64e-02 3.72e+03 9.57e+00 bond pdb=" N VAL R 432 " pdb=" CA VAL R 432 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.30e-02 5.92e+03 8.11e+00 bond pdb=" N GLN P 6 " pdb=" CA GLN P 6 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.91e+00 bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.28e-02 6.10e+03 7.90e+00 ... (remaining 8915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 11429 1.39 - 2.78: 571 2.78 - 4.17: 95 4.17 - 5.57: 30 5.57 - 6.96: 2 Bond angle restraints: 12127 Sorted by residual: angle pdb=" N LYS P 13 " pdb=" CA LYS P 13 " pdb=" C LYS P 13 " ideal model delta sigma weight residual 112.38 107.34 5.04 1.22e+00 6.72e-01 1.71e+01 angle pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" O GLY B 272 " ideal model delta sigma weight residual 121.64 118.03 3.61 9.20e-01 1.18e+00 1.54e+01 angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" C TYR B 59 " ideal model delta sigma weight residual 113.28 108.72 4.56 1.22e+00 6.72e-01 1.40e+01 angle pdb=" CA THR R 430 " pdb=" C THR R 430 " pdb=" O THR R 430 " ideal model delta sigma weight residual 121.81 117.60 4.21 1.18e+00 7.18e-01 1.28e+01 angle pdb=" N THR B 274 " pdb=" CA THR B 274 " pdb=" C THR B 274 " ideal model delta sigma weight residual 113.97 109.51 4.46 1.28e+00 6.10e-01 1.21e+01 ... (remaining 12122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4814 17.66 - 35.32: 329 35.32 - 52.98: 47 52.98 - 70.64: 17 70.64 - 88.30: 8 Dihedral angle restraints: 5215 sinusoidal: 1899 harmonic: 3316 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE R 314 " pdb=" C PHE R 314 " pdb=" N PHE R 315 " pdb=" CA PHE R 315 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 127.08 -34.08 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 5212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1038 0.047 - 0.094: 255 0.094 - 0.141: 62 0.141 - 0.188: 9 0.188 - 0.235: 3 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LYS P 13 " pdb=" N LYS P 13 " pdb=" C LYS P 13 " pdb=" CB LYS P 13 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1364 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO A 326 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 55 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C LEU B 55 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU B 55 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 428 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C PRO R 428 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO R 428 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR R 429 " -0.012 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1520 2.76 - 3.29: 8941 3.29 - 3.83: 15852 3.83 - 4.36: 19131 4.36 - 4.90: 31893 Nonbonded interactions: 77337 Sorted by model distance: nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.223 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.236 3.040 nonbonded pdb=" O PHE A 315 " pdb=" NH2 ARG A 336 " model vdw 2.249 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU P 4 " pdb=" OH TYR R 195 " model vdw 2.250 3.040 ... (remaining 77332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.210 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.110 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:14.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8920 Z= 0.269 Angle : 0.696 6.957 12127 Z= 0.439 Chirality : 0.045 0.235 1367 Planarity : 0.004 0.073 1544 Dihedral : 13.281 88.298 3053 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 0.35 % Allowed : 0.46 % Favored : 99.19 % 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 (0.25), residues: 1119 helix: 1.61 (0.25), residues: 428 sheet: -0.68 (0.32), residues: 209 loop : -0.15 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS B 266 PHE 0.014 0.002 PHE R 314 TYR 0.014 0.001 TYR R 459 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6085 (ttpp) cc_final: 0.5495 (tttt) REVERT: N 83 MET cc_start: 0.6321 (mtm) cc_final: 0.5300 (mtm) REVERT: R 36 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: R 221 TYR cc_start: 0.7269 (t80) cc_final: 0.6913 (t80) outliers start: 3 outliers final: 1 residues processed: 173 average time/residue: 1.3282 time to fit residues: 244.0967 