Starting phenix.real_space_refine on Sat Aug 23 03:29:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jit_36327/08_2025/8jit_36327_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jit_36327/08_2025/8jit_36327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jit_36327/08_2025/8jit_36327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jit_36327/08_2025/8jit_36327.map" model { file = "/net/cci-nas-00/data/ceres_data/8jit_36327/08_2025/8jit_36327_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jit_36327/08_2025/8jit_36327_neut_trim.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 56 5.16 5 C 5836 2.51 5 N 1617 2.21 5 O 1684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9193 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1868 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 233 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2574 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 420 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 964 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3108 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.81, per 1000 atoms: 0.20 Number of scatterers: 9193 At special positions: 0 Unit cell: (77.112, 99.603, 175.644, 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 56 16.00 O 1684 8.00 N 1617 7.00 C 5836 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=2.05 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 67 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 252.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 42.3% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 34 removed outlier: 3.806A pdb=" N ASN A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 30 " --> pdb=" O LYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 50 removed outlier: 3.625A pdb=" N ILE A 50 " --> pdb=" O LYS A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.641A pdb=" N GLN A 220 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 221 " --> pdb=" O TRP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 262 Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.658A pdb=" N TYR A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.520A pdb=" N ARG A 301 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 336 removed outlier: 4.511A pdb=" N SER A 336 " --> pdb=" O ILE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 375 removed outlier: 4.191A pdb=" N ASN A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.755A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.621A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'C' and resid 8 through 21 removed outlier: 4.099A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.855A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) 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 removed outlier: 3.786A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 49 removed outlier: 3.773A pdb=" N LEU R 49 " --> pdb=" O HIS R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 126 through 165 removed outlier: 3.757A pdb=" N VAL R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU R 158 " --> pdb=" O GLY R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 202 removed outlier: 3.583A pdb=" N ASN R 179 " --> pdb=" O ALA R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 217 Processing helix chain 'R' and resid 220 through 255 removed outlier: 3.787A pdb=" N CYS R 224 " --> pdb=" O ALA R 220 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU R 255 " --> pdb=" O ASN R 251 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 273 through 289 removed outlier: 3.822A pdb=" N LEU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) Proline residue: R 281 - end of helix Processing helix chain 'R' and resid 300 through 303 Processing helix chain 'R' and resid 304 through 317 Proline residue: R 310 - end of helix Processing helix chain 'R' and resid 318 through 334 Processing helix chain 'R' and resid 343 through 354 removed outlier: 3.837A pdb=" N THR R 351 " --> pdb=" O LEU R 347 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU R 352 " --> pdb=" O ALA R 348 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 402 removed outlier: 3.566A pdb=" N ARG R 378 " --> pdb=" O GLN R 374 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 420 removed outlier: 3.966A pdb=" N LEU R 420 " --> pdb=" O HIS R 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 198 removed outlier: 6.823A pdb=" N HIS A 35 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE A 206 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 37 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARG A 36 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE A 229 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU A 38 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 231 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 40 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ALA A 233 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.644A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.565A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.721A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.613A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.917A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.583A 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: 3.527A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.803A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (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 11 through 12 removed outlier: 6.895A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 75 through 80 453 hydrogen bonds defined for protein. 