Starting phenix.real_space_refine on Tue Mar 3 23:21:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbh_31879/03_2026/7vbh_31879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbh_31879/03_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_31879/03_2026/7vbh_31879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_2026/7vbh_31879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_2026/7vbh_31879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_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-5986/lib/python3.9/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: 2.10, per 1000 atoms: 0.23 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: 0.67 Conformation dependent library (CDL) restraints added in 318.0 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: 0.28 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: 1.49 Time building geometry restraints manager: 0.91 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: 4867 17.97 - 35.95: 521 35.95 - 53.92: 90 53.92 - 71.90: 27 71.90 - 89.87: 12 Dihedral angle restraints: 5517 sinusoidal: 2193 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 5514 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: 1.460 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 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 : 15.915 89.873 3349 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 covalent geometry : bond 0.01029 ( 9322) covalent geometry : angle 1.11731 (12633) SS BOND : bond 0.00403 ( 6) SS BOND : angle 2.20183 ( 12) hydrogen bonds : bond 0.18185 ( 441) hydrogen bonds : angle 8.36656 ( 1263) Misc. bond : bond 0.10469 ( 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 : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 166 average time/residue: 0.5123 time to fit residues: 91.1893 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 : 0.325 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: N 31 ASN P 20 GLN ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN R 304 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.207385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.163614 restraints weight = 10601.780| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.86 r_work: 0.3599 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9329 Z= 0.192 Angle : 0.751 9.518 12645 Z= 0.387 Chirality : 0.045 0.167 1392 Planarity : 0.006 0.065 1604 Dihedral : 7.190 59.607 1279 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 4.33 % Allowed : 16.00 % Favored : 79.67 % 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: -1.89 (0.24), residues: 1117 helix: -0.01 (0.24), residues: 441 sheet: -1.79 (0.31), residues: 210 loop : -2.16 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 356 TYR 0.029 0.002 TYR R 148 PHE 0.018 0.002 PHE N 108 TRP 0.021 0.002 TRP B 169 HIS 0.006 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9322) covalent geometry : angle 0.75039 (12633) SS BOND : bond 0.01121 ( 6) SS BOND : angle 1.45366 ( 12) hydrogen bonds : bond 0.05058 ( 441) hydrogen bonds : angle 5.22854 ( 1263) Misc. bond : bond 0.00023 ( 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 170 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8091 (m-30) cc_final: 0.7829 (m-30) REVERT: A 392 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7185 (mt-10) REVERT: B 259 GLN cc_start: 0.6675 (pt0) cc_final: 0.6412 (pt0) REVERT: G 38 MET cc_start: 0.6287 (tmm) cc_final: 0.5898 (ttp) outliers start: 42 outliers final: 10 residues processed: 157 average time/residue: 0.4772 time to fit residues: 80.8159 Evaluate side-chains 111 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain N residue 21 SER 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 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: 0.7980 chunk 53 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 73 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN B 88 ASN B 220 GLN 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 = 0.4220 r_free = 0.4220 target = 0.197831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154713 restraints weight = 10492.032| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.81 r_work: 0.3365 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5456 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= 0.163 Angle : 0.627 7.923 12645 Z= 0.333 Chirality : 0.044 0.153 1392 Planarity : 0.005 0.057 1604 Dihedral : 6.110 57.634 1273 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.92 % Allowed : 18.16 % Favored : 77.92 % 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: -1.09 (0.24), residues: 1117 helix: 0.90 (0.25), residues: 441 sheet: -1.32 (0.32), residues: 212 loop : -2.05 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 421 TYR 0.022 0.002 TYR R 148 PHE 0.020 0.002 PHE B 151 TRP 0.017 0.002 TRP R 243 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9322) covalent geometry : angle 0.62465 (12633) SS BOND : bond 0.00420 ( 6) SS BOND : angle 1.80712 ( 12) hydrogen bonds : bond 0.04886 ( 441) hydrogen bonds : angle 4.69329 ( 1263) Misc. bond : bond 0.00019 ( 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 178 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 380 ARG cc_start: 0.7333 (ttp-110) cc_final: 0.6511 (mtp85) REVERT: A 392 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7205 (mt-10) REVERT: N 77 ASN cc_start: 0.5991 (p0) cc_final: 0.5740 (p0) REVERT: N 94 TYR cc_start: 0.7899 (m-80) cc_final: 0.7697 (m-80) REVERT: R 202 