Starting phenix.real_space_refine on Thu Jul 2 16:11:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbh_31879/07_2026/7vbh_31879.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.089 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 53 5.16 5 C 5817 2.51 5 N 1577 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1761 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3105 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.80, per 1000 atoms: 0.20 Number of scatterers: 9116 At special positions: 0 Unit cell: (81.396, 96.39, 170.289, 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 53 16.00 O 1669 8.00 N 1577 7.00 C 5817 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=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 216.4 milliseconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 41.2% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.661A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.834A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.660A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.756A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.750A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.628A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 removed outlier: 3.993A pdb=" N ASP P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.715A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 168 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.727A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.813A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.538A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.541A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 377 through 403 removed outlier: 3.862A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.642A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.589A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.322A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.563A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.543A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.382A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.643A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.687A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.135A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.845A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1478 1.29 - 1.42: 2571 1.42 - 1.56: 5198 1.56 - 1.69: 3 1.69 - 1.83: 72 Bond restraints: 9322 Sorted by residual: bond pdb=" C02 D6M P 501 " pdb=" C12 D6M P 501 " ideal model delta sigma weight residual 1.517 1.795 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.23e-02 6.61e+03 2.75e+01 bond pdb=" C07 D6M P 501 " pdb=" O08 D6M P 501 " ideal model delta sigma weight residual 1.247 1.154 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C SER B 227 " pdb=" O SER B 227 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.28e-02 6.10e+03 1.97e+01 bond pdb=" N SER B 227 " pdb=" CA SER B 227 " ideal model delta sigma weight residual 1.455 1.394 0.061 1.41e-02 5.03e+03 1.87e+01 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 12176 2.49 - 4.99: 379 4.99 - 7.48: 47 7.48 - 9.97: 18 9.97 - 12.47: 13 Bond angle restraints: 12633 Sorted by residual: angle pdb=" N TYR P 13 " pdb=" CA TYR P 13 " pdb=" C TYR P 13 " ideal model delta sigma weight residual 112.23 100.11 12.12 1.26e+00 6.30e-01 9.25e+01 angle pdb=" C THR P 5 " pdb=" CA THR P 5 " pdb=" CB THR P 5 " ideal model delta sigma weight residual 110.92 100.58 10.34 1.59e+00 3.96e-01 4.23e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.47 121.65 -8.18 1.43e+00 4.89e-01 3.28e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.42 118.66 -8.24 1.46e+00 4.69e-01 3.18e+01 angle pdb=" CA LYS A 305 " pdb=" CB LYS A 305 " pdb=" CG LYS A 305 " ideal model delta sigma weight residual 114.10 125.33 -11.23 2.00e+00 2.50e-01 3.15e+01 ... (remaining 12628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4864 17.97 - 35.95: 520 35.95 - 53.92: 86 53.92 - 71.90: 27 71.90 - 89.87: 12 Dihedral angle restraints: 5509 sinusoidal: 2185 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.71 74.71 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.87 48.13 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA GLU A 327 " pdb=" C GLU A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 -151.95 -28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1154 0.077 - 0.155: 209 0.155 - 0.232: 24 0.232 - 0.310: 2 0.310 - 0.387: 3 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1389 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 501 " -0.095 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C04 D6M P 501 " 0.348 2.00e-02 2.50e+03 pdb=" C12 