1287 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: 1.07 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1902 1.33 - 1.45: 2394 1.45 - 1.57: 5025 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9397 Sorted by residual: bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.341 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C04 D6M P 101 " pdb=" C09 D6M P 101 " ideal model delta sigma weight residual 1.550 1.486 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C THR A 309 " pdb=" N PRO A 310 " ideal model delta sigma weight residual 1.329 1.367 -0.037 1.22e-02 6.72e+03 9.28e+00 bond pdb=" CA THR N 111 " pdb=" C THR N 111 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.40e-02 5.10e+03 9.01e+00 bond pdb=" CA CYS N 99 " pdb=" C CYS N 99 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.02e-02 9.61e+03 8.85e+00 ... (remaining 9392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 12684 4.22 - 8.45: 55 8.45 - 12.67: 3 12.67 - 16.90: 0 16.90 - 21.12: 1 Bond angle restraints: 12743 Sorted by residual: angle pdb=" C06 D6M P 101 " pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 118.04 96.92 21.12 3.00e+00 1.11e-01 4.96e+01 angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 113.30 122.71 -9.41 1.34e+00 5.57e-01 4.93e+01 angle pdb=" C THR A 309 " pdb=" N PRO A 310 " pdb=" CA PRO A 310 " ideal model delta sigma weight residual 120.66 113.02 7.64 1.09e+00 8.42e-01 4.92e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.38 105.27 8.11 1.23e+00 6.61e-01 4.34e+01 angle pdb=" N TRP P 25 " pdb=" CA TRP P 25 " pdb=" C TRP P 25 " ideal model delta sigma weight residual 111.71 105.02 6.69 1.15e+00 7.56e-01 3.39e+01 ... (remaining 12738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5005 17.83 - 35.66: 430 35.66 - 53.48: 94 53.48 - 71.31: 23 71.31 - 89.14: 10 Dihedral angle restraints: 5562 sinusoidal: 2156 harmonic: 3406 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 -14.49 -71.51 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" N ASN C 59 " pdb=" C ASN C 59 " pdb=" CA ASN C 59 " pdb=" CB ASN C 59 " ideal model delta harmonic sigma weight residual 122.80 133.65 -10.85 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" C ASN C 59 " pdb=" N ASN C 59 " pdb=" CA ASN C 59 " pdb=" CB ASN C 59 " ideal model delta harmonic sigma weight residual -122.60 -132.44 9.84 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 5559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1319 0.095 - 0.191: 85 0.191 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.477: 2 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA ASN C 59 " pdb=" N ASN C 59 " pdb=" C ASN C 59 " pdb=" CB ASN C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL R 212 " pdb=" CA VAL R 212 " pdb=" CG1 VAL R 212 " pdb=" CG2 VAL R 212 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1411 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER N 25 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C SER N 25 " -0.049 2.00e-02 2.50e+03 pdb=" O SER N 25 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY N 26 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 355 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO R 356 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " 0.035 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO R 275 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " 0.030 5.00e-02 4.00e+02 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1110 2.74 - 3.28: 9587 3.28 - 3.82: 15650 3.82 - 4.36: 18095 4.36 - 4.90: 30824 Nonbonded interactions: 75266 Sorted by model distance: nonbonded pdb=" O ALA R 175 " pdb=" ND2 ASN R 179 " model vdw 2.204 3.120 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.223 3.040 nonbonded pdb=" O TYR A 302 " pdb=" NH2 ARG A 320 " model vdw 2.260 3.120 nonbonded pdb=" O ARG B 22 " pdb=" NH1 ARG B 22 " model vdw 2.263 3.120 nonbonded pdb=" OE1 GLN P 3 " pdb=" OH TYR R 149 " model vdw 2.269 3.040 ... (remaining 75261 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: 0.980 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.070 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.006 0.094 9404 Z= 0.392 Angle : 0.789 21.123 12755 Z= 0.498 Chirality : 0.052 0.477 1414 Planarity : 0.004 0.065 1634 Dihedral : 14.715 89.141 3342 