Starting phenix.real_space_refine on Mon May 12 22:41:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jit_36327/05_2025/8jit_36327_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jit_36327/05_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_36327/05_2025/8jit_36327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jit_36327/05_2025/8jit_36327.map" model { file = "/net/cci-nas-00/data/ceres_data/8jit_36327/05_2025/8jit_36327_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jit_36327/05_2025/8jit_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-5687/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: 5.00, per 1000 atoms: 0.54 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 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: 0.97 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: 2.43 Time building geometry restraints manager: 2.72 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.330 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.17735 ( 453) hydrogen bonds : angle 6.74498 ( 1287) SS BOND : bond 0.00783 ( 6) SS BOND : angle 2.15500 ( 12) covalent geometry : bond 0.00544 ( 9397) covalent geometry : angle 0.78623 (12743) 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 : 1.060 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: 1.2829 time to fit residues: 296.3442 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 : 0.976 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.100863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071117 restraints weight = 19163.498| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.39 r_work: 0.2937 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 9404 Z= 0.160 Angle : 0.658 9.862 12755 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 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 453) hydrogen bonds : angle 4.59863 ( 1287) SS BOND : bond 0.00537 ( 6) SS BOND : angle 1.58525 ( 12) covalent geometry : bond 0.00375 ( 9397) covalent geometry : angle 0.65634 (12743) Misc. bond : bond 0.00026 ( 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 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8751 (mm-30) REVERT: B 8 ARG cc_start: 0.9410 (mtp180) cc_final: 0.8787 (mtt180) REVERT: B 15 LYS cc_start: 0.9344 (tttt) cc_final: 0.8956 (tmmt) REVERT: B 32 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: B 188 MET cc_start: 0.9172 (mmm) cc_final: 0.8766 (mmm) REVERT: B 254 ASP cc_start: 0.8255 (t70) cc_final: 0.7913 (t0) REVERT: B 260 GLU cc_start: 0.8359 (pt0) cc_final: 0.7743 (tt0) REVERT: B 262 MET cc_start: 0.8719 (tpt) cc_final: 0.8257 (tpp) REVERT: B 298 ASP cc_start: 0.8759 (t0) cc_final: 0.8373 (t0) REVERT: B 301 LYS cc_start: 0.7794 (mmpt) cc_final: 0.7452 (mmmt) REVERT: C 13 ARG cc_start: 0.9347 (ttm110) cc_final: 0.9133 (ttm110) REVERT: C 29 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8493 (mmmm) REVERT: C 42 GLU cc_start: 0.8826 (pp20) cc_final: 0.8467 (pp20) REVERT: C 58 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8827 (mt-10) REVERT: N 87 LYS cc_start: 0.8606 (tppp) cc_final: 0.8228 (ttmp) REVERT: N 89 GLU cc_start: 0.8791 (pm20) cc_final: 0.8532 (pm20) REVERT: N 94 TYR cc_start: 0.9038 (m-80) cc_final: 0.8730 (m-80) REVERT: R 34 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8971 (tm-30) REVERT: R 349 LYS cc_start: 0.6218 (mmtt) cc_final: 0.5968 (mptt) REVERT: R 354 LEU cc_start: 0.9054 (tp) cc_final: 0.8771 (tp) REVERT: R 410 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8548 (tm-30) outliers start: 22 outliers final: 14 residues processed: 167 average time/residue: 1.1390 time to fit residues: 203.7759 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 : 0.963 ------------------------------------------------------------------------------- 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 77 optimal weight: 0.0270 chunk 109 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- 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 1 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.071431 restraints weight = 