Starting phenix.real_space_refine on Tue Mar 3 23:26:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbi_31880/03_2026/7vbi_31880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbi_31880/03_2026/7vbi_31880.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2026/7vbi_31880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2026/7vbi_31880.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2026/7vbi_31880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbi_31880/03_2026/7vbi_31880.cif" } 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= -0.001 sd= 0.108 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 54 5.16 5 C 5882 2.51 5 N 1596 2.21 5 O 1691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 9223 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1891 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 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: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3115 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 33 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} Time building chain proxies: 2.56, per 1000 atoms: 0.28 Number of scatterers: 9223 At special positions: 0 Unit cell: (76.041, 100.674, 173.502, 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 54 16.00 O 1691 8.00 N 1596 7.00 C 5882 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 404.7 milliseconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.8% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.547A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.758A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.565A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.646A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.416A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.833A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.912A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'P' and resid 2 through 29 removed outlier: 3.669A pdb=" N VAL P 23 " --> pdb=" O GLN P 19 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.577A pdb=" N TYR R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.583A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.725A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.748A 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: 4.037A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 237 " --> pdb=" O MET R 233 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 removed outlier: 3.761A pdb=" N SER R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 280 removed outlier: 3.786A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 291 Processing helix chain 'R' and resid 293 through 298 removed outlier: 4.496A pdb=" N CYS R 296 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 336 Proline residue: R 312 - end of helix removed outlier: 3.663A pdb=" N ALA R 316 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N CYS R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 377 through 389 Processing helix chain 'R' and resid 390 through 403 removed outlier: 3.635A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 removed outlier: 3.962A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.877A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 4.006A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.794A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.521A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.185A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.626A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.454A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.573A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.670A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.928A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.698A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.996A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.351A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.063A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1221 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: 1.36 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2583 1.33 - 1.46: 2487 1.46 - 1.58: 4288 1.58 - 1.71: 0 1.71 - 1.84: 73 Bond restraints: 9431 Sorted by residual: bond pdb=" C PHE B 234 " pdb=" N PHE B 235 " ideal model delta sigma weight residual 1.328 1.274 0.054 1.44e-02 4.82e+03 1.41e+01 