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.52 % Favored : 93.97 % Rotamer: Outliers : 4.69 % Allowed : 3.34 % Favored : 91.97 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.26), residues: 1160 helix: 1.12 (0.27), residues: 429 sheet: -0.78 (0.35), residues: 232 loop : -1.33 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 32 TYR 0.015 0.001 TYR N 115 PHE 0.024 0.001 PHE B 253 TRP 0.024 0.001 TRP N 36 HIS 0.005 0.001 HIS R 44 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9397) covalent geometry : angle 0.78623 (12743) SS BOND : bond 0.00783 ( 6) SS BOND : angle 2.15500 ( 12) hydrogen bonds : bond 0.17735 ( 453) hydrogen bonds : angle 6.74498 ( 1287) Misc. bond : bond 0.09027 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 THR cc_start: 0.5987 (t) cc_final: 0.5655 (t) REVERT: A 278 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: B 17 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8795 (pp30) REVERT: B 188 MET cc_start: 0.8680 (mmm) cc_final: 0.8290 (mmm) REVERT: B 254 ASP cc_start: 0.8054 (t70) cc_final: 0.7834 (t0) REVERT: C 13 ARG cc_start: 0.9337 (ttm110) cc_final: 0.9136 (ttm110) REVERT: C 42 GLU cc_start: 0.8809 (pp20) cc_final: 0.8443 (pp20) REVERT: N 2 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8201 (p) REVERT: R 34 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8753 (tm-30) REVERT: R 142 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8161 (mt0) REVERT: R 354 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8546 (tt) REVERT: R 362 GLU cc_start: 0.8769 (tp30) cc_final: 0.8552 (tp30) REVERT: R 407 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8825 (p) outliers start: 45 outliers final: 7 residues processed: 217 average time/residue: 0.5286 time to fit residues: 121.5098 Evaluate side-chains 140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 317 ARG Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 358 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 409 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.0010 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS A 197 GLN B 340 ASN C 24 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 HIS ** R 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 337 GLN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.099288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.069448 restraints weight = 19447.065| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.40 r_work: 0.2902 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9404 Z= 0.190 Angle : 0.675 9.581 12755 Z= 0.348 Chirality : 0.044 0.224 1414 Planarity : 0.005 0.069 1634 Dihedral : 6.830 73.951 1324 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 2.92 % Allowed : 13.76 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.25), residues: 1160 helix: 1.49 (0.26), residues: 438 sheet: -0.60 (0.34), residues: 233 loop : -1.21 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.029 0.002 TYR R 145 PHE 0.024 0.002 PHE P 6 TRP 0.035 0.002 TRP N 36 HIS 0.008 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9397) covalent geometry : angle 0.67337 (12743) SS BOND : bond 0.00355 ( 6) SS BOND : angle 1.61937 ( 12) hydrogen bonds : bond 0.04103 ( 453) hydrogen bonds : angle 4.60443 ( 1287) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.9372 (mtp180) cc_final: 0.8842 (mtt180) REVERT: B 15 LYS cc_start: 0.9364 (tttt) cc_final: 0.8875 (tmmt) REVERT: B 32 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7300 (pm20) REVERT: B 188 MET cc_start: 0.9196 (mmm) cc_final: 0.8759 (mmm) REVERT: B 254 ASP cc_start: 0.8276 (t70) cc_final: 0.7939 (t0) REVERT: B 260 GLU cc_start: 0.8444 (pt0) cc_final: 0.8061 (tt0) REVERT: C 13 ARG cc_start: 0.9339 (ttm110) cc_final: 0.9050 (ttm110) REVERT: C 17 GLU cc_start: 0.8914 (tp30) cc_final: 0.8596 (mp0) REVERT: C 29 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8521 (mmmm) REVERT: C 42 GLU cc_start: 0.8850 (pp20) cc_final: 0.8490 (pp20) REVERT: C 58 GLU cc_start: 0.9379 (mm-30) cc_final: 0.8823 (mt-10) REVERT: N 1 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7198 (tp-100) REVERT: N 2 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8292 (p) REVERT: N 87 LYS cc_start: 0.8593 (tppp) cc_final: 0.8291 (ttmp) REVERT: N 89 GLU cc_start: 0.8756 (pm20) cc_final: 0.8511 (pm20) REVERT: R 34 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8984 (tm-30) REVERT: R 142 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: R 290 GLU cc_start: 0.6635 (pp20) cc_final: 0.6433 (pp20) REVERT: R 349 LYS cc_start: 0.6211 (mmtt) cc_final: 0.5967 (mptt) REVERT: R 354 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8802 (tt) outliers start: 28 outliers final: 16 residues processed: 161 average time/residue: 0.6020 time to fit residues: 102.8365 Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 25 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** R 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070050 restraints weight = 