19582.693| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.43 r_work: 0.2878 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9404 Z= 0.159 Angle : 0.611 9.247 12755 Z= 0.318 Chirality : 0.042 0.156 1414 Planarity : 0.004 0.070 1634 Dihedral : 5.509 59.541 1304 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 3.13 % Allowed : 17.00 % Favored : 79.87 % 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: 0.17 (0.26), residues: 1160 helix: 1.80 (0.26), residues: 427 sheet: -0.48 (0.34), residues: 234 loop : -1.08 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.019 0.001 PHE P 6 TYR 0.025 0.002 TYR R 145 ARG 0.005 0.001 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 453) hydrogen bonds : angle 4.25123 ( 1287) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.42962 ( 12) covalent geometry : bond 0.00373 ( 9397) covalent geometry : angle 0.60972 (12743) Misc. bond : bond 0.00010 ( 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 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8838 (mm-30) REVERT: A 246 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: B 8 ARG cc_start: 0.9326 (mtp180) cc_final: 0.8938 (mtt180) REVERT: B 15 LYS cc_start: 0.9389 (tttt) cc_final: 0.8994 (tmmt) REVERT: B 17 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8664 (pp30) REVERT: B 32 GLN cc_start: 0.7619 (pm20) cc_final: 0.7303 (pm20) REVERT: B 158 VAL cc_start: 0.9295 (t) cc_final: 0.8972 (p) REVERT: B 188 MET cc_start: 0.9180 (mmm) cc_final: 0.8701 (mmm) REVERT: B 260 GLU cc_start: 0.8452 (pt0) cc_final: 0.8056 (tt0) REVERT: B 262 MET cc_start: 0.8765 (tpt) cc_final: 0.8325 (tpp) REVERT: C 13 ARG cc_start: 0.9328 (ttm110) cc_final: 0.9115 (ttm110) REVERT: C 20 LYS cc_start: 0.8892 (tmmt) cc_final: 0.8605 (tmmt) REVERT: C 29 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8530 (tppp) REVERT: C 42 GLU cc_start: 0.8858 (pp20) cc_final: 0.8458 (pp20) REVERT: C 58 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8859 (mt-10) REVERT: N 87 LYS cc_start: 0.8520 (tppp) cc_final: 0.8073 (ttmp) REVERT: N 89 GLU cc_start: 0.8824 (pm20) cc_final: 0.8612 (pm20) REVERT: R 34 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8977 (tm-30) REVERT: R 115 TRP cc_start: 0.8728 (m100) cc_final: 0.8425 (m100) REVERT: R 133 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8664 (mp0) REVERT: R 290 GLU cc_start: 0.6734 (pp20) cc_final: 0.6382 (pp20) REVERT: R 354 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8852 (tp) outliers start: 30 outliers final: 16 residues processed: 163 average time/residue: 1.1715 time to fit residues: 204.3585 Evaluate side-chains 149 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 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 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 38 optimal weight: 0.0980 chunk 98 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 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 = 0.3618 r_free = 0.3618 target = 0.103464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.072828 restraints weight = 19226.350| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 3.42 r_work: 0.2920 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9404 Z= 0.125 Angle : 0.599 10.084 12755 Z= 0.307 Chirality : 0.041 0.167 1414 Planarity : 0.004 0.072 1634 Dihedral : 5.278 57.929 1304 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 3.13 % Allowed : 18.98 % 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 (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: 0.27 (0.26), residues: 1160 helix: 1.79 (0.26), residues: 433 sheet: -0.37 (0.34), residues: 239 loop : -0.99 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 36 HIS 0.009 0.001 HIS R 361 PHE 0.016 0.001 PHE P 6 TYR 0.023 0.001 TYR R 145 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 453) hydrogen bonds : angle 4.10557 ( 1287) SS BOND : bond 0.00290 ( 6) SS BOND : angle 1.01729 ( 12) covalent geometry : bond 0.00289 ( 9397) covalent geometry : angle 0.59820 (12743) Misc. bond : bond 0.00008 ( 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 178 