D6M P 501 " 0.123 2.00e-02 2.50e+03 pdb=" N03 D6M P 501 " -0.518 2.00e-02 2.50e+03 pdb=" O01 D6M P 501 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 385 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PHE R 385 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE R 385 " -0.024 2.00e-02 2.50e+03 pdb=" N THR R 386 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 226 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLU B 226 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 226 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 41 2.41 - 3.03: 4872 3.03 - 3.65: 14461 3.65 - 4.28: 22223 4.28 - 4.90: 37221 Nonbonded interactions: 78818 Sorted by model distance: nonbonded pdb=" O LEU P 27 " pdb=" NH2 ARG R 121 " model vdw 1.784 3.120 nonbonded pdb=" CD2 LEU P 26 " pdb=" O GLU R 68 " model vdw 1.908 3.460 nonbonded pdb=" OD1 ASP P 15 " pdb=" N LEU R 32 " model vdw 1.947 3.120 nonbonded pdb=" N HIS P 1 " pdb=" CH2 TRP R 306 " model vdw 1.950 3.420 nonbonded pdb=" O GLY P 29 " pdb=" OE2 GLU R 68 " model vdw 2.182 3.040 ... (remaining 78813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 : 0.010 0.278 9329 Z= 0.483 Angle : 1.119 12.466 12645 Z= 0.621 Chirality : 0.062 0.387 1392 Planarity : 0.011 0.294 1604 Dihedral : 15.865 89.873 3341 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.52 % Allowed : 9.91 % Favored : 89.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.19), residues: 1117 helix: -2.58 (0.18), residues: 439 sheet: -2.61 (0.29), residues: 212 loop : -2.66 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 38 TYR 0.025 0.003 TYR R 148 PHE 0.034 0.003 PHE B 151 TRP 0.035 0.003 TRP R 214 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.01029 / 0.47 ( 9322) covalent geometry : angle 1.11731 / 0.62 (12633) SS BOND : bond 0.00403 / 0.22 ( 6) SS BOND : angle 2.20183 / 1.23 ( 12) hydrogen bonds : bond 0.18185 / 11.89 ( 441) hydrogen bonds : angle 8.36656 / 5.94 ( 1263) Misc. bond : bond 0.10469 / 5.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 166 average time/residue: 0.4513 time to fit residues: 80.5626 Evaluate side-chains 92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN P 20 GLN ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN R 304 ASN R 394 GLN B 9 GLN B 35 ASN B 155 ASN B 176 GLN B 237 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.207480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.164319 restraints weight = 10597.658| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.78 r_work: 0.3533 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9329 Z= 0.194 Angle : 0.726 9.016 12645 Z= 0.377 Chirality : 0.045 0.159 1392 Planarity : 0.006 0.065 1604 Dihedral : 6.925 59.314 1271 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.88 % Rotamer: Outliers : 4.13 % Allowed : 16.00 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.23), residues: 1117 helix: -0.04 (0.24), residues: 441 sheet: -1.81 (0.31), residues: 212 loop : -2.16 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.029 0.002 TYR R 148 PHE 0.017 0.002 PHE N 108 TRP 0.021 0.002 TRP B 169 HIS 0.006 0.002 HIS A 387 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 9322) covalent geometry : angle 0.72558 / 0.38 (12633) SS BOND : bond 0.01179 / 0.57 ( 6) SS BOND : angle 1.36688 / 0.78 ( 12) hydrogen bonds : bond 0.05000 / 3.22 ( 441) hydrogen bonds : angle 5.21649 / 3.68 ( 1263) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8121 (m-30) cc_final: 0.7852 (m-30) REVERT: A 392 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7167 (mt-10) REVERT: N 53 GLN cc_start: 0.7599 (mp10) cc_final: 0.7267 (mp10) REVERT: R 233 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6649 (ttp) REVERT: B 259 GLN cc_start: 0.6670 (pt0) cc_final: 0.6392 (pt0) REVERT: G 38 MET cc_start: 0.6238 (tmm) cc_final: 0.5852 (ttp) outliers start: 40 outliers final: 9 residues processed: 156 average time/residue: 0.4516 time to fit residues: 76.1671 Evaluate side-chains 114 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 223 SER Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 103 optimal weight: 0.0060 chunk 66 optimal weight: 0.1980 chunk 39 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 HIS P 1 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN B 88 ASN B 230 ASN B 237 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.205132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.161373 restraints weight = 10527.711| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.84 r_work: 0.3557 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9329 Z= 0.127 Angle : 0.578 7.769 12645 Z= 0.307 Chirality : 0.041 0.145 1392 Planarity : 0.005 