19534.863| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.42 r_work: 0.2857 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9404 Z= 0.176 Angle : 0.627 9.514 12755 Z= 0.325 Chirality : 0.042 0.155 1414 Planarity : 0.004 0.075 1634 Dihedral : 5.846 59.924 1310 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 3.55 % Allowed : 17.10 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.26), residues: 1160 helix: 1.79 (0.26), residues: 427 sheet: -0.48 (0.34), residues: 239 loop : -1.10 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.024 0.002 TYR R 145 PHE 0.020 0.002 PHE P 6 TRP 0.030 0.002 TRP N 36 HIS 0.010 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9397) covalent geometry : angle 0.62565 (12743) SS BOND : bond 0.00341 ( 6) SS BOND : angle 1.50663 ( 12) hydrogen bonds : bond 0.03916 ( 453) hydrogen bonds : angle 4.31042 ( 1287) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8830 (mm-30) REVERT: A 246 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: B 8 ARG cc_start: 0.9332 (mtp180) cc_final: 0.8834 (mtt180) REVERT: B 9 GLN cc_start: 0.9613 (mm-40) cc_final: 0.9376 (mm-40) REVERT: B 15 LYS cc_start: 0.9388 (tttt) cc_final: 0.9007 (tmmt) REVERT: B 17 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8686 (pp30) REVERT: B 32 GLN cc_start: 0.7666 (pm20) cc_final: 0.7332 (pm20) REVERT: B 188 MET cc_start: 0.9174 (mmm) cc_final: 0.8754 (mmm) REVERT: B 217 MET cc_start: 0.7312 (pmm) cc_final: 0.6899 (pmm) REVERT: B 254 ASP cc_start: 0.8201 (t70) cc_final: 0.7810 (t0) REVERT: B 260 GLU cc_start: 0.8652 (pt0) cc_final: 0.8156 (tt0) REVERT: B 301 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7882 (mmmm) REVERT: C 13 ARG cc_start: 0.9347 (ttm110) cc_final: 0.9113 (ttm110) REVERT: C 17 GLU cc_start: 0.9074 (tp30) cc_final: 0.8783 (tp30) REVERT: C 21 MET cc_start: 0.7952 (mpp) cc_final: 0.7163 (mpp) REVERT: C 28 ILE cc_start: 0.9113 (pt) cc_final: 0.8849 (pp) REVERT: C 29 LYS cc_start: 0.8724 (mmmm) cc_final: 0.8513 (tppp) REVERT: C 42 GLU cc_start: 0.8860 (pp20) cc_final: 0.8466 (pp20) REVERT: C 58 GLU cc_start: 0.9421 (mm-30) cc_final: 0.8852 (mt-10) REVERT: N 87 LYS cc_start: 0.8572 (tppp) cc_final: 0.8210 (ttmp) REVERT: N 89 GLU cc_start: 0.8770 (pm20) cc_final: 0.8527 (pm20) REVERT: R 34 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8987 (tm-30) REVERT: R 115 TRP cc_start: 0.8650 (m100) cc_final: 0.8421 (m100) REVERT: R 127 GLU cc_start: 0.7630 (mp0) cc_final: 0.7275 (mp0) REVERT: R 142 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8390 (mt0) REVERT: R 290 GLU cc_start: 0.6748 (pp20) cc_final: 0.6532 (pp20) REVERT: R 354 LEU cc_start: 0.9079 (tp) cc_final: 0.8831 (tp) outliers start: 34 outliers final: 19 residues processed: 162 average time/residue: 0.5161 time to fit residues: 88.9208 Evaluate side-chains 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 142 GLN Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 52 optimal weight: 0.4980 chunk 104 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 ASN R 142 GLN R 179 ASN ** R 361 HIS ** 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 = 0.3585 r_free = 0.3585 target = 0.098926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.069221 restraints weight = 19367.141| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.36 r_work: 0.2891 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9404 Z= 0.129 Angle : 0.590 9.881 12755 Z= 0.303 Chirality : 0.041 0.150 1414 Planarity : 0.004 0.072 1634 Dihedral : 5.496 57.328 1307 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 3.34 % Allowed : 18.77 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1160 helix: 1.86 (0.26), residues: 433 sheet: -0.39 (0.34), residues: 241 loop : -1.00 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.023 0.001 TYR R 145 PHE 0.017 0.001 PHE P 6 TRP 0.022 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9397) covalent geometry : angle 0.58920 (12743) SS BOND : bond 0.00295 ( 6) SS BOND : angle 1.14360 ( 12) hydrogen bonds : bond 0.03512 ( 453) hydrogen bonds : angle 4.11626 ( 1287) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8873 (mm-30) REVERT: B 8 ARG cc_start: 0.9264 (mtp180) cc_final: 0.8760 (mtt180) REVERT: B 9 GLN cc_start: 0.9661 (mm-40) cc_final: 0.9458 (mm-40) REVERT: B 15 LYS cc_start: 0.9378 (tttt) cc_final: 0.9044 (tmmt) REVERT: B 32 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: B 188 MET cc_start: 0.9189 (mmm) cc_final: 0.8702 (mmm) REVERT: B 217 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7079 (pmm) REVERT: B 254 ASP cc_start: 0.8172 (t70) cc_final: 0.7795 (t0) REVERT: B 260 GLU cc_start: 0.8573 (pt0) cc_final: 0.8268 (tt0) REVERT: C 13 ARG cc_start: 0.9358 (ttm110) cc_final: 0.9130 (ttm110) REVERT: C 17 GLU cc_start: 0.9096 (tp30) cc_final: 0.8725 (tp30) REVERT: C 20 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8736 (tmmm) REVERT: C 21 MET cc_start: 0.7809 (mpp) cc_final: 0.6914 (mpp) REVERT: C 28 ILE cc_start: 0.9161 (pt) cc_final: 0.8899 (pp) REVERT: C 29 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8547 (tppp) REVERT: C 42 GLU cc_start: 0.8842 (pp20) cc_final: 0.8445 (pp20) REVERT: C 48 ASP cc_start: 0.8917 (t0) cc_final: 0.8714 (t0) REVERT: C 58 GLU cc_start: 0.9426 (mm-30) cc_final: 0.8879 (mt-10) REVERT: N 38 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8625 (ptm-80) REVERT: N 82 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8073 (tp-100) REVERT: N 87 LYS cc_start: 0.8546 (tppp) cc_final: 0.8207 (ttmm) REVERT: N 89 GLU cc_start: 0.8852 (pm20) cc_final: 0.8568 (pm20) REVERT: N 120 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7581 (tm-30) REVERT: R 34 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8974 (tm-30) REVERT: R 50 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (tp) REVERT: R 115 TRP cc_start: 0.8707 (m100) cc_final: 0.8447 (m100) REVERT: R 127 GLU cc_start: 0.7586 (mp0) cc_final: 0.7308 (mp0) REVERT: R 354 LEU cc_start: 0.9066 (tp) cc_final: 0.8839 (tp) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 0.5083 time to fit residues: 90.4532 Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 67 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 ASN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.064069 restraints weight = 19580.738| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.41 r_work: 0.2774 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 9404 Z= 0.283 Angle : 0.685 8.672 12755 Z= 0.356 Chirality : 0.045 0.169 1414 Planarity : 0.005 0.078 1634 Dihedral : 5.923 58.680 1304 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 4.48 % Allowed : 19.50 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.26), residues: 1160 helix: 1.87 (0.26), residues: 430 sheet: -0.32 (0.34), residues: 241 loop : -1.04 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 105 TYR 0.025 0.002 TYR R 145 PHE 0.019 0.002 PHE N 108 TRP 0.033 0.002 TRP N 36 HIS 0.010 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 9397) covalent geometry : angle 0.68360 (12743) SS BOND : bond 0.00425 ( 6) SS BOND : angle 1.67858 ( 12) hydrogen bonds : bond 0.04352 ( 453) hydrogen bonds : angle 4.28420 ( 1287) Misc. bond : bond 0.00056 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8781 (mm-30) REVERT: B 5 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.9017 (p0) REVERT: B 8 ARG cc_start: 0.9278 (mtp180) cc_final: 0.8878 (mtt180) REVERT: B 9 GLN cc_start: 0.9692 (mm-40) cc_final: 0.9438 (mm-40) REVERT: B 15 LYS cc_start: 0.9411 (tttt) cc_final: 0.9120 (tmmt) REVERT: B 23 LYS cc_start: 0.9573 (tppp) cc_final: 0.9333 (tptp) REVERT: B 188 MET cc_start: 0.9131 (mmm) cc_final: 0.8872 (mmm) REVERT: B 217 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7342 (pmm) REVERT: B 254 ASP cc_start: 0.8285 (t70) cc_final: 0.7922 (t0) REVERT: B 260 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: C 13 ARG cc_start: 0.9354 (ttm110) cc_final: 0.9120 (ttm110) REVERT: C 17 GLU cc_start: 0.9161 (tp30) cc_final: 0.8740 (tp30) REVERT: C 21 MET cc_start: 0.8170 (mpp) cc_final: 0.7253 (mpp) REVERT: C 28 ILE cc_start: 0.9091 (pt) cc_final: 0.8878 (pp) REVERT: C 29 LYS cc_start: 0.8804 (mmmm) cc_final: 0.8569 (tppp) REVERT: C 42 GLU cc_start: 0.8966 (pp20) cc_final: 0.8539 (pp20) REVERT: C 58 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8766 (mt-10) REVERT: N 38 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8673 (ptm-80) REVERT: N 46 GLU cc_start: 0.8595 (pt0) cc_final: 0.8394 (pt0) REVERT: N 87 LYS cc_start: 0.8604 (tppp) cc_final: 0.8246 (ttmm) REVERT: N 89 GLU cc_start: 0.8853 (pm20) cc_final: 0.8609 (pm20) REVERT: R 34 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9017 (tm-30) REVERT: R 115 TRP cc_start: 0.8614 (m100) cc_final: 0.8388 (m100) REVERT: R 124 ASP cc_start: 0.8968 (t0) cc_final: 0.8734 (t0) REVERT: R 127 GLU cc_start: 0.7733 (mp0) cc_final: 0.7211 (mp0) REVERT: R 354 LEU cc_start: 0.9048 (tp) cc_final: 0.8834 (tp) outliers start: 43 outliers final: 25 residues processed: 164 average time/residue: 0.4994 time to fit residues: 87.4645 Evaluate side-chains 160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 HIS ** 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 = 0.3543 r_free = 0.3543 target = 0.098470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.067681 restraints weight = 19599.166| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.40 r_work: 0.2815 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9404 Z= 0.199 Angle : 0.650 10.972 12755 Z= 0.331 Chirality : 0.043 0.156 1414 Planarity : 0.004 0.080 1634 Dihedral : 5.718 59.607 1304 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 4.07 % Allowed : 20.65 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.26), residues: 1160 helix: 1.76 (0.25), residues: 443 sheet: -0.20 (0.34), residues: 239 loop : -0.93 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 105 TYR 0.022 0.002 TYR R 145 PHE 0.018 0.001 PHE P 6 TRP 0.021 