bond pdb=" CA PHE A 238 " pdb=" CB PHE A 238 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.51e-02 4.39e+03 1.33e+01 bond pdb=" CG1 ILE B 81 " pdb=" CD1 ILE B 81 " ideal model delta sigma weight residual 1.513 1.398 0.115 3.90e-02 6.57e+02 8.62e+00 bond pdb=" C PHE B 235 " pdb=" N PRO B 236 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.91e+00 ... (remaining 9426 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 12321 2.56 - 5.12: 400 5.12 - 7.69: 48 7.69 - 10.25: 12 10.25 - 12.81: 6 Bond angle restraints: 12787 Sorted by residual: angle pdb=" C THR A 319 " pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta sigma weight residual 120.51 130.15 -9.64 1.45e+00 4.76e-01 4.42e+01 angle pdb=" O ASP B 291 " pdb=" C ASP B 291 " pdb=" N PHE B 292 " ideal model delta sigma weight residual 122.39 129.37 -6.98 1.29e+00 6.01e-01 2.93e+01 angle pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta sigma weight residual 120.39 127.58 -7.19 1.39e+00 5.18e-01 2.67e+01 angle pdb=" C ARG N 98 " pdb=" N CYS N 99 " pdb=" CA CYS N 99 " ideal model delta sigma weight residual 122.74 110.14 12.60 2.44e+00 1.68e-01 2.67e+01 angle pdb=" N VAL R 405 " pdb=" CA VAL R 405 " pdb=" C VAL R 405 " ideal model delta sigma weight residual 113.10 108.34 4.76 9.70e-01 1.06e+00 2.41e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 4972 18.13 - 36.25: 488 36.25 - 54.38: 83 54.38 - 72.50: 21 72.50 - 90.63: 9 Dihedral angle restraints: 5573 sinusoidal: 2202 harmonic: 3371 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 93.00 162.50 -69.50 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -144.63 -35.37 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA LEU R 217 " pdb=" C LEU R 217 " pdb=" N LEU R 218 " pdb=" CA LEU R 218 " ideal model delta harmonic sigma weight residual 180.00 146.84 33.16 0 5.00e+00 4.00e-02 4.40e+01 ... (remaining 5570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 873 0.050 - 0.101: 396 0.101 - 0.151: 110 0.151 - 0.201: 23 0.201 - 0.251: 10 Chirality restraints: 1412 Sorted by residual: 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 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB ILE A 308 " pdb=" CA ILE A 308 " pdb=" CG1 ILE A 308 " pdb=" CG2 ILE A 308 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA VAL R 282 " pdb=" N VAL R 282 " pdb=" C VAL R 282 " pdb=" CB VAL R 282 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1409 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 384 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU R 384 " -0.058 2.00e-02 2.50e+03 pdb=" O LEU R 384 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE R 385 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 55 " -0.051 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO R 56 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 56 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO R 56 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 395 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C GLY R 395 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY R 395 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU R 396 " -0.017 2.00e-02 2.50e+03 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 745 2.73 - 3.27: 8443 3.27 - 3.81: 14905 3.81 - 4.36: 18454 4.36 - 4.90: 32142 Nonbonded interactions: 74689 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.181 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.265 3.040 nonbonded pdb=" O TYR R 69 " pdb=" OH TYR R 88 " model vdw 2.267 3.040 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.290 3.120 nonbonded pdb=" OE2 GLU P 3 " pdb=" OH TYR R 152 " model vdw 2.315 3.040 ... (remaining 74684 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: 1.130 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.990 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 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 : 0.011 0.115 9437 Z= 0.482 Angle : 1.128 12.808 12799 Z= 0.634 Chirality : 0.063 0.251 1412 Planarity : 0.008 0.076 1623 Dihedral : 14.914 90.630 3377 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.81 % Allowed : 7.42 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.18 % 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: -3.46 (0.20), residues: 1133 helix: -2.64 (0.18), residues: 429 sheet: -1.08 (0.32), residues: 229 loop : -2.44 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 8 TYR 0.027 0.003 TYR R 148 PHE 0.044 0.004 PHE N 108 TRP 0.031 0.004 TRP R 72 HIS 0.020 0.003 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.01118 ( 9431) covalent geometry : angle 1.12522 (12787) SS BOND : bond 0.00604 ( 6) SS BOND : angle 2.74903 ( 12) hydrogen bonds : bond 0.19655 ( 424) hydrogen bonds : angle 7.43376 ( 1221) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.387 Fit side-chains REVERT: A 272 LEU cc_start: 0.8286 (mt) cc_final: 0.8052 (mm) REVERT: A 339 TYR cc_start: 0.8678 (m-80) cc_final: 0.8439 (m-80) REVERT: N 34 MET cc_start: 0.8108 (mmm) cc_final: 0.7733 (mmm) REVERT: N 46 GLU cc_start: 0.7187 (mp0) cc_final: 0.6890 (mp0) REVERT: N 94 TYR cc_start: 0.8429 (m-80) cc_final: 0.8141 (m-80) REVERT: N 95 TYR cc_start: 0.8513 (m-80) cc_final: 0.8165 (m-80) REVERT: P 9 ASP cc_start: 0.8069 (m-30) cc_final: 0.7473 (m-30) REVERT: R 146 ILE cc_start: 0.8759 (mt) cc_final: 0.8484 (mp) REVERT: R 267 ARG cc_start: 0.7041 (tpt170) cc_final: 0.6324 (mpp80) REVERT: R 336 LYS cc_start: 0.8081 (mttp) cc_final: 0.7778 (mmtm) REVERT: R 348 ARG cc_start: 0.7395 (tpm170) cc_final: 0.6602 (mtp180) REVERT: R 376 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7274 (mtt90) REVERT: R 415 LYS cc_start: 0.7048 (mtmt) cc_final: 0.6696 (mttt) REVERT: B 42 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7058 (ttm-80) outliers start: 8 outliers final: 4 residues processed: 177 average time/residue: 0.6911 time to fit residues: 129.4997 Evaluate side-chains 135 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.0020 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN A 227 GLN A 371 ASN N 1 GLN N 31 ASN N 77 ASN R 45 GLN R 140 GLN R 211 GLN R 221 GLN B 119 ASN B 132 ASN B 230 ASN B 239 ASN G 24 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.192809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.148539 restraints weight = 10139.315| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.02 r_work: 0.3347 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9437 Z= 0.144 Angle : 0.614 10.051 12799 Z= 0.328 Chirality : 0.042 0.150 1412 Planarity : 0.005 0.063 1623 Dihedral : 5.849 52.325 1273 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.76 % Allowed : 13.82 % Favored : 82.42 % 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: -1.72 (0.23), residues: 1133 helix: -0.51 (0.24), residues: 433 sheet: -0.51 (0.32), residues: 242 loop : -2.03 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 283 TYR 0.022 0.001 TYR R 148 PHE 0.017 0.001 PHE A 212 TRP 0.021 0.002 TRP R 214 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9431) covalent geometry : angle 0.60944 (12787) SS BOND : bond 0.00284 ( 6) SS BOND : angle 2.58309 ( 12) hydrogen bonds : bond 0.04840 ( 424) hydrogen bonds : angle 4.91622 ( 1221) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 time to evaluate : 0.381 Fit side-chains REVERT: A 272 LEU cc_start: 0.8371 (mt) cc_final: 0.8117 (mm) REVERT: A 283 ARG cc_start: 0.7832 (ptp-110) cc_final: 0.7518 (mtm110) REVERT: A 347 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7600 (ttp80) REVERT: A 356 ARG cc_start: 0.7196 (mtm110) cc_final: 0.6981 (mtm110) REVERT: N 34 MET cc_start: 0.8468 (mmm) cc_final: 0.8082 (mmm) REVERT: N 39 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: N 46 GLU cc_start: 0.8214 (mp0) cc_final: 0.7928 (mp0) REVERT: N 95 TYR cc_start: 0.8456 (m-80) cc_final: 0.8195 (m-80) REVERT: P 3 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: R 146 ILE cc_start: 0.8838 (mt) cc_final: 0.8625 (mp) REVERT: R 167 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7669 (pp) REVERT: R 202 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7468 (tttp) REVERT: R 267 ARG cc_start: 0.7282 (tpt170) cc_final: 0.6338 (mpp80) REVERT: R 336 LYS cc_start: 0.7839 (mttp) cc_final: 0.7575 (mmtm) REVERT: R 376 ARG cc_start: 0.7684 (ptp-170) cc_final: 0.6965 (mtt90) REVERT: R 387 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5769 (mt-10) REVERT: B 42 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.6760 (ttm-80) REVERT: B 217 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7874 (pmm) REVERT: G 21 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.5023 (tmm) outliers start: 37 outliers final: 14 residues processed: 164 average time/residue: 