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8871 (mm-30) REVERT: B 8 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8844 (ptt-90) REVERT: B 9 GLN cc_start: 0.9584 (mm-40) cc_final: 0.9327 (mm-40) REVERT: B 15 LYS cc_start: 0.9394 (tttt) cc_final: 0.9046 (tmmt) REVERT: B 32 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7392 (pm20) REVERT: B 158 VAL cc_start: 0.9313 (t) cc_final: 0.9010 (p) REVERT: B 188 MET cc_start: 0.9181 (mmm) cc_final: 0.8723 (mmm) REVERT: B 217 MET cc_start: 0.7442 (pmm) cc_final: 0.7004 (pmm) REVERT: B 254 ASP cc_start: 0.8158 (t70) cc_final: 0.7808 (t0) REVERT: B 260 GLU cc_start: 0.8387 (pt0) cc_final: 0.7970 (tt0) REVERT: B 262 MET cc_start: 0.8719 (tpt) cc_final: 0.8297 (tpp) REVERT: B 298 ASP cc_start: 0.8655 (t0) cc_final: 0.8354 (t0) REVERT: C 13 ARG cc_start: 0.9335 (ttm110) cc_final: 0.9118 (ttm110) REVERT: C 42 GLU cc_start: 0.8823 (pp20) cc_final: 0.8428 (pp20) REVERT: C 58 GLU cc_start: 0.9435 (mm-30) cc_final: 0.8907 (mt-10) REVERT: N 38 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8930 (ptm-80) REVERT: N 82 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8061 (tp-100) REVERT: N 87 LYS cc_start: 0.8513 (tppp) cc_final: 0.8155 (ttmm) REVERT: N 89 GLU cc_start: 0.8888 (pm20) cc_final: 0.8652 (pm20) REVERT: R 34 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8971 (tm-30) REVERT: R 50 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8181 (tp) REVERT: R 115 TRP cc_start: 0.8738 (m100) cc_final: 0.8460 (m100) REVERT: R 166 LEU cc_start: 0.8017 (tp) cc_final: 0.7790 (tp) REVERT: R 354 LEU cc_start: 0.9122 (tp) cc_final: 0.8912 (tp) outliers start: 30 outliers final: 14 residues processed: 167 average time/residue: 1.1386 time to fit residues: 203.8539 Evaluate side-chains 152 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 8 ARG 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 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 Chi-restraints excluded: chain R residue 235 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 ** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.070833 restraints weight = 19708.084| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.42 r_work: 0.2850 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9404 Z= 0.170 Angle : 0.614 9.182 12755 Z= 0.317 Chirality : 0.042 0.155 1414 Planarity : 0.004 0.075 1634 Dihedral : 5.316 54.509 1302 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.40 % Favored : 95.43 % Rotamer: Outliers : 3.55 % Allowed : 20.65 % Favored : 75.81 % 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: 0.34 (0.26), residues: 1160 helix: 1.82 (0.26), residues: 437 sheet: -0.35 (0.34), residues: 240 loop : -0.95 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 36 HIS 0.010 0.001 HIS R 361 PHE 0.016 0.001 PHE P 6 TYR 0.024 0.002 TYR R 145 ARG 0.009 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 453) hydrogen bonds : angle 4.06486 ( 1287) SS BOND : bond 0.00284 ( 6) SS BOND : angle 1.12725 ( 12) covalent geometry : bond 0.00401 ( 9397) covalent geometry : angle 0.61300 (12743) Misc. bond : bond 0.00009 ( 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 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8789 (mm-30) REVERT: B 8 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8994 (mtt180) REVERT: B 15 LYS cc_start: 0.9397 (tttt) cc_final: 0.9114 (tmmt) REVERT: B 158 VAL cc_start: 0.9323 (t) cc_final: 0.9018 (p) REVERT: B 188 MET cc_start: 0.9151 (mmm) cc_final: 0.8693 (mmm) REVERT: B 217 MET cc_start: 0.7608 (pmm) cc_final: 0.7241 (pmm) REVERT: B 254 ASP cc_start: 0.8221 (t70) cc_final: 0.7857 (t0) REVERT: B 260 GLU cc_start: 0.8485 (pt0) cc_final: 0.8008 (tt0) REVERT: B 262 MET cc_start: 0.8720 (tpt) cc_final: 0.8258 (tpp) REVERT: C 13 ARG cc_start: 0.9356 (ttm110) cc_final: 0.9130 (ttm110) REVERT: C 42 GLU cc_start: 0.8876 (pp20) cc_final: 0.8447 (pp20) REVERT: C 58 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8876 (mt-10) REVERT: N 38 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8554 (ptm160) REVERT: N 46 GLU cc_start: 0.8386 (pt0) cc_final: 0.8168 (pt0) REVERT: N 60 TYR cc_start: 0.8817 (m-80) cc_final: 0.8603 (m-80) REVERT: N 87 LYS cc_start: 0.8525 (tppp) cc_final: 0.8104 (ttmm) REVERT: R 34 GLU cc_start: 0.9269 (tm-30) cc_final: 0.9005 (tm-30) REVERT: R 115 TRP cc_start: 0.8685 (m100) cc_final: 0.8430 (m100) REVERT: R 127 GLU cc_start: 0.7685 (mp0) cc_final: 0.7127 (mp0) REVERT: R 290 GLU cc_start: 0.6948 (pp20) cc_final: 0.6388 (pp20) REVERT: R 354 LEU cc_start: 0.9127 (tp) cc_final: 0.8898 (tp) outliers start: 34 outliers final: 19 residues processed: 162 average time/residue: 1.1292 time to fit residues: 196.7594 Evaluate side-chains 153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.096567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.066406 restraints weight = 19234.572| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.39 r_work: 0.2838 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9404 Z= 0.187 Angle : 0.648 9.729 12755 Z= 0.329 Chirality : 0.042 0.156 1414 Planarity : 0.004 0.077 1634 Dihedral : 5.475 56.133 1302 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.74 % Favored : 95.09 % Rotamer: Outliers : 4.38 % Allowed : 20.44 % 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 (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: 0.40 (0.26), residues: 1160 helix: 1.81 (0.25), residues: 443 sheet: -0.32 (0.34), residues: 240 loop : -0.87 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 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 0.010 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 453) hydrogen bonds : angle 4.07390 ( 1287) SS BOND : bond 0.00320 ( 6) SS BOND : angle 1.22858 ( 12) covalent geometry : bond 0.00443 ( 9397) covalent geometry : angle 0.64759 (12743) Misc. bond : bond 0.00029 ( 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: 42 poor density : 132 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8789 (mm-30) REVERT: P 27 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 15 LYS cc_start: 0.9342 (tttt) cc_final: 0.9122 (tmmt) REVERT: B 32 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: B 59 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8832 (t80) REVERT: B 188 MET cc_start: 0.9184 (mmm) cc_final: 0.8770 (mmm) REVERT: B 217 MET cc_start: 0.7737 (pmm) cc_final: 0.7341 (pmm) REVERT: B 254 ASP cc_start: 0.8221 (t70) cc_final: 0.7852 (t0) REVERT: B 260 GLU cc_start: 0.8532 (pt0) cc_final: 0.8039 (tt0) REVERT: B 262 MET cc_start: 0.8739 (tpt) cc_final: 0.8241 (tpp) REVERT: C 13 ARG cc_start: 0.9352 (ttm110) cc_final: 0.9119 (ttm110) REVERT: C 42 GLU cc_start: 0.8902 (pp20) cc_final: 0.8476 (pp20) REVERT: C 58 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8829 (mt-10) REVERT: N 87 LYS cc_start: 0.8607 (tppp) cc_final: 0.8299 (ttmm) REVERT: N 89 GLU cc_start: 0.8834 (pm20) cc_final: 0.8591 (pm20) REVERT: R 34 GLU cc_start: 0.9288 (tm-30) cc_final: 0.9011 (tm-30) REVERT: R 127 GLU cc_start: 0.7835 (mp0) cc_final: 0.7289 (mp0) REVERT: R 290 GLU cc_start: 0.7022 (pp20) cc_final: 0.6442 (pp20) outliers start: 42 outliers final: 26 residues processed: 156 average time/residue: 1.1054 time to fit residues: 185.6219 Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 156 GLN 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 25 ILE Chi-restraints excluded: chain C residue 41 CYS 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 30 ASP 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 83 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 104 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069729 restraints weight = 19343.101| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.35 r_work: 0.2921 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9404 Z= 0.121 Angle : 0.632 11.501 12755 Z= 0.318 Chirality : 0.041 0.154 1414 Planarity : 0.004 0.079 1634 Dihedral : 5.228 54.317 1302 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 3.02 % Allowed : 21.