Starting phenix.real_space_refine on Sun Dec 29 00:24:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jit_36327/12_2024/8jit_36327_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jit_36327/12_2024/8jit_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_36327/12_2024/8jit_36327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jit_36327/12_2024/8jit_36327.map" model { file = "/net/cci-nas-00/data/ceres_data/8jit_36327/12_2024/8jit_36327_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jit_36327/12_2024/8jit_36327_neut_trim.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 3, 'ASP:plan': 2} 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, 'GLU:plan': 3, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG: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: 5.14, per 1000 atoms: 0.56 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: 2.88 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.00 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: 3.04 Time building geometry restraints manager: 3.26 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: 1.200 Set stop_for_unknowns flag: 0.010 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.170 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:14.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- 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 : 0.005 0.094 9397 Z= 0.362 Angle : 0.786 21.123 12743 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (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 TRP 0.024 0.001 TRP N 36 HIS 0.005 0.001 HIS R 44 PHE 0.024 0.001 PHE B 253 TYR 0.015 0.001 TYR N 115 ARG 0.004 0.000 ARG A 32 *********************** 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 : 1.072 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: 0.8200 (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: 1.3878 time to fit residues: 319.6257 Evaluate side-chains 139 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 95 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 R 177 HIS R 179 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9397 Z= 0.245 Angle : 0.656 9.862 12743 Z= 0.339 Chirality : 0.043 0.226 1414 Planarity : 0.005 0.068 1634 Dihedral : 6.722 74.355 1324 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.22 % Favored : 95.60 % Rotamer: Outliers : 2.29 % Allowed : 14.60 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1160 helix: 1.51 (0.26), residues: 438 sheet: -0.60 (0.35), residues: 232 loop : -1.22 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 36 HIS 0.008 0.001 HIS R 361 PHE 0.023 0.002 PHE P 6 TYR 0.027 0.002 TYR R 145 ARG 0.006 0.001 ARG B 19 *********************** 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 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 8 ARG cc_start: 0.9449 (mtp180) cc_final: 0.8838 (mtt180) REVERT: B 15 LYS cc_start: 0.9401 (tttt) cc_final: 0.9032 (tmmt) REVERT: B 32 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7171 (pm20) REVERT: B 188 MET cc_start: 0.8948 (mmm) cc_final: 0.8576 (mmm) REVERT: B 254 ASP cc_start: 0.7825 (t70) cc_final: 0.7570 (t0) REVERT: B 260 GLU cc_start: 0.8141 (pt0) cc_final: 0.7628 (tt0) REVERT: B 262 MET cc_start: 0.7896 (tpt) cc_final: 0.7598 (tpp) REVERT: B 298 ASP cc_start: 0.8403 (t0) cc_final: 0.8084 (t0) REVERT: B 301 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7501 (mmmt) REVERT: C 13 ARG cc_start: 0.9300 (ttm110) cc_final: 0.9093 (ttm110) REVERT: C 29 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8573 (mmmm) REVERT: C 42 GLU cc_start: 0.8697 (pp20) cc_final: 0.8360 (pp20) REVERT: C 58 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8818 (mt-10) REVERT: N 46 GLU cc_start: 0.7904 (pt0) cc_final: 0.7694 (pt0) REVERT: N 87 LYS cc_start: 0.8825 (tppp) cc_final: 0.8399 (ttmp) REVERT: N 89 GLU cc_start: 0.8613 (pm20) cc_final: 0.8365 (pm20) REVERT: N 94 TYR cc_start: 0.9020 (m-80) cc_final: 0.8811 (m-80) REVERT: R 