LYS cc_start: 0.6041 (ttpp) cc_final: 0.5716 (tptp) REVERT: R 292 GLU cc_start: 0.7839 (tp30) cc_final: 0.7461 (mp0) REVERT: R 346 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7651 (mtpm) REVERT: B 46 ARG cc_start: 0.8326 (mtp-110) cc_final: 0.7928 (mtp-110) REVERT: B 215 GLU cc_start: 0.8179 (mp0) cc_final: 0.7606 (tt0) REVERT: G 21 MET cc_start: 0.3866 (ttt) cc_final: 0.3142 (pp-130) REVERT: G 38 MET cc_start: 0.6291 (tmm) cc_final: 0.6063 (ttp) outliers start: 38 outliers final: 12 residues processed: 164 average time/residue: 0.5006 time to fit residues: 88.1262 Evaluate side-chains 131 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 386 MET 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 R residue 89 LEU Chi-restraints excluded: chain R residue 355 THR 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: 0.5980 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 39 GLN R 213 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.195718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.152450 restraints weight = 10546.830| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.99 r_work: 0.3410 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6163 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= 0.139 Angle : 0.577 7.806 12645 Z= 0.305 Chirality : 0.042 0.137 1392 Planarity : 0.004 0.058 1604 Dihedral : 5.777 54.245 1273 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.82 % Allowed : 21.05 % Favored : 75.13 % 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: -0.53 (0.25), residues: 1117 helix: 1.42 (0.25), residues: 436 sheet: -0.74 (0.34), residues: 216 loop : -1.93 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 421 TYR 0.021 0.002 TYR R 148 PHE 0.015 0.001 PHE R 280 TRP 0.015 0.001 TRP R 243 HIS 0.007 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9322) covalent geometry : angle 0.57581 (12633) SS BOND : bond 0.00229 ( 6) SS BOND : angle 1.39958 ( 12) hydrogen bonds : bond 0.04350 ( 441) hydrogen bonds : angle 4.48370 ( 1263) Misc. bond : bond 0.00036 ( 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 174 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8435 (tttt) cc_final: 0.8055 (mmpt) REVERT: A 292 ASN cc_start: 0.8208 (t0) cc_final: 0.7805 (t0) REVERT: A 380 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.6620 (mtp85) REVERT: A 392 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7295 (mt-10) REVERT: N 77 ASN cc_start: 0.6077 (p0) cc_final: 0.5867 (p0) REVERT: R 202 LYS cc_start: 0.6316 (ttpp) cc_final: 0.5928 (tptp) REVERT: R 346 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7734 (mtpm) REVERT: B 46 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7912 (mtp-110) REVERT: G 21 MET cc_start: 0.4209 (OUTLIER) cc_final: 0.3429 (pp-130) REVERT: G 38 MET cc_start: 0.6429 (tmm) cc_final: 0.6200 (ttp) outliers start: 37 outliers final: 23 residues processed: 161 average time/residue: 0.5246 time to fit residues: 90.5972 Evaluate side-chains 142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 320 THR 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 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 411 LEU Chi-restraints excluded: chain B residue 70 LEU 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 228 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.0170 chunk 61 optimal weight: 2.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 230 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.191948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.148163 restraints weight = 10649.480| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.94 r_work: 0.3401 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.6696 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= 0.164 Angle : 0.610 10.017 12645 Z= 0.320 Chirality : 0.043 0.151 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.771 59.600 1273 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.13 % Allowed : 21.67 % Favored : 74.20 % 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: -0.40 (0.26), residues: 1117 helix: 1.55 (0.25), residues: 434 sheet: -0.66 (0.35), residues: 223 loop : -1.87 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 421 TYR 0.022 0.002 TYR R 289 PHE 0.016 0.002 PHE N 108 TRP 0.014 0.002 TRP R 243 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9322) covalent geometry : angle 0.60816 (12633) SS BOND : bond 0.00366 ( 6) SS BOND : angle 1.77674 ( 12) hydrogen bonds : bond 0.04686 ( 441) hydrogen bonds : angle 4.47754 ( 1263) Misc. bond : bond 0.00013 ( 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 170 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8448 (tttt) cc_final: 0.8082 (mmpt) REVERT: A 266 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.7971 (tm) REVERT: A 380 ARG cc_start: 0.7540 (ttp-110) cc_final: 0.6682 (mtp85) REVERT: A 392 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7354 (mt-10) REVERT: P 12 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7607 (mtpm) REVERT: R 202 LYS cc_start: 0.7150 (ttpp) cc_final: 0.6645 (tptp) REVERT: R 271 SER cc_start: 0.8381 (t) cc_final: 0.7931 (m) REVERT: R 288 LYS cc_start: 0.8364 (tptt) cc_final: 0.7838 (mptp) REVERT: R 346 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7867 (mtpm) REVERT: B 46 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.7918 (mtp-110) REVERT: B 118 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6761 (p0) REVERT: B 264 TYR cc_start: 0.8050 (m-80) cc_final: 0.7507 (m-80) outliers start: 40 outliers final: 23 residues processed: 156 average time/residue: 0.4911 time to fit residues: 82.3996 Evaluate side-chains 145 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 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 386 MET Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER 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 R residue 89 LEU 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 70 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 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 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: 3.