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9397) covalent geometry : angle 0.64888 (12743) SS BOND : bond 0.00290 ( 6) SS BOND : angle 1.35390 ( 12) hydrogen bonds : bond 0.03862 ( 453) hydrogen bonds : angle 4.16227 ( 1287) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8771 (mm-30) REVERT: B 5 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.8972 (p0) REVERT: B 8 ARG cc_start: 0.9241 (mtp180) cc_final: 0.9001 (mtt180) REVERT: B 9 GLN cc_start: 0.9702 (mm-40) cc_final: 0.9439 (mm-40) REVERT: B 15 LYS cc_start: 0.9362 (tttt) cc_final: 0.9106 (tmmt) REVERT: B 23 LYS cc_start: 0.9566 (tppp) cc_final: 0.9354 (tptp) REVERT: B 32 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 59 TYR cc_start: 0.9391 (OUTLIER) cc_final: 0.8711 (t80) REVERT: B 188 MET cc_start: 0.9159 (mmm) cc_final: 0.8764 (mmm) REVERT: B 217 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7645 (pmm) REVERT: B 254 ASP cc_start: 0.8345 (t70) cc_final: 0.7974 (t0) REVERT: B 260 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: C 13 ARG cc_start: 0.9339 (ttm110) cc_final: 0.9102 (ttm110) REVERT: C 17 GLU cc_start: 0.9150 (tp30) cc_final: 0.8730 (tp30) REVERT: C 21 MET cc_start: 0.8049 (mpp) cc_final: 0.7129 (mpp) REVERT: C 29 LYS cc_start: 0.8836 (mmmm) cc_final: 0.8593 (tppp) REVERT: C 42 GLU cc_start: 0.8897 (pp20) cc_final: 0.8457 (pp20) REVERT: C 58 GLU cc_start: 0.9418 (mm-30) cc_final: 0.8815 (mt-10) REVERT: N 38 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8748 (ptm-80) REVERT: N 87 LYS cc_start: 0.8796 (tppp) cc_final: 0.8419 (ttmm) REVERT: N 89 GLU cc_start: 0.8885 (pm20) cc_final: 0.8602 (pm20) REVERT: R 34 GLU cc_start: 0.9313 (tm-30) cc_final: 0.9035 (tm-30) REVERT: R 115 TRP cc_start: 0.8646 (m100) cc_final: 0.8444 (m100) REVERT: R 124 ASP cc_start: 0.9038 (t0) cc_final: 0.8735 (t0) REVERT: R 127 GLU cc_start: 0.7794 (mp0) cc_final: 0.7222 (mp0) REVERT: R 349 LYS cc_start: 0.5966 (tptt) cc_final: 0.5582 (mptt) REVERT: R 354 LEU cc_start: 0.9076 (tp) cc_final: 0.8840 (tp) REVERT: R 406 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 39 outliers final: 23 residues processed: 159 average time/residue: 0.5141 time to fit residues: 87.2334 Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 361 HIS ** 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 = 0.3594 r_free = 0.3594 target = 0.101958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.071274 restraints weight = 19358.398| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.45 r_work: 0.2887 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9404 Z= 0.124 Angle : 0.626 11.673 12755 Z= 0.315 Chirality : 0.041 0.148 1414 Planarity : 0.004 0.080 1634 Dihedral : 5.343 57.640 1304 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 3.44 % Allowed : 21.38 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1160 helix: 1.93 (0.25), residues: 443 sheet: -0.16 (0.35), residues: 238 loop : -0.85 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 105 TYR 0.021 0.001 TYR R 145 PHE 0.017 0.001 PHE R 303 TRP 0.015 0.001 TRP N 36 HIS 0.009 0.001 HIS R 361 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9397) covalent geometry : angle 0.62504 (12743) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.14183 ( 12) hydrogen bonds : bond 0.03394 ( 453) hydrogen bonds : angle 4.00577 ( 1287) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8760 (mm-30) REVERT: P 27 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 8 ARG cc_start: 0.9347 (mtp180) cc_final: 0.9050 (mtt-85) REVERT: B 9 GLN cc_start: 0.9728 (mm-40) cc_final: 0.9507 (mm-40) REVERT: B 15 LYS cc_start: 0.9394 (tttt) cc_final: 0.9134 (tmmt) REVERT: B 32 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: B 59 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.8670 (t80) REVERT: B 158 VAL cc_start: 0.9308 (t) cc_final: 0.9028 (p) REVERT: B 188 MET cc_start: 0.9149 (mmm) cc_final: 0.8694 (mmm) REVERT: B 217 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7926 (pmm) REVERT: B 254 ASP cc_start: 0.8290 (t70) cc_final: 0.7927 (t0) REVERT: B 260 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: C 13 ARG cc_start: 0.9351 (ttm110) cc_final: 0.9127 (ttm110) REVERT: C 17 GLU cc_start: 0.9162 (tp30) cc_final: 0.8751 (tp30) REVERT: C 21 MET cc_start: 0.7898 (mpp) cc_final: 0.7030 (mpp) REVERT: C 42 GLU cc_start: 0.8838 (pp20) cc_final: 0.8381 (pp20) REVERT: C 58 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8850 (mt-10) REVERT: N 38 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8735 (ptm-80) REVERT: N 87 LYS cc_start: 0.8687 (tppp) cc_final: 0.8090 (ttmm) REVERT: N 89 GLU cc_start: 0.8883 (pm20) cc_final: 0.8520 (pm20) REVERT: R 34 GLU cc_start: 0.9311 (tm-30) cc_final: 0.9021 (tm-30) REVERT: R 115 TRP cc_start: 0.8644 (m100) cc_final: 0.8418 (m100) REVERT: R 124 ASP cc_start: 0.9024 (t0) cc_final: 0.8751 (t0) REVERT: R 127 GLU cc_start: 0.7848 (mp0) cc_final: 0.7159 (mp0) REVERT: R 354 LEU cc_start: 0.9061 (tp) cc_final: 0.8837 (tp) outliers