34 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8777 (tm-30) REVERT: R 290 GLU cc_start: 0.6664 (pp20) cc_final: 0.6451 (pp20) REVERT: R 349 LYS cc_start: 0.6230 (mmtt) cc_final: 0.5996 (mptt) REVERT: R 354 LEU cc_start: 0.9009 (tp) cc_final: 0.8711 (tp) REVERT: R 410 GLU cc_start: 0.8865 (tm-30) cc_final: 0.8586 (tm-30) outliers start: 22 outliers final: 14 residues processed: 167 average time/residue: 1.2809 time to fit residues: 228.6956 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 8 SER Chi-restraints excluded: chain P residue 23 VAL 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 392 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9397 Z= 0.188 Angle : 0.592 9.306 12743 Z= 0.307 Chirality : 0.041 0.153 1414 Planarity : 0.004 0.069 1634 Dihedral : 5.351 57.811 1304 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 2.92 % Allowed : 17.10 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1160 helix: 1.86 (0.26), residues: 427 sheet: -0.47 (0.34), residues: 234 loop : -1.09 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.017 0.001 PHE P 6 TYR 0.024 0.001 TYR R 145 ARG 0.005 0.000 ARG N 105 *********************** 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 182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8586 (mm-30) REVERT: B 8 ARG cc_start: 0.9355 (OUTLIER) cc_final: 0.8971 (mtt180) REVERT: B 15 LYS cc_start: 0.9434 (tttt) cc_final: 0.9090 (tmmt) REVERT: B 17 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8758 (pp30) REVERT: B 32 GLN cc_start: 0.7514 (pm20) cc_final: 0.7300 (pm20) REVERT: B 158 VAL cc_start: 0.9267 (t) cc_final: 0.8952 (p) REVERT: B 188 MET cc_start: 0.8947 (mmm) cc_final: 0.8550 (mmm) REVERT: B 260 GLU cc_start: 0.8122 (pt0) cc_final: 0.7831 (tt0) REVERT: B 262 MET cc_start: 0.7857 (tpt) cc_final: 0.7585 (tpp) REVERT: B 298 ASP cc_start: 0.8277 (t0) cc_final: 0.8028 (t0) REVERT: C 13 ARG cc_start: 0.9302 (ttm110) cc_final: 0.9090 (ttm110) REVERT: C 42 GLU cc_start: 0.8682 (pp20) cc_final: 0.8311 (pp20) REVERT: C 58 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8822 (mt-10) REVERT: N 46 GLU cc_start: 0.7772 (pt0) cc_final: 0.7538 (pt0) REVERT: N 87 LYS cc_start: 0.8819 (tppp) cc_final: 0.8304 (ttmm) REVERT: R 34 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8765 (tm-30) REVERT: R 115 TRP cc_start: 0.8526 (m100) cc_final: 0.8291 (m100) REVERT: R 133 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8565 (mp0) REVERT: R 270 ILE cc_start: 0.9384 (tt) cc_final: 0.9052 (tp) REVERT: R 290 GLU cc_start: 0.6697 (pp20) cc_final: 0.5976 (pp20) REVERT: R 354 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8849 (tp) outliers start: 28 outliers final: 12 residues processed: 169 average time/residue: 1.2829 time to fit residues: 231.3086 Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 8 ARG 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 R residue 45 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 R 74 ASN ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 9397 Z= 0.470 Angle : 0.702 9.401 12743 Z= 0.364 Chirality : 0.045 0.171 1414 Planarity : 0.005 0.075 1634 Dihedral : 5.844 56.110 1304 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.83 % Favored : 95.00 % Rotamer: Outliers : 4.17 % Allowed : 19.29 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1160 helix: 1.68 (0.25), residues: 434 sheet: -0.40 (0.33), residues: 244 loop : -1.08 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP N 36 HIS 0.011 0.001 HIS R 361 PHE 0.021 0.002 PHE N 108 TYR 0.025 0.002 TYR R 145 ARG 0.005 0.001 ARG N 105 *********************** 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 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 136 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8511 (mm-30) REVERT: B 8 ARG cc_start: 0.9331 (mtp180) cc_final: 0.8952 (mtt180) REVERT: B 15 LYS cc_start: 0.9449 (tttt) cc_final: 0.9103 (tmmt) REVERT: B 32 