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.198839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155705 restraints weight = 10463.514| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.92 r_work: 0.3548 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.7093 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= 0.153 Angle : 0.598 8.113 12645 Z= 0.313 Chirality : 0.043 0.176 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.638 56.169 1273 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.75 % Allowed : 21.98 % 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: -0.23 (0.26), residues: 1117 helix: 1.73 (0.25), residues: 433 sheet: -0.41 (0.35), residues: 222 loop : -1.92 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 421 TYR 0.020 0.002 TYR R 148 PHE 0.014 0.001 PHE R 280 TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9322) covalent geometry : angle 0.59615 (12633) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.68867 ( 12) hydrogen bonds : bond 0.04508 ( 441) hydrogen bonds : angle 4.34924 ( 1263) Misc. bond : bond 0.00007 ( 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 177 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8517 (tttt) cc_final: 0.8177 (mmpt) REVERT: A 266 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8112 (tm) REVERT: A 380 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.6721 (mtp85) REVERT: A 392 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7268 (mm-30) REVERT: N 31 ASN cc_start: 0.8303 (m-40) cc_final: 0.8077 (m-40) REVERT: P 12 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7646 (mtpm) REVERT: R 202 LYS cc_start: 0.7231 (ttpp) cc_final: 0.6788 (tptp) REVERT: R 271 SER cc_start: 0.8514 (t) cc_final: 0.8086 (m) REVERT: R 288 LYS cc_start: 0.8556 (tptt) cc_final: 0.8141 (mptp) REVERT: R 346 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7952 (mtpm) REVERT: B 118 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6658 (p0) REVERT: B 168 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 264 TYR cc_start: 0.8040 (m-80) cc_final: 0.7493 (m-80) outliers start: 46 outliers final: 24 residues processed: 160 average time/residue: 0.4922 time to fit residues: 84.8441 Evaluate side-chains 151 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE 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 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 70 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 30.0000 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 6 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.197730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155802 restraints weight = 10405.253| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.81 r_work: 0.3514 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.7386 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= 0.158 Angle : 0.612 8.511 12645 Z= 0.318 Chirality : 0.043 0.155 1392 Planarity : 0.004 0.054 1604 Dihedral : 5.657 56.266 1273 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.44 % Allowed : 22.70 % Favored : 72.86 % 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: -0.19 (0.25), residues: 1117 helix: 1.72 (0.25), residues: 440 sheet: -0.38 (0.35), residues: 221 loop : -1.92 (0.27), 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 148 PHE 0.014 0.001 PHE N 108 TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9322) covalent geometry : angle 0.60966 (12633) SS BOND : bond 0.00314 ( 6) SS BOND : angle 1.77001 ( 12) hydrogen bonds : bond 0.04567 ( 441) hydrogen bonds : angle 4.31255 ( 1263) Misc. bond : bond 0.00014 ( 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 171 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8580 (tttt) cc_final: 0.8240 (mmpt) REVERT: A 266 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8137 (tm) REVERT: A 380 ARG cc_start: 0.7616 (ttp-110) cc_final: 0.6764 (mtp85) REVERT: A 392 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7304 (mm-30) REVERT: N 31 ASN cc_start: 0.8340 (m-40) cc_final: 0.8112 (m-40) REVERT: P 12 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7743 (mtpm) REVERT: R 202 LYS cc_start: 0.7327 (ttpp) cc_final: 0.6917 (tptp) REVERT: R 271 SER cc_start: 0.8587 (t) cc_final: 0.8122 (m) REVERT: R 346 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8038 (mtpm) REVERT: R 421 ARG cc_start: 0.6898 (tpp-160) cc_final: 0.6391 (tpp-160) REVERT: B 45 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7148 (mmt) REVERT: B 118 ASP cc_start: 0.7057 (OUTLIER) cc_final: 0.6701 (p0) REVERT: B 168 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8680 (tp) REVERT: B 234 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8567 (t80) outliers start: 43 outliers final: 29 residues processed: 157 average time/residue: 0.4677 time to fit residues: 79.4496 Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 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 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 272 ILE 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 45 MET Chi-restraints excluded: chain B residue 70 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 161 SER 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 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 B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS 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 = 0.4281 r_free = 0.4281 target = 0.197234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154002 restraints weight = 10391.849| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.90 r_work: 0.3547 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.7516 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= 0.153 Angle : 0.608 9.209 12645 Z= 0.317 Chirality : 0.043 0.156 1392 Planarity : 0.004 0.054 1604 Dihedral : 5.612 56.036 1273 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.44 % Allowed : 22.70 % Favored : 72.86 % 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: -0.08 (0.25), residues: 1117 helix: 1.79 (0.25), residues: 440 sheet: -0.36 (0.35), residues: 221 loop : -1.79 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 421 TYR 0.035 0.002 TYR R 220 PHE 0.014 0.001 PHE R 280 TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 9322) covalent geometry : angle 0.60601 (12633) SS BOND : bond 0.00227 ( 6) SS BOND : angle 1.72238 ( 12) hydrogen bonds : bond 0.04534 ( 441) hydrogen bonds : angle 4.27790 ( 1263) Misc. bond : bond 0.00014 ( 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 170 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8642 (tttt) cc_final: 0.8218 (mmpt) REVERT: A 266 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8236 (tm) REVERT: A 380 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.6869 (mtp85) REVERT: A 392 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7411 (mm-30) REVERT: N 31 ASN cc_start: 0.8392 (m-40) cc_final: 0.8165 (m-40) REVERT: P 12 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7860 (mtpm) REVERT: R 202 LYS cc_start: 0.7427 (ttpp) cc_final: 0.6972 (tptp) REVERT: R 271 SER cc_start: 0.8660 (t) cc_final: 0.8260 (m) REVERT: R 346 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7975 (mtpm) REVERT: B 45 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7280 (mmt) REVERT: B 118 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6918 (p0) REVERT: B 168 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8708 (tp) REVERT: B 234 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8594 (t80) REVERT: B 264 TYR cc_start: 0.8075 (m-80) cc_final: 0.7531 (m-80) outliers start: 43 outliers final: 32 residues processed: 156 average time/residue: 0.4773 time to fit residues: 80.6456 Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 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 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 23 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 289 TYR 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 45 MET Chi-restraints excluded: chain B residue 70 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 161 SER 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 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 72 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 35 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN N 5 GLN R 171 HIS R 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.197957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154768 restraints weight = 10402.500| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.68 r_work: 0.3554 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7623 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= 0.137 Angle : 0.610 8.604 12645 Z= 0.318 Chirality : 0.042 0.152 1392 Planarity : 0.004 0.069 1604 Dihedral : 5.563 55.138 1273 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.23 % Allowed : 24.05 % 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: 0.11 (0.26), residues: 1117 helix: 1.98 (0.25), residues: 435 sheet: -0.31 (0.35), residues: 221 loop : -1.66 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 421 TYR 0.027 0.002 TYR R 220 PHE 0.014 0.001 PHE R 280 TRP 0.015 0.001 TRP R 214 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9322) covalent geometry : angle 0.60852 (12633) SS BOND : bond 0.00204 ( 6) SS BOND : angle 1.60200 ( 12) hydrogen bonds : bond 0.04339 ( 441) hydrogen bonds : angle 4.21474 ( 1263) Misc. bond : bond 0.00010 ( 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 171 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8614 (tttt) cc_final: 0.8215 (mmpt) REVERT: A 266 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8236 (tm) REVERT: A 380 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.6862 (mtp85) REVERT: A 392 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7393 (mm-30) REVERT: N 31 ASN cc_start: 0.8359 (m-40) cc_final: 0.8135 (m-40) REVERT: P 12 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7827 (mtpm) REVERT: R 41 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8055 (tp30) REVERT: R 170 ARG cc_start: 0.7847 (tpt-90) cc_final: 0.7638 (tpt-90) REVERT: R 202 LYS cc_start: 0.7399 (ttpp) cc_final: 0.6939 (tptp) REVERT: R 271 SER cc_start: 0.8649 (t) cc_final: 0.8211 (m) REVERT: R 346 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7934 (mtpm) REVERT: R 421 