0.6730 time to fit residues: 117.0766 Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 387 HIS N 31 ASN N 77 ASN R 47 GLN B 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147891 restraints weight = 10228.424| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.80 r_work: 0.3344 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9437 Z= 0.149 Angle : 0.597 8.071 12799 Z= 0.318 Chirality : 0.042 0.183 1412 Planarity : 0.004 0.062 1623 Dihedral : 5.466 38.868 1269 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.96 % Allowed : 15.04 % Favored : 81.00 % 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: -1.12 (0.24), residues: 1133 helix: 0.35 (0.25), residues: 433 sheet: -0.43 (0.32), residues: 242 loop : -1.96 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 44 TYR 0.021 0.001 TYR R 148 PHE 0.015 0.001 PHE N 108 TRP 0.019 0.001 TRP R 214 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9431) covalent geometry : angle 0.59128 (12787) SS BOND : bond 0.00561 ( 6) SS BOND : angle 2.83323 ( 12) hydrogen bonds : bond 0.04508 ( 424) hydrogen bonds : angle 4.61841 ( 1221) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8336 (mt) cc_final: 0.8106 (mp) REVERT: A 283 ARG cc_start: 0.7873 (ptp-110) cc_final: 0.7590 (mtm110) REVERT: A 356 ARG cc_start: 0.7155 (mtm110) cc_final: 0.6939 (mtm110) REVERT: A 386 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8173 (ttm) REVERT: N 34 MET cc_start: 0.8362 (mmm) cc_final: 0.8038 (mmm) REVERT: N 39 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: N 46 GLU cc_start: 0.8268 (mp0) cc_final: 0.7971 (mp0) REVERT: N 95 TYR cc_start: 0.8535 (m-80) cc_final: 0.8313 (m-80) REVERT: P 3 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: R 44 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8112 (ttp80) REVERT: R 146 ILE cc_start: 0.8822 (mt) cc_final: 0.8597 (mp) REVERT: R 167 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7600 (pp) REVERT: R 202 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7482 (tttp) REVERT: R 267 ARG cc_start: 0.7274 (tpt170) cc_final: 0.6373 (mpp80) REVERT: R 336 LYS cc_start: 0.7792 (mttp) cc_final: 0.7457 (mmtm) REVERT: R 348 ARG cc_start: 0.7402 (tpm-80) cc_final: 0.6262 (mtp180) REVERT: R 376 ARG cc_start: 0.7688 (ptp-170) cc_final: 0.7032 (mtt90) REVERT: R 387 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5902 (mt-10) REVERT: B 42 ARG cc_start: 0.7479 (ttp-110) cc_final: 0.6986 (ttm-80) REVERT: B 70 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8683 (pt) REVERT: B 171 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 217 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7757 (pmm) REVERT: G 21 MET cc_start: 0.5298 (tmt) cc_final: 0.4961 (tmm) outliers start: 39 outliers final: 16 residues processed: 173 average time/residue: 0.5864 time to fit residues: 107.7219 Evaluate side-chains 158 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 279 ASN N 77 ASN R 112 GLN R 394 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.187590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131562 restraints weight = 10281.406| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.67 r_work: 0.3265 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 9437 Z= 0.244 Angle : 0.662 9.421 12799 Z= 0.350 Chirality : 0.045 0.153 1412 Planarity : 0.005 0.062 1623 Dihedral : 5.513 36.603 1269 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.78 % Allowed : 16.87 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1133 helix: 0.60 (0.25), residues: 429 sheet: -0.34 (0.33), residues: 239 loop : -1.90 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 44 TYR 0.025 0.002 TYR R 148 PHE 0.020 0.002 PHE N 108 TRP 0.019 0.002 TRP R 214 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9431) covalent geometry : angle 0.66008 (12787) SS BOND : bond 0.00255 ( 6) SS BOND : angle 1.71152 ( 12) hydrogen bonds : bond 0.05199 ( 424) hydrogen bonds : angle 4.67981 ( 1221) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6290 (tt0) cc_final: 0.6051 (pt0) REVERT: A 272 LEU cc_start: 0.8332 (mt) cc_final: 0.8092 (mp) REVERT: A 283 ARG cc_start: 0.7768 (ptp-110) cc_final: 0.7436 (mtm110) REVERT: A 308 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7726 (tp) REVERT: A 347 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8053 (ttm170) REVERT: A 386 