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: B 188 MET cc_start: 0.8978 (mmm) cc_final: 0.8575 (mmm) REVERT: B 217 MET cc_start: 0.7496 (pmm) cc_final: 0.7092 (pmm) REVERT: B 254 ASP cc_start: 0.7901 (t70) cc_final: 0.7588 (t0) REVERT: B 260 GLU cc_start: 0.8400 (pt0) cc_final: 0.7909 (tt0) REVERT: C 13 ARG cc_start: 0.9292 (ttm110) cc_final: 0.9006 (ttm110) REVERT: C 17 GLU cc_start: 0.9059 (tp30) cc_final: 0.8606 (mp0) REVERT: C 29 LYS cc_start: 0.8796 (tppp) cc_final: 0.8550 (tppp) REVERT: C 42 GLU cc_start: 0.8831 (pp20) cc_final: 0.8451 (pp20) REVERT: C 58 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8801 (mt-10) REVERT: N 38 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8323 (ptm160) REVERT: N 46 GLU cc_start: 0.7911 (pt0) cc_final: 0.7581 (pt0) REVERT: N 87 LYS cc_start: 0.8844 (tppp) cc_final: 0.8561 (ttmm) REVERT: N 89 GLU cc_start: 0.8613 (pm20) cc_final: 0.8363 (pm20) REVERT: R 34 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8811 (tm-30) REVERT: R 115 TRP cc_start: 0.8525 (m100) cc_final: 0.8306 (m100) REVERT: R 124 ASP cc_start: 0.8983 (t0) cc_final: 0.8772 (t0) REVERT: R 354 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8846 (tp) outliers start: 40 outliers final: 21 residues processed: 159 average time/residue: 1.2697 time to fit residues: 215.4050 Evaluate side-chains 152 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 32 GLN 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 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 89 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 133 GLU Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9397 Z= 0.246 Angle : 0.622 9.047 12743 Z= 0.321 Chirality : 0.042 0.154 1414 Planarity : 0.004 0.078 1634 Dihedral : 5.509 55.431 1304 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 3.55 % Allowed : 20.75 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1160 helix: 1.78 (0.26), residues: 437 sheet: -0.42 (0.34), residues: 240 loop : -0.96 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.018 0.001 PHE P 6 TYR 0.021 0.001 TYR R 145 ARG 0.010 0.000 ARG N 105 *********************** 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 172 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8479 (mm-30) REVERT: B 5 ASP cc_start: 0.9204 (OUTLIER) cc_final: 0.8958 (m-30) REVERT: B 8 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8924 (ptt-90) REVERT: B 9 GLN cc_start: 0.9456 (mm-40) cc_final: 0.9113 (mm-40) REVERT: B 15 LYS cc_start: 0.9449 (tttt) cc_final: 0.9156 (tmmt) REVERT: B 59 TYR cc_start: 0.9328 (OUTLIER) cc_final: 0.8640 (t80) REVERT: B 188 MET cc_start: 0.8933 (mmm) cc_final: 0.8549 (mmm) REVERT: B 217 MET cc_start: 0.7688 (pmm) cc_final: 0.7263 (pmm) REVERT: B 254 ASP cc_start: 0.7910 (t70) cc_final: 0.7587 (t0) REVERT: B 260 GLU cc_start: 0.8348 (pt0) cc_final: 0.7930 (tt0) REVERT: B 262 MET cc_start: 0.7816 (tpt) cc_final: 0.7534 (tpp) REVERT: B 301 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8262 (mmmt) REVERT: C 13 ARG cc_start: 0.9298 (ttm110) cc_final: 0.9081 (ttm110) REVERT: C 17 GLU cc_start: 0.9057 (tp30) cc_final: 0.8854 (tp30) REVERT: C 42 GLU cc_start: 0.8743 (pp20) cc_final: 0.8325 (pp20) REVERT: C 58 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8832 (mt-10) REVERT: N 38 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8693 (ptm160) REVERT: N 87 LYS cc_start: 0.8967 (tppp) cc_final: 0.8621 (ttmm) REVERT: N 89 GLU cc_start: 0.8580 (pm20) cc_final: 0.8234 (pm20) REVERT: R 34 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8807 (tm-30) REVERT: R 50 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8111 (tp) REVERT: R 115 TRP cc_start: 0.8529 (m100) cc_final: 0.8275 (m100) REVERT: R 127 GLU cc_start: 0.7574 (mp0) cc_final: 0.7148 (mp0) REVERT: R 290 GLU cc_start: 0.7046 (pp20) cc_final: 0.6788 (pp20) REVERT: R 354 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8857 (tp) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 