Evaluate side-chains 116 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 36 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 156 GLN B 220 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.214679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173383 restraints weight = 9922.920| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.84 r_work: 0.4062 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 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 : 0.003 0.043 8920 Z= 0.220 Angle : 0.604 10.736 12127 Z= 0.326 Chirality : 0.043 0.221 1367 Planarity : 0.004 0.056 1544 Dihedral : 5.674 85.328 1236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.43 % Allowed : 9.71 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.98 (0.25), residues: 1119 helix: 2.22 (0.25), residues: 432 sheet: -0.79 (0.31), residues: 212 loop : -0.05 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.010 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.034 0.002 TYR R 191 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.973 Fit side-chains REVERT: A 53 LYS cc_start: 0.6357 (ttpp) cc_final: 0.5621 (ttpt) REVERT: A 208 PHE cc_start: 0.7631 (m-80) cc_final: 0.7316 (m-10) REVERT: A 373 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7058 (mmm-85) REVERT: B 44 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.5815 (mp-120) REVERT: B 170 ASP cc_start: 0.7943 (t70) cc_final: 0.7702 (p0) REVERT: B 175 GLN cc_start: 0.7262 (mm110) cc_final: 0.6377 (pt0) REVERT: G 50 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.5869 (mp) REVERT: N 83 MET cc_start: 0.6820 (mtm) cc_final: 0.5995 (mtm) REVERT: R 180 GLU cc_start: 0.6091 (tp30) cc_final: 0.5390 (mt-10) REVERT: R 221 TYR cc_start: 0.7331 (t80) cc_final: 0.6850 (t80) REVERT: R 438 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7175 (mm-40) outliers start: 21 outliers final: 5 residues processed: 142 average time/residue: 1.3562 time to fit residues: 204.9332 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 438 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN G 18 GLN P 10 GLN R 37 GLN R 380 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.212349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170542 restraints weight = 10039.922| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.82 r_work: 0.4037 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8920 Z= 0.251 Angle : 0.589 9.752 12127 Z= 0.316 Chirality : 0.043 0.235 1367 Planarity : 0.004 0.048 1544 Dihedral : 4.872 35.626 1231 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.54 % Allowed : 13.18 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.92 (0.26), residues: 1119 helix: 2.18 (0.24), residues: 437 sheet: -0.93 (0.31), residues: 217 loop : -0.04 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 14 HIS 0.010 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.031 0.002 TYR R 191 ARG 0.004 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 1.014 Fit side-chains REVERT: A 27 GLU cc_start: 0.7152 (tp30) cc_final: 0.6725 (tp30) REVERT: A 53 LYS cc_start: 0.6387 (ttpp) cc_final: 0.5615 (ttpt) REVERT: A 373 ARG cc_start: 0.7383 (mmt-90) cc_final: 0.7095 (mmm-85) REVERT: B 87 THR cc_start: 0.7882 (t) cc_final: 0.7511 (m) REVERT: B 170 ASP cc_start: 0.8006 (t70) cc_final: 0.7705 (p0) REVERT: B 175 GLN cc_start: 0.7313 (mm110) cc_final: 0.6374 (pt0) REVERT: B 197 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6719 (mpp80) REVERT: B 219 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7196 (mmt-90) REVERT: B 280 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7711 (mtpt) REVERT: G 50 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.5892 (mp) REVERT: N 83 MET cc_start: 0.6859 (mtm) cc_final: 0.6243 (mtm) REVERT: R 180 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5460 (mp0) REVERT: R 181 ARG cc_start: 0.6545 (ttp-110) cc_final: 0.6343 (ttp-110) REVERT: R 195 TYR cc_start: 0.8294 (m-80) cc_final: 0.7964 (m-80) REVERT: R 221 TYR cc_start: 0.7249 (t80) cc_final: 0.6786 (t80) REVERT: R 438 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7177 (mm-40) outliers start: 22 outliers final: 8 residues processed: 137 average time/residue: 