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1160 helix: 1.92 (0.26), residues: 443 sheet: -0.27 (0.34), residues: 237 loop : -0.83 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 115 HIS 0.009 0.001 HIS R 361 PHE 0.016 0.001 PHE R 303 TYR 0.022 0.001 TYR R 145 ARG 0.011 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 453) hydrogen bonds : angle 3.95227 ( 1287) SS BOND : bond 0.00296 ( 6) SS BOND : angle 1.15898 ( 12) covalent geometry : bond 0.00279 ( 9397) covalent geometry : angle 0.63112 (12743) Misc. bond : bond 0.00003 ( 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 163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8710 (mm-30) REVERT: B 15 LYS cc_start: 0.9350 (tttt) cc_final: 0.9128 (tmmt) REVERT: B 32 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: B 158 VAL cc_start: 0.9296 (t) cc_final: 0.9020 (p) REVERT: B 188 MET cc_start: 0.9201 (mmm) cc_final: 0.8783 (mmm) REVERT: B 217 MET cc_start: 0.7893 (pmm) cc_final: 0.7452 (pmm) REVERT: B 254 ASP cc_start: 0.8224 (t70) cc_final: 0.7867 (t0) REVERT: B 260 GLU cc_start: 0.8416 (pt0) cc_final: 0.8045 (tt0) REVERT: B 262 MET cc_start: 0.8687 (tpt) cc_final: 0.8260 (tpp) REVERT: B 298 ASP cc_start: 0.8638 (t0) cc_final: 0.8275 (t0) REVERT: C 13 ARG cc_start: 0.9329 (ttm110) cc_final: 0.9096 (ttm110) REVERT: C 42 GLU cc_start: 0.8874 (pp20) cc_final: 0.8412 (pp20) REVERT: C 58 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8905 (mt-10) REVERT: N 87 LYS cc_start: 0.8648 (tppp) cc_final: 0.8162 (ttmm) REVERT: N 89 GLU cc_start: 0.8776 (pm20) cc_final: 0.8560 (pm20) REVERT: R 34 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8980 (tm-30) REVERT: R 115 TRP cc_start: 0.8637 (m100) cc_final: 0.8320 (m100) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 1.1152 time to fit residues: 179.0952 Evaluate side-chains 157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 32 GLN Chi-restraints excluded: chain B residue 47 THR 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 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 69 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 360 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 48 optimal weight: 0.0970 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 24 ASN ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.097289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067947 restraints weight = 19512.377| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.35 r_work: 0.2880 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9404 Z= 0.153 Angle : 0.663 11.981 12755 Z= 0.330 Chirality : 0.042 0.161 1414 Planarity : 0.004 0.079 1634 Dihedral : 5.267 55.576 1302 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % Rotamer: Outliers : 3.02 % Allowed : 22.42 % 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: 0.53 (0.26), residues: 1160 helix: 1.99 (0.26), residues: 443 sheet: -0.33 (0.34), residues: 240 loop : -0.82 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 36 HIS 0.003 0.001 HIS A 341 PHE 0.015 0.001 PHE P 6 TYR 0.023 0.002 TYR R 145 ARG 0.013 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03457 ( 453) hydrogen bonds : angle 3.93311 ( 1287) SS BOND : bond 0.00259 ( 6) SS BOND : angle 1.07658 ( 12) covalent geometry : bond 0.00365 ( 9397) covalent geometry : angle 0.66218 (12743) Misc. bond : bond 0.00013 ( 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 167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8723 (mm-30) REVERT: B 15 LYS cc_start: 0.9364 (tttt) cc_final: 0.9142 (tmmt) REVERT: B 34 THR cc_start: 0.8911 (p) cc_final: 0.8630 (p) REVERT: B 59 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8826 (t80) REVERT: B 158 VAL cc_start: 0.9319 (t) cc_final: 0.9033 (p) REVERT: B 188 MET cc_start: 0.9186 (mmm) cc_final: 0.8746 (mmm) REVERT: B 217 MET cc_start: 0.8062 (pmm) cc_final: 0.7645 (pmm) REVERT: B 254 ASP cc_start: 0.8237 (t70) cc_final: 0.7880 (t0) REVERT: B 260 GLU cc_start: 0.8442 (pt0) cc_final: 0.8006 (tt0) REVERT: B 262 MET cc_start: 0.8713 (tpt) cc_final: 0.8275 (tpp) REVERT: C 13 ARG cc_start: 0.9338 (ttm110) cc_final: 0.9111 (ttm110) REVERT: C 42 GLU cc_start: 0.8887 (pp20) cc_final: 0.8441 (pp20) REVERT: C 58 GLU cc_start: 0.9409 (mm-30) cc_final: 0.8886 (mt-10) REVERT: N 87 LYS