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (ttm) REVERT: N 34 MET cc_start: 0.8396 (mmm) cc_final: 0.8096 (mmm) REVERT: N 39 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: N 46 GLU cc_start: 0.8303 (mp0) cc_final: 0.8011 (mp0) REVERT: P 3 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6889 (mm-30) REVERT: R 44 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8155 (ttp80) REVERT: R 146 ILE cc_start: 0.8803 (mt) cc_final: 0.8553 (mp) REVERT: R 167 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7626 (pp) REVERT: R 267 ARG cc_start: 0.7258 (tpt170) cc_final: 0.6231 (mpp80) REVERT: R 303 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7870 (mtt) REVERT: R 336 LYS cc_start: 0.7737 (mttp) cc_final: 0.7325 (mmtm) REVERT: R 348 ARG cc_start: 0.7500 (tpm-80) cc_final: 0.6260 (mtp180) REVERT: R 376 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7082 (mmt90) REVERT: R 387 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.5970 (mt-10) REVERT: B 42 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7381 (tpt170) REVERT: B 70 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8813 (pt) REVERT: B 100 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8897 (p) REVERT: B 171 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8580 (mm) REVERT: B 217 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7690 (pmm) REVERT: B 239 ASN cc_start: 0.7683 (m-40) cc_final: 0.7464 (m110) REVERT: G 21 MET cc_start: 0.5132 (OUTLIER) cc_final: 0.4845 (tmm) outliers start: 47 outliers final: 23 residues processed: 169 average time/residue: 0.5953 time to fit residues: 106.7994 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 105 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 279 ASN N 77 ASN B 230 ASN B 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.189733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135907 restraints weight = 10166.805| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.51 r_work: 0.3319 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9437 Z= 0.126 Angle : 0.563 8.186 12799 Z= 0.300 Chirality : 0.041 0.154 1412 Planarity : 0.004 0.063 1623 Dihedral : 5.182 37.085 1269 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.46 % Allowed : 20.02 % Favored : 76.52 % 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: -0.52 (0.25), residues: 1133 helix: 0.95 (0.25), residues: 442 sheet: -0.11 (0.33), residues: 239 loop : -1.80 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 44 TYR 0.019 0.001 TYR N 95 PHE 0.016 0.001 PHE N 108 TRP 0.017 0.001 TRP R 214 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9431) covalent geometry : angle 0.56307 (12787) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.90308 ( 12) hydrogen bonds : bond 0.04166 ( 424) hydrogen bonds : angle 4.42751 ( 1221) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8272 (mt) cc_final: 0.8032 (mp) REVERT: A 283 ARG cc_start: 0.7648 (ptp-110) cc_final: 0.7274 (mtm110) REVERT: A 308 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7496 (mt) REVERT: A 331 ASP cc_start: 0.8099 (t0) cc_final: 0.7663 (t0) REVERT: A 347 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8017 (ttm170) REVERT: N 46 GLU cc_start: 0.8357 (mp0) cc_final: 0.7955 (mp0) REVERT: P 3 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: R 109 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8123 (mm) REVERT: R 146 ILE cc_start: 0.8755 (mt) cc_final: 0.8501 (mp) REVERT: R 202 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7381 (tttp) REVERT: R 267 ARG cc_start: 0.7250 (tpt170) cc_final: 0.6241 (mpp80) REVERT: R 336 LYS cc_start: 0.7700 (mttp) cc_final: 0.7303 (mmtm) REVERT: R 348 ARG cc_start: 0.7348 (tpm-80) cc_final: 0.6132 (mtp180) REVERT: R 376 ARG cc_start: 0.7493 (ptp-170) cc_final: 0.6837 (mmt90) REVERT: R 387 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.5918 (mt-10) REVERT: B 42 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7331 (tpt170) REVERT: B 70 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8634 (pt) REVERT: B 100 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (p) REVERT: B 217 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7699 (pmm) outliers start: 34 outliers final: 15 residues processed: 167 average time/residue: 0.5847 time to fit residues: 104.1539 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 