1.2400 time to fit residues: 211.3579 Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 8 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 156 GLN 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 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE 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 Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 354 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 98 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9397 Z= 0.265 Angle : 0.636 14.427 12743 Z= 0.323 Chirality : 0.042 0.154 1414 Planarity : 0.004 0.080 1634 Dihedral : 5.490 56.249 1304 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 4.38 % Allowed : 21.06 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1160 helix: 1.87 (0.25), residues: 437 sheet: -0.36 (0.34), residues: 242 loop : -0.90 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.017 0.001 PHE P 6 TYR 0.023 0.002 TYR R 145 ARG 0.011 0.000 ARG N 105 *********************** 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 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8455 (mm-30) REVERT: B 8 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8973 (mtt180) REVERT: B 15 LYS cc_start: 0.9445 (tttt) cc_final: 0.9079 (tmmt) REVERT: B 32 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7514 (pm20) REVERT: B 59 TYR cc_start: 0.9299 (OUTLIER) cc_final: 0.8597 (t80) REVERT: B 188 MET cc_start: 0.8929 (mmm) cc_final: 0.8546 (mmm) REVERT: B 217 MET cc_start: 0.7756 (pmm) cc_final: 0.7307 (pmm) REVERT: B 254 ASP cc_start: 0.7928 (t70) cc_final: 0.7579 (t0) REVERT: B 260 GLU cc_start: 0.8357 (pt0) cc_final: 0.7939 (tt0) REVERT: B 262 MET cc_start: 0.7790 (tpt) cc_final: 0.7498 (tpp) REVERT: C 13 ARG cc_start: 0.9305 (ttm110) cc_final: 0.9080 (ttm110) REVERT: C 17 GLU cc_start: 0.9068 (tp30) cc_final: 0.8809 (tp30) REVERT: C 21 MET cc_start: 0.7847 (mpp) cc_final: 0.7564 (mpp) REVERT: C 42 GLU cc_start: 0.8740 (pp20) cc_final: 0.8334 (pp20) REVERT: C 58 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8796 (mt-10) REVERT: N 38 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8675 (ptm-80) REVERT: N 46 GLU cc_start: 0.8071 (pt0) cc_final: 0.7786 (pt0) REVERT: N 87 LYS cc_start: 0.8929 (tppp) cc_final: 0.8568 (ttmm) REVERT: N 89 GLU cc_start: 0.8613 (pm20) cc_final: 0.8386 (pm20) REVERT: R 34 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8826 (tm-30) REVERT: R 115 TRP cc_start: 0.8545 (m100) cc_final: 0.8324 (m100) REVERT: R 127 GLU cc_start: 0.7620 (mp0) cc_final: 0.7126 (mp0) REVERT: R 290 GLU cc_start: 0.7086 (pp20) cc_final: 0.6848 (pp20) REVERT: R 354 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8857 (tp) outliers start: 42 outliers final: 26 residues processed: 163 average time/residue: 1.1968 time to fit residues: 208.8773 Evaluate side-chains 159 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 8 ARG 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 247 ASP Chi-restraints excluded: chain B residue 277 SER 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 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 144 MET Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 354 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 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 0.0770 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9397 Z= 0.184 Angle : 0.622 12.855 12743 Z= 0.315 Chirality : 0.041 0.147 1414 Planarity : 0.004 0.076 1634 Dihedral : 5.240 54.813 1302 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 4.07 % Allowed : 21.38 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1160 helix: 1.89 (0.25), residues: 443 sheet: -0.40 (0.34), residues: 245 loop : -0.83 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 36 HIS 0.009 0.001 HIS R 361 PHE 0.017 0.001 PHE R 303 TYR 0.022 0.001 TYR N 60 ARG 0.012 0.000 ARG N 105 *********************** 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 187 