1.2481 time to fit residues: 182.4011 Evaluate side-chains 131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 438 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 0.0070 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 44 GLN B 176 GLN B 220 GLN N 77 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.214905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173492 restraints weight = 9960.963| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.84 r_work: 0.4063 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8920 Z= 0.185 Angle : 0.537 9.718 12127 Z= 0.290 Chirality : 0.041 0.252 1367 Planarity : 0.004 0.043 1544 Dihedral : 4.702 33.525 1231 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.66 % Allowed : 14.34 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.04 (0.26), residues: 1119 helix: 2.37 (0.24), residues: 435 sheet: -0.86 (0.31), residues: 222 loop : -0.05 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 14 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.029 0.001 TYR R 191 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.960 Fit side-chains REVERT: A 27 GLU cc_start: 0.7063 (tp30) cc_final: 0.6675 (tp30) REVERT: A 53 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5505 (ttpt) REVERT: A 208 PHE cc_start: 0.7571 (m-80) cc_final: 0.7220 (m-10) REVERT: A 390 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6095 (pt0) REVERT: B 44 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6653 (mm110) REVERT: B 87 THR cc_start: 0.7779 (t) cc_final: 0.7490 (m) REVERT: B 170 ASP cc_start: 0.8016 (t70) cc_final: 0.7749 (p0) REVERT: B 175 GLN cc_start: 0.7240 (mm110) cc_final: 0.6376 (pt0) REVERT: B 219 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.7213 (mmt-90) REVERT: B 280 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7701 (mtpt) REVERT: G 50 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.5745 (mp) REVERT: N 53 GLN cc_start: 0.7881 (mp10) cc_final: 0.7656 (mp10) REVERT: N 83 MET cc_start: 0.6787 (mtm) cc_final: 0.6063 (mtm) REVERT: R 180 GLU cc_start: 0.6275 (OUTLIER) cc_final: 0.5566 (mp0) REVERT: R 181 ARG cc_start: 0.6560 (ttp-110) cc_final: 0.6350 (ttp-110) REVERT: R 221 TYR cc_start: 0.7236 (t80) cc_final: 0.6807 (t80) REVERT: R 438 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.7180 (mm-40) REVERT: R 467 GLN cc_start: 0.7569 (tp40) cc_final: 0.7034 (tm-30) outliers start: 23 outliers final: 8 residues processed: 134 average time/residue: 1.2179 time to fit residues: 174.0856 Evaluate side-chains 125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 438 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 40.0000 chunk 2 optimal weight: 0.0270 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 49 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.213708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171710 restraints weight = 9906.177| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.85 r_work: 0.4044 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3929 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8920 Z= 0.229 Angle : 0.554 9.181 12127 Z= 0.300 Chirality : 0.043 0.264 1367 Planarity : 0.004 0.046 1544 Dihedral : 4.708 33.467 1231 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.24 % Allowed : 14.80 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.04 (0.26), residues: 1119 helix: 2.33 (0.24), residues: 437 sheet: -0.84 (0.31), residues: 221 loop : -0.03 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 14 HIS 0.008 0.001 HIS A 362 PHE 0.022 0.002 PHE A 222 TYR 0.027 0.002 TYR R 191 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5502 (ttpt) REVERT: A 208 PHE cc_start: 0.7567 (m-80) cc_final: 0.7255 (m-10) REVERT: A 390 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.6165 (pt0) REVERT: B 44 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.6904 (mm110) REVERT: B 87 THR cc_start: 0.7752 (t) cc_final: 0.7488 (m) REVERT: B 170 ASP cc_start: 0.8007 (t70) cc_final: 0.7754 (p0) REVERT: B 175 GLN cc_start: 0.7254 (mm110) cc_final: 0.6363 (pt0) REVERT: B 219 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7182 (mmt-90) REVERT: B 280 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7691 (mtpt) REVERT: G 50 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.5771 (mp) REVERT: N 53 GLN cc_start: 0.7895 (mp10) cc_final: 0.7659 (mp10) REVERT: N 83 MET cc_start: 0.6792 (mtm) cc_final: 0.6227 (mtm) REVERT: R 180 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5565 (mp0) REVERT: R 221 TYR cc_start: 0.7256 (t80) cc_final: 0.6819 (t80) REVERT: R 467 GLN cc_start: 0.7593 (tp40) cc_final: 0.7068 (tm-30) outliers start: 28 outliers final: 10 residues processed: 131 average time/residue: 1.5751 time to fit residues: 219.6313 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.0060 chunk 109 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 44 GLN B 176 GLN N 77 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS R 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.216658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.175688 restraints weight = 9827.574| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.82 r_work: 0.4081 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8920 Z= 0.172 Angle : 0.537 9.248 12127 Z= 0.290 Chirality : 0.042 0.283 1367 Planarity : 0.004 0.049 1544 Dihedral : 4.586 31.214 1231 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.54 % Allowed : 15.84 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.14 (0.26), residues: 1119 helix: 2.42 (0.24), residues: 437 sheet: -0.71 (0.32), residues: 216 loop : -0.05 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 14 HIS 0.006 0.001 HIS A 362 PHE 0.027 0.002 PHE A 222 TYR 0.026 0.001 TYR R 191 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6909 (tp30) cc_final: 0.6480 (tp30) REVERT: A 53 LYS cc_start: 0.6256 (ttpp) cc_final: 0.5484 (ttpt) REVERT: A 208 PHE cc_start: 0.7492 (m-80) cc_final: 0.7159 (m-10) REVERT: A 390 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.6044 (pt0) REVERT: B 87 THR cc_start: 0.7633 (t) cc_final: 0.7371 (m) REVERT: B 170 ASP cc_start: 0.7967 (t70) cc_final: 0.7747 (p0) REVERT: B 219 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7213 (mmt-90) REVERT: B 280 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7656 (ttpt) REVERT: G 50 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.5728 (mp) REVERT: N 53 GLN cc_start: 0.7865 (mp10) cc_final: 0.7643 (mp10) REVERT: N 83 MET cc_start: 0.6708 (mtm) cc_final: 0.6050 (mtm) REVERT: R 180 GLU cc_start: 0.6317 (tp30) cc_final: 0.5548 (mp0) REVERT: R 221 TYR cc_start: 0.7182 (t80) cc_final: 0.6766 (t80) REVERT: R 467 GLN cc_start: 0.7551 (tp40) cc_final: 0.7090 (tm-30) outliers start: 22 outliers final: 9 residues processed: 130 average time/residue: 1.2761 time to fit residues: 177.1822 Evaluate side-chains 118 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 100 optimal weight: 0.3980 chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 0.0980 chunk 66 optimal weight: 0.3980 overall best weight: 0.2558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** R 374 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 = 0.4571 r_free = 0.4571 target = 0.218036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.177275 restraints weight = 10053.804| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.85 r_work: 0.4097 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3987 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8920 Z= 0.151 Angle : 0.525 9.616 12127 Z= 0.284 Chirality : 0.042 0.292 1367 Planarity : 0.004 0.050 1544 Dihedral : 4.465 29.835 1231 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.85 % Allowed : 16.65 % Favored : 81.50 % 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: 1.22 (0.26), residues: 1119 helix: 2.51 (0.24), residues: 437 sheet: -0.69 (0.31), residues: 226 loop : 0.00 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.032 0.001 PHE A 222 TYR 0.026 0.001 TYR R 191 ARG 0.004 0.000 ARG R 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6890 (tp30) cc_final: 0.6475 (tp30) REVERT: A 53 LYS cc_start: 0.6251 (ttpp) cc_final: 0.5489 (ttpt) REVERT: A 208 PHE cc_start: 0.7455 (m-80) cc_final: 0.7121 (m-10) REVERT: A 373 ARG cc_start: 0.7351 (tpp-160) cc_final: 0.6935 (mmm-85) REVERT: A 390 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.6114 (pt0) REVERT: B 87 THR cc_start: 0.7627 (t) cc_final: 0.7381 (m) REVERT: B 170 ASP cc_start: 0.7934 (t70) cc_final: 0.7722 (p0) REVERT: B 219 ARG cc_start: 0.7735 (mtp-110) cc_final: 0.7176 (mmt-90) REVERT: B 280 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7652 (ttpt) REVERT: B 325 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6826 (mmt) REVERT: G 50 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.5606 (mp) REVERT: N 83 MET cc_start: 0.6644 (mtm) cc_final: 0.6069 (mtm) REVERT: R 180 GLU cc_start: 0.6296 (tp30) cc_final: 0.5557 (mp0) REVERT: R 221 TYR cc_start: 0.7143 (t80) cc_final: 0.6826 (t80) REVERT: R 467 GLN cc_start: 0.7538 (tp40) cc_final: 0.7098 (tm-30) outliers start: 16 outliers final: 7 residues processed: 124 average time/residue: 1.2124 time to fit residues: 160.6790 Evaluate side-chains 115 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 390 GLN B 220 GLN N 77 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.213085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.170445 restraints weight = 10064.424| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.88 r_work: 0.4036 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8920 Z= 0.254 Angle : 0.580 9.116 12127 Z= 0.311 Chirality : 0.044 0.305 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.687 31.989 1231 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.08 % Allowed : 16.65 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.13 (0.26), residues: 1119 helix: 2.36 (0.24), residues: 437 sheet: -0.71 (0.32), residues: 223 loop : 0.03 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 298 HIS 0.007 0.001 HIS A 357 PHE 0.042 0.002 PHE A 222 TYR 0.026 0.002 TYR R 191 ARG 0.004 0.000 ARG R 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7014 (tp30) cc_final: 0.6587 (tp30) REVERT: A 53 LYS cc_start: 0.6276 (ttpp) cc_final: 0.5548 (ttpt) REVERT: A 373 ARG cc_start: 0.7326 (tpp-160) cc_final: 0.6911 (mmm-85) REVERT: A 390 GLN cc_start: 0.6450 (OUTLIER) cc_final: 0.6079 (pt0) REVERT: A 392 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: B 87 THR cc_start: 0.7603 (t) cc_final: 0.7375 (m) REVERT: B 170 ASP cc_start: 0.7988 (t70) cc_final: 0.7759 (p0) REVERT: B 219 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7183 (mmt-90) REVERT: B 258 ASP cc_start: 0.6631 (t0) cc_final: 0.6407 (m-30) REVERT: B 280 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7662 (mtpt) REVERT: B 325 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7049 (mmt) REVERT: G 50 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.5877 (mp) REVERT: N 83 MET cc_start: 0.6760 (mtm) cc_final: 0.6352 (mtm) REVERT: R 180 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5670 (mp0) REVERT: R 221 TYR cc_start: 0.7216 (t80) cc_final: 0.6871 (t80) REVERT: R 467 GLN cc_start: 0.7521 (tp40) cc_final: 0.7106 (tm-30) outliers start: 18 outliers final: 10 residues processed: 115 average time/residue: 1.2695 time to fit residues: 155.7494 Evaluate side-chains 119 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 383 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.0970 chunk 81 optimal weight: 40.0000 chunk 84 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 390 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.211097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.168813 restraints weight = 9977.673| |-----------------------------------------------------------------------------| r_work (start): 0.4119 rms_B_bonded: 1.85 r_work: 0.4033 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8920 Z= 0.263 Angle : 0.580 8.340 12127 Z= 0.313 Chirality : 0.044 0.294 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.721 31.582 1231 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.43 % Allowed : 16.99 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.03 (0.26), residues: 1119 helix: 2.26 (0.24), residues: 437 sheet: -0.76 (0.32), residues: 223 loop : -0.01 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 352 HIS 0.008 0.001 HIS A 357 PHE 0.044 0.002 PHE A 222 TYR 0.025 0.002 TYR R 191 ARG 0.006 0.000 ARG R 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6984 (tp30) cc_final: 0.6573 (tp30) REVERT: A 53 LYS cc_start: 0.6291 (ttpp) cc_final: 0.5569 (ttpt) REVERT: A 373 ARG cc_start: 0.7347 (tpp-160) cc_final: 0.6917 (mmm-85) REVERT: A 392 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7425 (mt-10) REVERT: B 87 THR cc_start: 0.7596 (t) cc_final: 0.7373 (m) REVERT: B 170 ASP cc_start: 0.7971 (t70) cc_final: 0.7739 (p0) REVERT: B 219 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7195 (mmt-90) REVERT: B 280 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7703 (mtpt) REVERT: B 325 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7031 (mmt) REVERT: G 50 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.5855 (mp) REVERT: N 83 MET cc_start: 0.6745 (mtm) cc_final: 0.6333 (mtm) REVERT: R 178 THR cc_start: 0.6761 (t) cc_final: 0.6359 (p) REVERT: R 180 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: R 221 TYR cc_start: 0.7208 (t80) cc_final: 0.6858 (t80) REVERT: R 467 GLN cc_start: 0.7525 (tp40) cc_final: 0.7121 (tm-30) outliers start: 21 outliers final: 13 residues processed: 117 average time/residue: 1.4232 time to fit residues: 179.8170 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 383 ARG Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.212804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171229 restraints weight = 9988.104| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 1.84 r_work: 0.4062 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8920 Z= 0.211 Angle : 0.559 8.890 12127 Z= 0.303 Chirality : 0.043 0.299 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.643 30.669 1231 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.08 % Allowed : 17.11 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.12 (0.26), residues: 1119 helix: 2.29 (0.25), residues: 438 sheet: -0.67 (0.32), residues: 228 loop : 0.07 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 352 HIS 0.007 0.001 HIS A 357 PHE 0.044 0.002 PHE A 222 TYR 0.025 0.002 TYR R 191 ARG 0.005 0.000 ARG R 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6939 (tp30) cc_final: 0.6515 (tp30) REVERT: A 53 LYS cc_start: 0.6285 (ttpp) cc_final: 0.5562 (ttpt) REVERT: A 373 ARG cc_start: 0.7334 (tpp-160) cc_final: 0.6903 (mmm-85) REVERT: B 87 THR cc_start: 0.7541 (t) cc_final: 0.7328 (m) REVERT: B 219 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7157 (mmt-90) REVERT: B 280 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7682 (mtpt) REVERT: B 325 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6925 (mmt) REVERT: G 50 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.5837 (mp) REVERT: N 83 MET cc_start: 0.6681 (mtm) cc_final: 0.6222 (mtm) REVERT: R 178 THR cc_start: 0.6765 (t) cc_final: 0.6367 (p) REVERT: R 180 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5771 (mp0) REVERT: R 221 TYR cc_start: 0.7176 (t80) cc_final: 0.6832 (t80) REVERT: R 231 MET cc_start: 0.6977 (mmt) cc_final: 0.6713 (mmm) REVERT: R 467 GLN cc_start: 0.7495 (tp40) cc_final: 0.7132 (tm-30) outliers start: 18 outliers final: 10 residues processed: 120 average time/residue: 1.3732 time to fit residues: 175.3329 Evaluate side-chains 121 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 44 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 155 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.214220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.173639 restraints weight = 10038.837| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.78 r_work: 0.4084 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8920 Z= 0.187 Angle : 0.552 8.853 12127 Z= 0.299 Chirality : 0.043 0.303 1367 Planarity : 0.004 0.052 1544 Dihedral : 4.582 29.831 1231 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.62 % Allowed : 17.92 % Favored : 80.46 % 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: 1.20 (0.26), residues: 1119 helix: 2.37 (0.25), residues: 437 sheet: -0.68 (0.32), residues: 229 loop : 0.15 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 352 HIS 0.006 0.001 HIS A 357 PHE 0.049 0.002 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.005 0.000 ARG R 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7603.29 seconds wall clock time: 133 minutes 54.24 seconds (8034.24 seconds total)