start: 33 outliers final: 18 residues processed: 171 average time/residue: 0.4718 time to fit residues: 86.3009 Evaluate side-chains 160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 45 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 93 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.071562 restraints weight = 19441.161| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.42 r_work: 0.2878 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9404 Z= 0.130 Angle : 0.647 11.583 12755 Z= 0.324 Chirality : 0.041 0.165 1414 Planarity : 0.004 0.078 1634 Dihedral : 5.275 57.644 1302 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 3.65 % Allowed : 22.42 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1160 helix: 1.98 (0.25), residues: 443 sheet: -0.21 (0.34), residues: 241 loop : -0.81 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 105 TYR 0.022 0.002 TYR R 145 PHE 0.015 0.001 PHE P 6 TRP 0.018 0.001 TRP N 36 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9397) covalent geometry : angle 0.64607 (12743) SS BOND : bond 0.00280 ( 6) SS BOND : angle 1.13243 ( 12) hydrogen bonds : bond 0.03354 ( 453) hydrogen bonds : angle 3.92817 ( 1287) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8732 (mm-30) REVERT: B 9 GLN cc_start: 0.9725 (mm-40) cc_final: 0.9517 (mm110) REVERT: B 15 LYS cc_start: 0.9398 (tttt) cc_final: 0.9119 (tmmt) REVERT: B 32 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: B 59 TYR cc_start: 0.9308 (OUTLIER) cc_final: 0.8732 (t80) REVERT: B 158 VAL cc_start: 0.9293 (t) cc_final: 0.9018 (p) REVERT: B 188 MET cc_start: 0.9138 (mmm) cc_final: 0.8676 (mmm) REVERT: B 217 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8034 (pmm) REVERT: B 247 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: B 254 ASP cc_start: 0.8167 (t70) cc_final: 0.7841 (t0) REVERT: B 260 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8355 (tt0) REVERT: C 13 ARG cc_start: 0.9335 (ttm110) cc_final: 0.9110 (ttm110) REVERT: C 29 LYS cc_start: 0.8738 (tppp) cc_final: 0.8508 (tppp) REVERT: C 42 GLU cc_start: 0.8843 (pp20) cc_final: 0.8382 (pp20) REVERT: C 58 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8843 (mt-10) REVERT: N 38 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8690 (ptm-80) REVERT: N 87 LYS cc_start: 0.8728 (tppp) cc_final: 0.8089 (ttmm) REVERT: N 89 GLU cc_start: 0.8910 (pm20) cc_final: 0.8591 (pm20) REVERT: R 34 GLU cc_start: 0.9306 (tm-30) cc_final: 0.9013 (tm-30) REVERT: R 115 TRP cc_start: 0.8659 (m100) cc_final: 0.8456 (m100) REVERT: R 124 ASP cc_start: 0.9072 (t0) cc_final: 0.8799 (t0) REVERT: R 127 GLU cc_start: 0.7900 (mp0) cc_final: 0.7279 (mp0) REVERT: R 354 LEU cc_start: 0.9082 (tp) cc_final: 0.8862 (tp) outliers start: 35 outliers final: 21 residues processed: 163 average time/residue: 0.5147 time to fit residues: 89.5612 Evaluate side-chains 161 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 43 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.102443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.072014 restraints weight = 19683.800| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.33 r_work: 0.2888 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9404 Z= 0.137 Angle : 0.665 12.523 12755 Z= 0.331 Chirality : 0.041 0.159 1414 Planarity : 0.004 0.079 1634 Dihedral : 5.219 57.883 1302 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 3.34 % Allowed : 23.15 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1160 helix: 1.98 (0.26), residues: 442 sheet: -0.20 (0.34), residues: 245 loop : -0.77 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.022 0.001 TYR R 145 PHE 0.015 0.001 PHE R 303 TRP 0.019 0.001 TRP N 36 HIS 0.003 0.001 HIS A 341 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9397) covalent geometry : angle 0.66455 (12743) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.94003 ( 12) hydrogen bonds : bond 0.03350 ( 453) hydrogen bonds : angle 3.91974 ( 1287) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8726 (mm-30) REVERT: A 246 GLN cc_start: 0.6577 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: B 9 GLN cc_start: 0.9738 (mm-40) cc_final: 0.9449 (mm-40) REVERT: B 15 LYS cc_start: 0.9384 (tttt) cc_final: 0.9146 (tmmt) REVERT: B 59 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8673 (t80) REVERT: B 101 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8897 (mtp) REVERT: B 158 VAL cc_start: 0.9318 (t) cc_final: 0.9051 (p) REVERT: B 188 MET cc_start: 0.9159 (mmm) cc_final: 0.8706 (mmm) REVERT: B 217 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8156 (pmm) REVERT: B 247 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: B 254 ASP cc_start: 0.8220 (t70) cc_final: 0.7873 (t0) REVERT: B 260 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: C 13 ARG cc_start: 0.9370 (ttm110) cc_final: 0.9142 (ttm110) REVERT: C 42 GLU cc_start: 0.8852 (pp20) cc_final: 0.8397 (pp20) REVERT: C 58 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8867 (mt-10) REVERT: N 38 ARG cc_start: 0.9201 (OUTLIER) cc_final: 0.8746 (ptm-80) REVERT: N 87 LYS cc_start: 0.8747 (tppp) cc_final: 0.8118 (ttmm) REVERT: N 89 GLU cc_start: 0.8927 (pm20) cc_final: 0.8594 (pm20) REVERT: R 34 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8986 (tm-30) REVERT: R 123 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8177 (tpp) REVERT: R 124 ASP cc_start: 0.9063 (t0) cc_final: 0.8781 (t0) REVERT: R 127 GLU cc_start: 0.7877 (mp0) cc_final: 0.7015 (mp0) outliers start: 32 outliers final: 18 residues processed: 156 average time/residue: 0.5177 time to fit residues: 86.4638 Evaluate side-chains 162 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 18 GLN C 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.103297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.073167 restraints weight = 19773.117| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.31 r_work: 0.2907 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9404 Z= 0.133 Angle : 0.694 12.927 12755 Z= 0.342 Chirality : 0.041 0.155 1414 Planarity : 0.004 0.079 1634 Dihedral : 5.182 57.694 1302 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 3.34 % Allowed : 23.36 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.26), residues: 1160 helix: 1.98 (0.26), residues: 443 sheet: -0.21 (0.34), residues: 245 loop : -0.74 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG N 105 TYR 0.022 0.001 TYR R 145 PHE 0.014 0.001 PHE P 6 TRP 0.030 0.001 TRP R 115 HIS 0.005 0.001 HIS P 1 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9397) covalent geometry : angle 0.69387 (12743) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.81247 ( 12) hydrogen bonds : bond 0.03253 ( 453) hydrogen bonds : angle 3.86824 ( 1287) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8656 (mm-30) REVERT: A 246 GLN cc_start: 0.6569 (OUTLIER) cc_final: 0.6088 (tm130) REVERT: B 9 GLN cc_start: 0.9708 (mm110) cc_final: 0.9498 (mm-40) REVERT: B 15 LYS cc_start: 0.9389 (tttt) cc_final: 0.9159 (tmmt) REVERT: B 59 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8775 (t80) REVERT: B 101 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8921 (mtp) REVERT: B 158 VAL cc_start: 0.9301 (t) cc_final: 0.9038 (p) REVERT: B 188 MET cc_start: 0.9147 (mmm) cc_final: 0.8737 (mmm) REVERT: B 217 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8208 (pmm) REVERT: B 247 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: B 254 ASP cc_start: 0.8220 (t70) cc_final: 0.7884 (t0) REVERT: B 260 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: B 262 MET cc_start: 0.8554 (tpt) cc_final: 0.7931 (tmt) REVERT: C 42 GLU cc_start: 0.8821 (pp20) cc_final: 0.8380 (pp20) REVERT: C 58 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8880 (mt-10) REVERT: N 1 GLN cc_start: 0.8013 (tp40) cc_final: 0.7785 (tp-100) REVERT: N 38 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8747 (ptm-80) REVERT: N 87 LYS cc_start: 0.8731 (tppp) cc_final: 0.8027 (ttmm) REVERT: N 89 GLU cc_start: 0.8970 (pm20) cc_final: 0.8675 (pm20) REVERT: R 34 GLU cc_start: 0.9283 (tm-30) cc_final: 0.9015 (tm-30) REVERT: R 115 TRP cc_start: 0.8632 (m100) cc_final: 0.8356 (m100) REVERT: R 123 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8151 (tpp) REVERT: R 124 ASP cc_start: 0.9073 (t0) cc_final: 0.8790 (t0) REVERT: R 127 GLU cc_start: 0.7829 (mp0) cc_final: 0.7056 (mp0) REVERT: R 352 LEU cc_start: 0.8364 (tm) cc_final: 0.8067 (tt) outliers start: 32 outliers final: 20 residues processed: 159 average time/residue: 0.4817 time to fit residues: 81.6456 Evaluate side-chains 164 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 246 GLN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 30 ASP Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 ASN ** R 74 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 = 0.3599 r_free = 0.3599 target = 0.102947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072685 restraints weight = 19557.001| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.30 r_work: 0.2902 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9404 Z= 0.142 Angle : 0.706 13.667 12755 Z= 0.348 Chirality : 0.042 0.149 1414 Planarity : 0.005 0.080 1634 Dihedral : 5.178 58.026 1302 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 3.02 % Allowed : 24.50 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1160 helix: 1.95 (0.26), residues: 443 sheet: -0.22 (0.34), residues: 245 loop : -0.74 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 105 TYR 0.023 0.001 TYR R 145 PHE 0.022 0.001 PHE R 33 TRP 0.024 0.001 TRP R 115 HIS 0.004 0.001 HIS P 1 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9397) covalent geometry : angle 0.70599 (12743) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.80491 ( 12) hydrogen bonds : bond 0.03333 ( 453) hydrogen bonds : angle 3.88365 ( 1287) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2754.61 seconds wall clock time: 47 minutes 42.02 seconds (2862.02 seconds total)