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8397 (mm-30) REVERT: P 27 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 8 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.9037 (mtt-85) REVERT: B 15 LYS cc_start: 0.9438 (tttt) cc_final: 0.9106 (tmmt) REVERT: B 32 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: B 34 THR cc_start: 0.8779 (p) cc_final: 0.8548 (p) REVERT: B 59 TYR cc_start: 0.9231 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 158 VAL cc_start: 0.9270 (t) cc_final: 0.8982 (p) REVERT: B 188 MET cc_start: 0.8937 (mmm) cc_final: 0.8517 (mmm) REVERT: B 217 MET cc_start: 0.7949 (pmm) cc_final: 0.7539 (pmm) REVERT: B 247 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6923 (m-30) REVERT: B 254 ASP cc_start: 0.7876 (t70) cc_final: 0.7537 (t0) REVERT: B 260 GLU cc_start: 0.8267 (pt0) cc_final: 0.8007 (tt0) REVERT: B 262 MET cc_start: 0.7706 (tpt) cc_final: 0.7449 (tpp) REVERT: C 13 ARG cc_start: 0.9302 (ttm110) cc_final: 0.9085 (ttm110) REVERT: C 42 GLU cc_start: 0.8708 (pp20) cc_final: 0.8269 (pp20) REVERT: C 58 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8811 (mt-10) REVERT: N 38 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8706 (ptm-80) REVERT: N 46 GLU cc_start: 0.7972 (pt0) cc_final: 0.7753 (pt0) REVERT: N 87 LYS cc_start: 0.8952 (tppp) cc_final: 0.8725 (ttmm) REVERT: N 89 GLU cc_start: 0.8601 (pm20) cc_final: 0.8215 (mp0) REVERT: R 34 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8797 (tm-30) REVERT: R 115 TRP cc_start: 0.8515 (m100) cc_final: 0.8303 (m100) REVERT: R 133 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8553 (mp0) outliers start: 39 outliers final: 18 residues processed: 168 average time/residue: 1.1162 time to fit residues: 201.8926 Evaluate side-chains 161 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 8 ARG 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 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 317 CYS 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 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 133 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9397 Z= 0.196 Angle : 0.655 15.630 12743 Z= 0.326 Chirality : 0.041 0.160 1414 Planarity : 0.004 0.077 1634 Dihedral : 5.163 55.193 1302 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 3.44 % Allowed : 22.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1160 helix: 2.02 (0.26), residues: 443 sheet: -0.40 (0.33), residues: 246 loop : -0.77 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 36 HIS 0.003 0.001 HIS P 1 PHE 0.014 0.001 PHE R 303 TYR 0.022 0.002 TYR R 145 ARG 0.013 0.000 ARG N 105 *********************** 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 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8404 (mm-30) REVERT: B 15 LYS cc_start: 0.9448 (tttt) cc_final: 0.9106 (tmmt) REVERT: B 32 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7578 (pm20) REVERT: B 34 THR cc_start: 0.8769 (p) cc_final: 0.8541 (p) REVERT: B 59 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8561 (t80) REVERT: B 101 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8824 (mtp) REVERT: B 158 VAL cc_start: 0.9272 (t) cc_final: 0.8991 (p) REVERT: B 188 MET cc_start: 0.8931 (mmm) cc_final: 0.8524 (mmm) REVERT: B 217 MET cc_start: 0.8079 (pmm) cc_final: 0.7807 (pmm) REVERT: B 247 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.6954 (m-30) REVERT: B 254 ASP cc_start: 0.7833 (t70) cc_final: 0.7474 (t0) REVERT: B 260 GLU cc_start: 0.8281 (pt0) cc_final: 0.8018 (tt0) REVERT: B 262 MET cc_start: 0.7744 (tpt) cc_final: 0.7475 (tpp) REVERT: B 291 ASP cc_start: 0.8504 (m-30) cc_final: 0.8288 (m-30) REVERT: C 13 ARG cc_start: 0.9296 (ttm110) cc_final: 0.9083 (ttm110) REVERT: C 20 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8650 (tmmm) REVERT: C 21 MET cc_start: 0.8175 (mpp) cc_final: 0.7299 (mpp) REVERT: C 42 GLU cc_start: 0.8692 (pp20) cc_final: 0.8273 (pp20) REVERT: C 58 