ARG cc_start: 0.7123 (tpp-160) cc_final: 0.6515 (tpp-160) REVERT: B 118 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6903 (p0) REVERT: B 168 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8701 (tp) REVERT: B 212 ASP cc_start: 0.8371 (p0) cc_final: 0.7474 (p0) REVERT: B 215 GLU cc_start: 0.7813 (mp0) cc_final: 0.7476 (pm20) REVERT: B 234 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8546 (t80) REVERT: B 264 TYR cc_start: 0.8127 (m-80) cc_final: 0.7624 (m-80) REVERT: B 318 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8747 (tp) outliers start: 41 outliers final: 30 residues processed: 158 average time/residue: 0.4853 time to fit residues: 82.5721 Evaluate side-chains 162 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 126 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 7 SER 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 N residue 83 MET Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 70 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 161 SER 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 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS R 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.195350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.153239 restraints weight = 10395.850| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.84 r_work: 0.3479 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9329 Z= 0.187 Angle : 0.652 8.632 12645 Z= 0.340 Chirality : 0.044 0.167 1392 Planarity : 0.005 0.065 1604 Dihedral : 5.789 57.664 1273 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.72 % Allowed : 24.66 % Favored : 71.62 % 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: 1.74 (0.25), residues: 443 sheet: -0.34 (0.35), residues: 221 loop : -1.75 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 421 TYR 0.020 0.002 TYR R 148 PHE 0.017 0.002 PHE N 108 TRP 0.017 0.002 TRP R 214 HIS 0.007 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9322) covalent geometry : angle 0.64959 (12633) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.78661 ( 12) hydrogen bonds : bond 0.04937 ( 441) hydrogen bonds : angle 4.38581 ( 1263) Misc. bond : bond 0.00015 ( 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 169 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8632 (tttt) cc_final: 0.8273 (mmpt) REVERT: A 266 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8204 (tm) REVERT: A 380 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.6775 (mtp85) REVERT: A 392 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7345 (mm-30) REVERT: N 31 ASN cc_start: 0.8409 (m-40) cc_final: 0.8170 (m-40) REVERT: N 60 TYR cc_start: 0.8699 (m-80) cc_final: 0.8341 (m-80) REVERT: P 12 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7753 (mtpm) REVERT: R 41 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7943 (tp30) REVERT: R 202 LYS cc_start: 0.7658 (ttpp) cc_final: 0.7198 (tptp) REVERT: R 271 SER cc_start: 0.8654 (t) cc_final: 0.8225 (m) REVERT: R 279 LEU cc_start: 0.8392 (tm) cc_final: 0.7697 (mp) REVERT: R 346 LYS cc_start: 0.8272 (mtmm) cc_final: 0.8026 (mtpm) REVERT: R 421 ARG cc_start: 0.7004 (tpp-160) cc_final: 0.6440 (tpp-160) REVERT: B 118 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6764 (p0) REVERT: B 168 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8699 (tp) REVERT: B 212 ASP cc_start: 0.8220 (p0) cc_final: 0.7310 (p0) REVERT: B 234 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8595 (t80) outliers start: 36 outliers final: 25 residues processed: 159 average time/residue: 0.4935 time to fit residues: 84.5156 Evaluate side-chains 154 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE 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 83 MET Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE 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 161 SER 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 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 1.9990 chunk 87 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 17 optimal weight: 0.0170 chunk 106 optimal weight: 9.9990 chunk 68 optimal weight: 0.0570 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.0870 chunk 20 optimal weight: 2.9990 overall best weight: 0.1312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN P 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.199452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.159334 restraints weight = 10155.649| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.24 r_work: 0.3616 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.7972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9329 Z= 0.108 Angle : 0.571 8.758 12645 Z= 0.300 Chirality : 0.041 0.151 1392 Planarity : 0.004 0.055 1604 Dihedral : 5.387 59.325 1273 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.68 % Allowed : 25.70 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.33 (0.26), residues: 1117 helix: 2.22 (0.26), residues: 434 sheet: -0.23 (0.35), residues: 221 loop : -1.57 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 421 TYR 0.025 0.001 TYR R 220 PHE 0.016 0.001 PHE R 280 TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9322) covalent geometry : angle 0.56953 (12633) SS BOND : bond 0.00167 ( 6) SS BOND : angle 1.36069 ( 12) hydrogen bonds : bond 0.03730 ( 441) hydrogen bonds : angle 4.05592 ( 1263) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3172.23 seconds wall clock time: 54 minutes 42.16 seconds (3282.16 seconds total)