cc_start: 0.8668 (tppp) cc_final: 0.7981 (ttmm) REVERT: N 89 GLU cc_start: 0.8754 (pm20) cc_final: 0.8546 (pm20) REVERT: R 34 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8991 (tm-30) REVERT: R 115 TRP cc_start: 0.8590 (m100) cc_final: 0.8299 (m100) REVERT: R 123 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8090 (tpp) outliers start: 29 outliers final: 20 residues processed: 151 average time/residue: 1.0462 time to fit residues: 170.7349 Evaluate side-chains 159 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL 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 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 69 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 360 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.102929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.073070 restraints weight = 19638.267| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.29 r_work: 0.2898 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9404 Z= 0.135 Angle : 0.673 12.121 12755 Z= 0.333 Chirality : 0.041 0.157 1414 Planarity : 0.004 0.079 1634 Dihedral : 5.171 55.607 1302 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 2.92 % Allowed : 22.84 % Favored : 74.24 % 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: 0.57 (0.26), residues: 1160 helix: 2.01 (0.26), residues: 443 sheet: -0.31 (0.34), residues: 239 loop : -0.80 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 36 HIS 0.003 0.001 HIS A 341 PHE 0.014 0.001 PHE R 303 TYR 0.022 0.001 TYR R 145 ARG 0.015 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 453) hydrogen bonds : angle 3.89397 ( 1287) SS BOND : bond 0.00290 ( 6) SS BOND : angle 1.09672 ( 12) covalent geometry : bond 0.00319 ( 9397) covalent geometry : angle 0.67214 (12743) 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 170 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8709 (mm-30) REVERT: B 15 LYS cc_start: 0.9385 (tttt) cc_final: 0.9168 (tmmt) REVERT: B 34 THR cc_start: 0.8843 (p) cc_final: 0.8589 (p) REVERT: B 59 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8750 (t80) REVERT: B 101 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8910 (mtp) REVERT: B 158 VAL cc_start: 0.9315 (t) cc_final: 0.9036 (p) REVERT: B 188 MET cc_start: 0.9183 (mmm) cc_final: 0.8736 (mmm) REVERT: B 217 MET cc_start: 0.8223 (pmm) cc_final: 0.7899 (pmm) REVERT: B 254 ASP cc_start: 0.8254 (t70) cc_final: 0.7878 (t0) REVERT: B 260 GLU cc_start: 0.8383 (pt0) cc_final: 0.7998 (tt0) REVERT: B 262 MET cc_start: 0.8641 (tpt) cc_final: 0.8208 (tpp) REVERT: C 13 ARG cc_start: 0.9333 (ttm110) cc_final: 0.9110 (ttm110) REVERT: C 42 GLU cc_start: 0.8869 (pp20) cc_final: 0.8411 (pp20) REVERT: C 58 GLU cc_start: 0.9420 (mm-30) cc_final: 0.8908 (mt-10) REVERT: N 82 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8288 (tp-100) REVERT: N 87 LYS cc_start: 0.8712 (tppp) cc_final: 0.8010 (ttmm) REVERT: R 34 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8998 (tm-30) REVERT: R 115 TRP cc_start: 0.8611 (m100) cc_final: 0.8299 (m100) REVERT: R 123 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8129 (tpp) REVERT: R 127 GLU cc_start: 0.7864 (mp0) cc_final: 0.7217 (mp0) REVERT: R 290 GLU cc_start: 0.7024 (pp20) cc_final: 0.6412 (pp20) outliers start: 28 outliers final: 19 residues processed: 155 average time/residue: 1.1229 time to fit residues: 186.6051 Evaluate side-chains 157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 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 308 LEU 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 69 THR 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 45 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 123 MET 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 85 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 43 optimal weight: 0.0470 chunk 86 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 74 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.104112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.074235 restraints weight = 19879.064| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.31 