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8817 (mt-10) REVERT: N 38 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8729 (ptm-80) REVERT: N 46 GLU cc_start: 0.8046 (pt0) cc_final: 0.7838 (pt0) REVERT: N 87 LYS cc_start: 0.8930 (tppp) cc_final: 0.8385 (ttmm) REVERT: N 89 GLU cc_start: 0.8598 (pm20) cc_final: 0.8371 (pm20) REVERT: R 34 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8789 (tm-30) REVERT: R 123 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8101 (tpp) REVERT: R 127 GLU cc_start: 0.7706 (mp0) cc_final: 0.6909 (mp0) REVERT: R 133 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: R 290 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6385 (pp20) outliers start: 33 outliers final: 18 residues processed: 162 average time/residue: 1.2478 time to fit residues: 216.2062 Evaluate side-chains 163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 247 ASP 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 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 133 GLU Chi-restraints excluded: chain R residue 290 GLU 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 101 optimal weight: 0.0570 chunk 104 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9397 Z= 0.197 Angle : 0.680 15.047 12743 Z= 0.334 Chirality : 0.041 0.155 1414 Planarity : 0.004 0.077 1634 Dihedral : 5.064 55.365 1302 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.71 % Favored : 96.21 % Rotamer: Outliers : 3.34 % Allowed : 23.57 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1160 helix: 2.08 (0.26), residues: 442 sheet: -0.36 (0.34), residues: 240 loop : -0.77 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 115 HIS 0.003 0.000 HIS A 341 PHE 0.015 0.001 PHE R 303 TYR 0.023 0.001 TYR R 145 ARG 0.014 0.000 ARG N 105 *********************** 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 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8394 (mm-30) REVERT: B 15 LYS cc_start: 0.9439 (tttt) cc_final: 0.9100 (tmmt) REVERT: B 32 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: B 34 THR cc_start: 0.8759 (p) cc_final: 0.8549 (p) REVERT: B 59 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8606 (t80) REVERT: B 158 VAL cc_start: 0.9271 (t) cc_final: 0.8989 (p) REVERT: B 188 MET cc_start: 0.8926 (mmm) cc_final: 0.8532 (mmm) REVERT: B 217 MET cc_start: 0.8144 (pmm) cc_final: 0.7882 (pmm) REVERT: B 254 ASP cc_start: 0.7879 (t70) cc_final: 0.7483 (t0) REVERT: B 260 GLU cc_start: 0.8314 (pt0) cc_final: 0.8063 (tt0) REVERT: B 262 MET cc_start: 0.7754 (tpt) cc_final: 0.7466 (tpp) REVERT: C 13 ARG cc_start: 0.9295 (ttm110) cc_final: 0.9087 (ttm110) REVERT: C 42 GLU cc_start: 0.8709 (pp20) cc_final: 0.8336 (pp20) REVERT: C 58 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8826 (mt-10) REVERT: N 38 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8696 (ptm160) REVERT: N 46 GLU cc_start: 0.8077 (pt0) cc_final: 0.7793 (pt0) REVERT: N 87 LYS cc_start: 0.8906 (tppp) cc_final: 0.8306 (ttmm) REVERT: N 89 GLU cc_start: 0.8621 (pm20) cc_final: 0.8374 (pm20) REVERT: R 34 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8790 (tm-30) REVERT: R 115 TRP cc_start: 0.8484 (m100) cc_final: 0.8195 (m100) REVERT: R 123 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8058 (tpp) REVERT: R 127 GLU cc_start: 0.7713 (mp0) cc_final: 0.6966 (mp0) REVERT: R 133 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: R 290 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6342 (pp20) REVERT: R 352 LEU cc_start: 0.8302 (tm) cc_final: 0.7922 (tt) outliers start: 32 outliers final: 20 residues processed: 163 average time/residue: 1.1593 time to fit residues: 202.8045 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 : 1.092 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 308 LEU 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 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 133 GLU Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 290 GLU 