0.058 1604 Dihedral : 5.903 53.305 1265 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.10 % Allowed : 19.09 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.25), residues: 1117 helix: 1.06 (0.25), residues: 436 sheet: -1.31 (0.32), residues: 211 loop : -2.00 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 44 TYR 0.022 0.001 TYR R 148 PHE 0.016 0.001 PHE B 151 TRP 0.016 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9322) covalent geometry : angle 0.57579 / 0.31 (12633) SS BOND : bond 0.00393 / 0.23 ( 6) SS BOND : angle 1.56954 / 0.86 ( 12) hydrogen bonds : bond 0.04162 / 2.65 ( 441) hydrogen bonds : angle 4.64517 / 3.28 ( 1263) Misc. bond : bond 0.00091 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.7883 (m-30) cc_final: 0.7556 (m-30) REVERT: A 392 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7154 (mt-10) REVERT: N 94 TYR cc_start: 0.7853 (m-80) cc_final: 0.7612 (m-80) REVERT: P 27 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7373 (mm) REVERT: B 46 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7899 (mtp-110) REVERT: B 215 GLU cc_start: 0.8264 (mp0) cc_final: 0.7591 (tt0) REVERT: G 38 MET cc_start: 0.6141 (tmm) cc_final: 0.5818 (ttp) outliers start: 30 outliers final: 8 residues processed: 145 average time/residue: 0.4804 time to fit residues: 75.0157 Evaluate side-chains 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 40.0000 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 213 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.197094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153767 restraints weight = 10593.266| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.90 r_work: 0.3455 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.142 Angle : 0.587 7.557 12645 Z= 0.312 Chirality : 0.042 0.139 1392 Planarity : 0.004 0.059 1604 Dihedral : 5.684 56.510 1265 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.33 % Allowed : 18.99 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.25), residues: 1117 helix: 1.48 (0.25), residues: 436 sheet: -0.87 (0.34), residues: 220 loop : -1.83 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 421 TYR 0.021 0.002 TYR R 148 PHE 0.015 0.002 PHE B 151 TRP 0.013 0.001 TRP R 243 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9322) covalent geometry : angle 0.58336 / 0.31 (12633) SS BOND : bond 0.00271 / 0.15 ( 6) SS BOND : angle 2.10592 / 1.28 ( 12) hydrogen bonds : bond 0.04377 / 2.81 ( 441) hydrogen bonds : angle 4.41912 / 3.12 ( 1263) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8978 (mm) REVERT: A 292 ASN cc_start: 0.8235 (t0) cc_final: 0.7841 (t0) REVERT: A 380 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6660 (mtp85) REVERT: A 392 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7316 (mt-10) REVERT: N 31 ASN cc_start: 0.8225 (m110) cc_final: 0.7949 (m110) REVERT: N 46 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7534 (pt0) REVERT: N 77 ASN cc_start: 0.6326 (p0) cc_final: 0.6084 (p0) REVERT: N 94 TYR cc_start: 0.7928 (m-80) cc_final: 0.7677 (m-80) REVERT: P 12 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7642 (mtpm) REVERT: R 202 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5914 (tptp) REVERT: R 293 ASP cc_start: 0.7077 (t0) cc_final: 0.6851 (t0) REVERT: B 46 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7983 (mtp-110) outliers start: 42 outliers final: 19 residues processed: 165 average time/residue: 0.4806 time to fit residues: 85.3694 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 0.0470 chunk 61 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151491 restraints weight = 10677.263| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.75 r_work: 0.3422 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.144 Angle : 0.582 8.200 12645 Z= 0.305 Chirality : 0.042 0.150 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.481 54.411 1265 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.54 % Allowed : 20.54 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.26), residues: 1117 helix: 1.65 (0.25), residues: 435 sheet: -0.66 (0.35), residues: 223 loop : -1.79 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 421 TYR 0.020 0.002 TYR R 148 PHE 0.015 0.001 PHE R 280 TRP 0.014 0.001 TRP R 243 HIS 0.010 0.001 HIS R 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 9322) covalent geometry : angle 0.57978 / 0.30 (12633) SS BOND : bond 0.00222 / 0.11 ( 6) SS BOND : angle 1.68156 / 1.07 ( 12) hydrogen bonds : bond 0.04361 / 2.78 ( 441) hydrogen bonds : angle 4.36384 / 3.09 ( 1263) Misc. bond : bond 0.00002 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 127 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8423 (tttt) cc_final: 0.8023 (mmpt) REVERT: A 266 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7979 (tm) REVERT: A 276 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8950 (mm) REVERT: A 380 ARG cc_start: 0.7442 (ttp-110) cc_final: 0.6596 (mtp85) REVERT: A 392 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7325 (mt-10) REVERT: N 31 ASN cc_start: 0.8265 (m-40) cc_final: 0.8043 (m-40) REVERT: N 46 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: N 94 TYR cc_start: 0.7837 (m-80) cc_final: 0.7550 (m-80) REVERT: P 12 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7569 (mtpm) REVERT: R 202 LYS cc_start: 0.6484 (ttpp) cc_final: 0.6050 (tptp) REVERT: B 46 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7880 (mtp-110) REVERT: B 118 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6620 (p0) REVERT: B 237 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.7459 (m110) REVERT: B 264 TYR cc_start: 0.7992 (m-80) cc_final: 0.7753 (m-10) outliers start: 44 outliers final: 21 residues processed: 153 average time/residue: 0.4286 time to fit residues: 70.8534 Evaluate side-chains 142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN R 263 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.191739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.149348 restraints weight = 10649.544| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.67 r_work: 0.3331 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9329 Z= 0.166 Angle : 0.613 8.154 12645 Z= 0.322 Chirality : 0.043 0.182 1392 Planarity : 0.004 0.055 1604 Dihedral : 5.516 57.698 1265 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.54 % Allowed : 22.19 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.26), residues: 1117 helix: 1.71 (0.25), residues: 435 sheet: -0.58 (0.35), residues: 224 loop : -1.74 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 421 TYR 0.027 0.002 TYR R 289 PHE 0.016 0.002 PHE N 108 TRP 0.015 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9322) covalent geometry : angle 0.61162 / 0.32 (12633) SS BOND : bond 0.00205 / 0.10 ( 6) SS BOND : angle 1.65193 / 0.94 ( 12) hydrogen bonds : bond 0.04590 / 2.94 ( 441) hydrogen bonds : angle 4.37721 / 3.10 ( 1263) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8483 (tttt) cc_final: 0.8073 (mmpt) REVERT: A 266 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8057 (tm) REVERT: A 276 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8978 (mm) REVERT: A 372 ILE cc_start: 0.8465 (mm) cc_final: 0.8257 (mp) REVERT: A 380 ARG cc_start: 0.7549 (ttp-110) cc_final: 0.6680 (mtp85) REVERT: A 392 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7350 (mt-10) REVERT: N 46 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: P 12 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7665 (mtpm) REVERT: R 202 LYS cc_start: 0.7238 (ttpp) cc_final: 0.6738 (tptp) REVERT: R 271 SER cc_start: 0.8418 (t) cc_final: 0.7968 (m) REVERT: R 411 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7457 (tp) REVERT: B 118 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6721 (p0) outliers start: 44 outliers final: 23 residues processed: 158 average time/residue: 0.4204 time to fit residues: 72.2846 Evaluate side-chains 144 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 5 GLN R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.191027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.147674 restraints weight = 10598.279| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.87 r_work: 0.3293 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9329 Z= 0.154 Angle : 0.602 8.600 12645 Z= 0.314 Chirality : 0.043 0.160 1392 Planarity : 0.004 0.054 1604 Dihedral : 5.546 58.072 1265 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.44 % Allowed : 23.53 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1117 helix: 1.82 (0.25), residues: 436 sheet: -0.51 (0.35), residues: 225 loop : -1.68 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 421 TYR 0.024 0.002 TYR R 289 PHE 0.015 0.001 PHE N 108 TRP 0.013 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 9322) covalent geometry : angle 0.60024 / 0.31 (12633) SS BOND : bond 0.00257 / 0.13 ( 6) SS BOND : angle 1.53941 / 0.82 ( 12) hydrogen bonds : bond 0.04503 / 2.88 ( 441) hydrogen bonds : angle 4.30608 / 3.06 ( 1263) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8439 (tttt) cc_final: 0.7933 (mmpt) REVERT: A 266 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8105 (tm) REVERT: A 276 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 372 ILE cc_start: 0.8455 (mm) cc_final: 0.8216 (mp) REVERT: A 380 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.6655 (mtp85) REVERT: A 392 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7451 (mm-30) REVERT: N 31 ASN cc_start: 0.8328 (m-40) cc_final: 0.8106 (m-40) REVERT: N 46 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: P 12 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7795 (mtpm) REVERT: R 202 LYS cc_start: 0.7147 (ttpp) cc_final: 0.6608 (tptp) REVERT: R 271 SER cc_start: 0.8483 (t) cc_final: 0.8033 (m) REVERT: R 289 TYR cc_start: 0.7461 (t80) cc_final: 0.7190 (t80) REVERT: R 411 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7319 (tp) REVERT: B 96 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7152 (mtm-85) REVERT: B 118 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6837 (p0) REVERT: B 217 MET cc_start: 0.7986 (mtp) cc_final: 0.7737 (ttp) REVERT: B 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8570 (t80) REVERT: G 21 MET cc_start: 0.4571 (OUTLIER) cc_final: 0.4367 (mmm) outliers start: 43 outliers final: 21 residues processed: 154 average time/residue: 0.3946 time to fit residues: 66.5320 Evaluate side-chains 146 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.0570 chunk 104 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155714 restraints weight = 10278.503| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.66 r_work: 0.3554 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.124 Angle : 0.589 8.513 12645 Z= 0.304 Chirality : 0.042 0.157 1392 Planarity : 0.004 0.061 1604 Dihedral : 5.429 58.649 1265 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.72 % Allowed : 24.46 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.26), residues: 1117 helix: 1.89 (0.25), residues: 440 sheet: -0.37 (0.35), residues: 220 loop : -1.57 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 421 TYR 0.019 0.001 TYR R 289 PHE 0.014 0.001 PHE R 280 TRP 0.014 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9322) covalent geometry : angle 0.58669 / 0.30 (12633) SS BOND : bond 0.00256 / 0.13 ( 6) SS BOND : angle 1.64193 / 0.87 ( 12) hydrogen bonds : bond 0.04170 / 2.64 ( 441) hydrogen bonds : angle 4.18356 / 2.97 ( 1263) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7719 (mmtt) REVERT: A 32 LYS cc_start: 0.8515 (tttt) cc_final: 0.8146 (mmpt) REVERT: A 266 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8102 (tm) REVERT: A 380 ARG cc_start: 0.7541 (ttp-110) cc_final: 0.6737 (mtp85) REVERT: A 392 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7325 (mm-30) REVERT: N 31 ASN cc_start: 0.8222 (m-40) cc_final: 0.7998 (m-40) REVERT: N 46 GLU cc_start: 0.7836 (pm20) cc_final: 0.7536 (pt0) REVERT: P 12 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7531 (mtpt) REVERT: R 202 LYS cc_start: 0.7150 (ttpp) cc_final: 0.6731 (tptp) REVERT: R 271 SER cc_start: 0.8494 (t) cc_final: 0.8010 (m) REVERT: R 289 TYR cc_start: 0.7342 (t80) cc_final: 0.7028 (t80) REVERT: R 291 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: R 411 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7555 (tp) REVERT: R 421 ARG cc_start: 0.6887 (tpp-160) cc_final: 0.6351 (tpp-160) REVERT: B 118 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.6672 (p0) REVERT: B 234 PHE cc_start: 0.8890 (OUTLIER) cc_final: 0.8523 (t80) REVERT: B 264 TYR cc_start: 0.7988 (m-80) cc_final: 0.7477 (m-80) outliers start: 36 outliers final: 22 residues processed: 154 average time/residue: 0.4312 time to fit residues: 72.0199 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 291 TYR Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 85 optimal weight: 0.0040 chunk 93 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN N 5 GLN R 302 ASN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.159117 restraints weight = 10300.387| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.39 r_work: 0.3594 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9329 Z= 0.115 Angle : 0.572 8.632 12645 Z= 0.300 Chirality : 0.041 0.154 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.314 59.429 1265 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.61 % Allowed : 24.56 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1117 helix: 2.08 (0.25), residues: 434 sheet: -0.28 (0.35), residues: 218 loop : -1.54 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 421 TYR 0.020 0.001 TYR R 148 PHE 0.014 0.001 PHE R 280 TRP 0.013 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9322) covalent geometry : angle 0.57044 / 0.30 (12633) SS BOND : bond 0.00183 / 0.09 ( 6) SS BOND : angle 1.49392 / 0.80 ( 12) hydrogen bonds : bond 0.03949 / 2.50 ( 441) hydrogen bonds : angle 4.12331 / 2.93 ( 1263) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7745 (mmtt) REVERT: A 32 LYS cc_start: 0.8544 (tttt) cc_final: 0.8131 (mmpt) REVERT: A 266 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8209 (tm) REVERT: A 380 ARG cc_start: 0.7710 (ttp-110) cc_final: 0.6881 (mtp85) REVERT: A 392 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7297 (tt0) REVERT: N 46 GLU cc_start: 0.8074 (pm20) cc_final: 0.7749 (pt0) REVERT: P 12 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7689 (mtpt) REVERT: R 202 LYS cc_start: 0.7308 (ttpp) cc_final: 0.6792 (tptp) REVERT: R 271 SER cc_start: 0.8598 (t) cc_final: 0.8173 (m) REVERT: R 289 TYR cc_start: 0.7413 (t80) cc_final: 0.7158 (t80) REVERT: R 411 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7578 (tp) REVERT: B 118 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6958 (p0) REVERT: B 234 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8451 (t80) REVERT: B 264 TYR cc_start: 0.8086 (m-80) cc_final: 0.7614 (m-80) outliers start: 35 outliers final: 22 residues processed: 152 average time/residue: 0.4549 time to fit residues: 74.8746 Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 5 GLN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.198668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.155165 restraints weight = 10399.908| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.80 r_work: 0.3573 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9329 Z= 0.140 Angle : 0.602 8.669 12645 Z= 0.315 Chirality : 0.042 0.158 1392 Planarity : 0.004 0.061 1604 Dihedral : 5.360 55.878 1265 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.99 % Allowed : 25.28 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1117 helix: 2.02 (0.25), residues: 438 sheet: -0.26 (0.35), residues: 218 loop : -1.57 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 421 TYR 0.020 0.002 TYR R 148 PHE 0.014 0.001 PHE R 169 TRP 0.013 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9322) covalent geometry : angle 0.59989 / 0.31 (12633) SS BOND : bond 0.00168 / 0.08 ( 6) SS BOND : angle 1.66269 / 0.89 ( 12) hydrogen bonds : bond 0.04324 / 2.75 ( 441) hydrogen bonds : angle 4.17504 / 2.96 ( 1263) Misc. bond : bond 0.00002 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7722 (mmtt) REVERT: A 32 LYS cc_start: 0.8539 (tttt) cc_final: 0.8101 (mmpt) REVERT: A 266 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8226 (tm) REVERT: A 380 ARG cc_start: 0.7788 (ttp-110) cc_final: 0.6894 (mtp85) REVERT: A 392 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7283 (tt0) REVERT: N 46 GLU cc_start: 0.8091 (pm20) cc_final: 0.7764 (pt0) REVERT: P 12 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7709 (mtpt) REVERT: R 38 LYS cc_start: 0.8268 (ttpt) cc_final: 0.8059 (ttpt) REVERT: R 170 ARG cc_start: 0.7932 (tpt-90) cc_final: 0.7729 (tpt-90) REVERT: R 202 LYS cc_start: 0.7327 (ttpp) cc_final: 0.6872 (tptp) REVERT: R 271 SER cc_start: 0.8689 (t) cc_final: 0.8283 (m) REVERT: R 289 TYR cc_start: 0.7429 (t80) cc_final: 0.7098 (t80) REVERT: R 421 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6526 (tpp-160) REVERT: B 118 ASP cc_start: 0.7306 (OUTLIER) cc_final: 0.6948 (p0) REVERT: B 234 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 264 TYR cc_start: 0.8116 (m-80) cc_final: 0.7662 (m-80) outliers start: 29 outliers final: 20 residues processed: 150 average time/residue: 0.4169 time to fit residues: 67.4263 Evaluate side-chains 149 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 63 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 17 optimal weight: 0.0010 chunk 106 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.200203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158885 restraints weight = 10264.480| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.38 r_work: 0.3569 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9329 Z= 0.119 Angle : 0.577 8.796 12645 Z= 0.301 Chirality : 0.041 0.156 1392 Planarity : 0.004 0.066 1604 Dihedral : 5.234 57.152 1265 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.58 % Allowed : 26.11 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.26), residues: 1117 helix: 2.18 (0.26), residues: 435 sheet: -0.21 (0.35), residues: 218 loop : -1.47 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 421 TYR 0.032 0.001 TYR R 220 PHE 0.014 0.001 PHE R 280 TRP 0.013 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9322) covalent geometry : angle 0.57507 / 0.30 (12633) SS BOND : bond 0.00150 / 0.08 ( 6) SS BOND : angle 1.51262 / 0.82 ( 12) hydrogen bonds : bond 0.03957 / 2.51 ( 441) hydrogen bonds : angle 4.06114 / 2.89 ( 1263) Misc. bond : bond 0.00008 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2961.61 seconds wall clock time: 51 minutes 13.09 seconds (3073.09 seconds total)