r_work: 0.2931 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9404 Z= 0.125 Angle : 0.697 12.275 12755 Z= 0.344 Chirality : 0.041 0.151 1414 Planarity : 0.004 0.079 1634 Dihedral : 5.047 55.042 1302 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 2.61 % Allowed : 23.77 % Favored : 73.62 % 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: 0.57 (0.26), residues: 1160 helix: 2.01 (0.26), residues: 443 sheet: -0.30 (0.34), residues: 239 loop : -0.79 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 36 HIS 0.003 0.000 HIS A 341 PHE 0.015 0.001 PHE R 230 TYR 0.022 0.001 TYR R 145 ARG 0.015 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 453) hydrogen bonds : angle 3.90894 ( 1287) SS BOND : bond 0.00267 ( 6) SS BOND : angle 0.79570 ( 12) covalent geometry : bond 0.00292 ( 9397) covalent geometry : angle 0.69640 (12743) Misc. bond : bond 0.00002 ( 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 169 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8699 (mm-30) REVERT: A 280 LEU cc_start: 0.9399 (tm) cc_final: 0.8764 (tm) REVERT: B 15 LYS cc_start: 0.9374 (tttt) cc_final: 0.9163 (tmmt) REVERT: B 101 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8968 (mtp) REVERT: B 158 VAL cc_start: 0.9314 (t) cc_final: 0.9057 (p) REVERT: B 188 MET cc_start: 0.9195 (mmm) cc_final: 0.8779 (mmm) REVERT: B 217 MET cc_start: 0.8263 (pmm) cc_final: 0.7955 (pmm) REVERT: B 254 ASP cc_start: 0.8222 (t70) cc_final: 0.7826 (t0) REVERT: B 260 GLU cc_start: 0.8391 (pt0) cc_final: 0.8049 (tt0) REVERT: B 262 MET cc_start: 0.8641 (tpt) cc_final: 0.8226 (tpp) REVERT: B 291 ASP cc_start: 0.8762 (m-30) cc_final: 0.8529 (m-30) REVERT: C 13 ARG cc_start: 0.9327 (ttm110) cc_final: 0.9117 (ttm110) REVERT: C 42 GLU cc_start: 0.8859 (pp20) cc_final: 0.8422 (pp20) REVERT: C 58 GLU cc_start: 0.9421 (mm-30) cc_final: 0.8920 (mt-10) REVERT: N 87 LYS cc_start: 0.8736 (tppp) cc_final: 0.8519 (ttmm) REVERT: N 89 GLU cc_start: 0.8853 (pm20) cc_final: 0.8513 (pm20) REVERT: R 34 GLU cc_start: 0.9269 (tm-30) cc_final: 0.8984 (tm-30) REVERT: R 115 TRP cc_start: 0.8597 (m100) cc_final: 0.8288 (m100) REVERT: R 123 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8026 (tpp) REVERT: R 127 GLU cc_start: 0.7885 (mp0) cc_final: 0.7144 (mp0) REVERT: R 290 GLU cc_start: 0.6955 (pp20) cc_final: 0.6297 (pp20) REVERT: R 352 LEU cc_start: 0.8300 (tm) cc_final: 0.8025 (tp) outliers start: 25 outliers final: 16 residues processed: 158 average time/residue: 1.1107 time to fit residues: 188.5346 Evaluate side-chains 145 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL 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 C residue 16 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain N residue 69 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 360 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.102373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072342 restraints weight = 19677.558| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.28 r_work: 0.2897 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3697 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= 0.155 Angle : 0.715 12.599 12755 Z= 0.355 Chirality : 0.042 0.193 1414 Planarity : 0.005 0.080 1634 Dihedral : 5.186 56.967 1302 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 2.61 % Allowed : 23.88 % 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 (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: 1.98 (0.26), residues: 443 sheet: -0.20 (0.35), residues: 238 loop : -0.77 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 36 HIS 0.008 0.001 HIS P 1 PHE 0.014 0.001 PHE R 230 TYR 0.023 0.002 TYR R 145 ARG 0.014 0.000 ARG N 105 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 453) hydrogen bonds : angle 3.92508 ( 1287) SS BOND : bond 0.00261 ( 6) SS BOND : angle 0.89069 ( 12) covalent geometry : bond 0.00369 ( 9397) covalent geometry : angle 0.71434 (12743) Misc. bond : bond 0.00013 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6432.48 seconds wall clock time: 111 minutes 47.97 seconds (6707.97 seconds total)