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 50 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9397 Z= 0.223 Angle : 0.696 15.147 12743 Z= 0.342 Chirality : 0.042 0.193 1414 Planarity : 0.004 0.077 1634 Dihedral : 5.155 56.837 1302 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 3.23 % Allowed : 24.40 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1160 helix: 2.06 (0.26), residues: 441 sheet: -0.26 (0.34), residues: 241 loop : -0.79 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 36 HIS 0.004 0.001 HIS P 1 PHE 0.014 0.001 PHE P 6 TYR 0.023 0.002 TYR R 145 ARG 0.014 0.000 ARG N 105 ********************** 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 173 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 15 LYS cc_start: 0.9454 (tttt) cc_final: 0.9094 (tmmt) REVERT: B 32 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: B 34 THR cc_start: 0.8735 (p) cc_final: 0.8222 (p) REVERT: B 59 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8611 (t80) REVERT: B 158 VAL cc_start: 0.9266 (t) cc_final: 0.8972 (p) REVERT: B 188 MET cc_start: 0.8927 (mmm) cc_final: 0.8496 (mmm) REVERT: B 217 MET cc_start: 0.8188 (pmm) cc_final: 0.7922 (pmm) REVERT: B 254 ASP cc_start: 0.7925 (t70) cc_final: 0.7521 (t0) REVERT: B 260 GLU cc_start: 0.8303 (pt0) cc_final: 0.8026 (tt0) REVERT: B 262 MET cc_start: 0.7814 (tpt) cc_final: 0.7504 (tpp) REVERT: C 42 GLU cc_start: 0.8736 (pp20) cc_final: 0.8317 (pp20) REVERT: C 58 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8828 (mt-10) REVERT: N 1 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7784 (tp-100) REVERT: N 38 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8387 (ptm160) REVERT: N 46 GLU cc_start: 0.8148 (pt0) cc_final: 0.7832 (pt0) REVERT: N 87 LYS cc_start: 0.8943 (tppp) cc_final: 0.8182 (ttmm) REVERT: N 89 GLU cc_start: 0.8635 (pm20) cc_final: 0.8395 (pm20) REVERT: R 34 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8794 (tm-30) REVERT: R 115 TRP cc_start: 0.8457 (m100) cc_final: 0.8190 (m100) REVERT: R 123 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8060 (tpp) REVERT: R 127 GLU cc_start: 0.7634 (mp0) cc_final: 0.7099 (mp0) REVERT: R 129 GLU cc_start: 0.8445 (pm20) cc_final: 0.8241 (pm20) REVERT: R 133 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: R 290 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6372 (pp20) REVERT: R 352 LEU cc_start: 0.8327 (tm) cc_final: 0.7976 (tt) outliers start: 31 outliers final: 21 residues processed: 158 average time/residue: 1.2931 time to fit residues: 218.1027 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 : 0.990 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 308 LEU 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 1 GLN 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 133 GLU Chi-restraints excluded: chain R residue 144 MET Chi-restraints excluded: chain R residue 290 GLU 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 82 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.3560 r_free = 0.3560 target = 0.100006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069030 restraints weight = 19661.733| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.30 r_work: 0.2840 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9397 Z= 0.339 Angle : 0.738 15.059 12743 Z= 0.366 Chirality : 0.044 0.213 1414 Planarity : 0.005 0.080 1634 Dihedral : 5.504 59.990 1302 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.88 % Favored : 95.95 % Rotamer: Outliers : 3.13 % Allowed : 24.50 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1160 helix: 1.97 (0.26), residues: 441 sheet: -0.12 (0.34), residues: 239 loop : -0.87 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 36 HIS 0.005 0.001 HIS P 1 PHE 0.017 0.002 PHE N 108 TYR 0.024 0.002 TYR R 145 ARG 0.015 0.001 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3814.52 seconds wall clock time: 69 minutes 12.55 seconds (4152.55 seconds total)