45 GLN B 230 ASN B 239 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137464 restraints weight = 10211.102| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.43 r_work: 0.3314 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9437 Z= 0.146 Angle : 0.575 8.238 12799 Z= 0.304 Chirality : 0.042 0.154 1412 Planarity : 0.004 0.064 1623 Dihedral : 5.107 39.633 1269 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.47 % Allowed : 20.53 % Favored : 75.00 % 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: -0.34 (0.25), residues: 1133 helix: 1.16 (0.25), residues: 437 sheet: -0.01 (0.33), residues: 239 loop : -1.73 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.019 0.001 TYR N 95 PHE 0.019 0.001 PHE B 292 TRP 0.014 0.001 TRP R 214 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9431) covalent geometry : angle 0.57435 (12787) SS BOND : bond 0.00117 ( 6) SS BOND : angle 1.05782 ( 12) hydrogen bonds : bond 0.04280 ( 424) hydrogen bonds : angle 4.38467 ( 1221) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8348 (mt) cc_final: 0.8123 (mp) REVERT: A 283 ARG cc_start: 0.7777 (ptp-110) cc_final: 0.7428 (mtm110) REVERT: A 308 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7541 (mt) REVERT: A 331 ASP cc_start: 0.8132 (t0) cc_final: 0.7740 (t0) REVERT: A 347 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8086 (ttm170) REVERT: A 386 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8236 (ttm) REVERT: A 392 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: N 39 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: N 46 GLU cc_start: 0.8371 (mp0) cc_final: 0.8091 (mp0) REVERT: P 3 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6883 (mm-30) REVERT: R 41 GLU cc_start: 0.8448 (pp20) cc_final: 0.7839 (pp20) REVERT: R 68 GLU cc_start: 0.5407 (tt0) cc_final: 0.5095 (tt0) REVERT: R 146 ILE cc_start: 0.8772 (mt) cc_final: 0.8509 (mp) REVERT: R 202 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7457 (tttp) REVERT: R 267 ARG cc_start: 0.7293 (tpt170) cc_final: 0.6338 (mpp80) REVERT: R 303 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7785 (mtt) REVERT: R 336 LYS cc_start: 0.7739 (mttp) cc_final: 0.7356 (mmtm) REVERT: R 348 ARG cc_start: 0.7423 (tpm-80) cc_final: 0.6230 (mtp180) REVERT: R 376 ARG cc_start: 0.7413 (ptp-170) cc_final: 0.6784 (mmt90) REVERT: R 387 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5971 (mt-10) REVERT: B 42 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7169 (ttm-80) REVERT: B 70 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8669 (pt) REVERT: B 171 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 217 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7768 (pmm) REVERT: G 21 MET cc_start: 0.3731 (tmm) cc_final: 0.3454 (tpt) outliers start: 44 outliers final: 20 residues processed: 160 average time/residue: 0.6189 time to fit residues: 105.5243 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 45 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.191187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131931 restraints weight = 10189.898| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.26 r_work: 0.3299 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9437 Z= 0.161 Angle : 0.587 7.767 12799 Z= 0.310 Chirality : 0.042 0.176 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.138 45.739 1269 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.78 % Allowed : 20.63 % Favored : 74.59 % 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: -0.27 (0.25), residues: 1133 helix: 1.20 (0.25), residues: 443 sheet: -0.04 (0.33), residues: 241 loop : -1.69 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 44 TYR 0.019 0.001 TYR R 148 PHE 0.020 0.002 PHE N 108 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9431) covalent geometry : angle 0.58618 (12787) SS BOND : bond 0.00135 ( 6) SS BOND : angle 1.03486 ( 12) hydrogen bonds : bond 0.04366 ( 424) hydrogen bonds : angle 4.36946 ( 1221) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8354 (mt) cc_final: 0.8147 (mp) REVERT: A 283 ARG cc_start: 0.7806 (ptp-110) cc_final: 0.7442 (mtm110) REVERT: A 308 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7729 (tp) REVERT: A 331 ASP cc_start: 0.8106 (t0) cc_final: 0.7634 (t0) REVERT: A 347 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8105 (ttm170) REVERT: A 356 ARG cc_start: 0.7229 (mtm110) cc_final: 0.6992 (mtm110) REVERT: A 386 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8261 (ttm) REVERT: A 392 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: N 39 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7997 (tt0) REVERT: N 46 GLU cc_start: 0.8403 (mp0) cc_final: 0.8143 (mp0) REVERT: P 3 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: R 41 GLU cc_start: 0.8433 (pp20) cc_final: 0.7865 (pp20) REVERT: R 44 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8194 (ptp-110) REVERT: R 109 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7975 (mm) REVERT: R 146 ILE cc_start: 0.8773 (mt) cc_final: 0.8508 (mp) REVERT: R 202 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7467 (tttp) REVERT: R 267 ARG cc_start: 0.7303 (tpt170) cc_final: 0.6346 (mpp80) REVERT: R 336 LYS cc_start: 0.7775 (mttp) cc_final: 0.7473 (mmtm) REVERT: R 348 ARG cc_start: 0.7415 (tpm-80) cc_final: 0.6196 (mtp180) REVERT: R 376 ARG cc_start: 0.7454 (ptp-170) cc_final: 0.6833 (mmt90) REVERT: R 387 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5992 (mt-10) REVERT: R 418 GLU cc_start: 0.7289 (mm-30) cc_final: 0.7007 (tm-30) REVERT: B 42 ARG cc_start: 0.7673 (ttp-110) cc_final: 0.7201 (ttm-80) REVERT: B 70 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8694 (pt) REVERT: B 171 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8331 (mm) REVERT: B 217 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7804 (pmm) REVERT: G 21 MET cc_start: 0.3544 (tmm) cc_final: 0.3293 (tpt) outliers start: 47 outliers final: 21 residues processed: 163 average time/residue: 0.6383 time to fit residues: 110.8004 Evaluate side-chains 160 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 53 optimal weight: 0.0770 chunk 23 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.193873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139677 restraints weight = 10164.961| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.56 r_work: 0.3341 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9437 Z= 0.110 Angle : 0.545 7.692 12799 Z= 0.288 Chirality : 0.040 0.181 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.926 46.775 1269 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.35 % Allowed : 22.46 % Favored : 74.19 % 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: -0.08 (0.25), residues: 1133 helix: 1.40 (0.25), residues: 442 sheet: 0.04 (0.33), residues: 246 loop : -1.61 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 44 TYR 0.016 0.001 TYR N 95 PHE 0.014 0.001 PHE A 212 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9431) covalent geometry : angle 0.54424 (12787) SS BOND : bond 0.00096 ( 6) SS BOND : angle 0.86952 ( 12) hydrogen bonds : bond 0.03820 ( 424) hydrogen bonds : angle 4.19574 ( 1221) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 MET cc_start: 0.8229 (mmm) cc_final: 0.7258 (mtt) REVERT: A 272 LEU cc_start: 0.8332 (mt) cc_final: 0.8124 (mp) REVERT: A 283 ARG cc_start: 0.7703 (ptp-110) cc_final: 0.7349 (mtm110) REVERT: A 308 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7604 (mt) REVERT: A 331 ASP cc_start: 0.8082 (t0) cc_final: 0.7688 (t0) REVERT: A 343 ASP cc_start: 0.7350 (m-30) cc_final: 0.7005 (m-30) REVERT: A 347 ARG cc_start: 0.8297 (ttp80) cc_final: 0.7970 (ttm170) REVERT: A 356 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6916 (mtm110) REVERT: A 386 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8237 (ttm) REVERT: A 392 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: N 46 GLU cc_start: 0.8384 (mp0) cc_final: 0.8168 (mp0) REVERT: P 3 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: R 41 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7833 (pp20) REVERT: R 44 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8071 (ptp-110) REVERT: R 109 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8035 (mm) REVERT: R 146 ILE cc_start: 0.8758 (mt) cc_final: 0.8493 (mp) REVERT: R 202 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7470 (tttp) REVERT: R 233 MET cc_start: 0.8251 (tmm) cc_final: 0.8033 (ttt) REVERT: R 267 ARG cc_start: 0.7363 (tpt170) cc_final: 0.6397 (mpp80) REVERT: R 336 LYS cc_start: 0.7751 (mttp) cc_final: 0.7431 (mmtm) REVERT: R 348 ARG cc_start: 0.7409 (tpm-80) cc_final: 0.6206 (mtp180) REVERT: R 376 ARG cc_start: 0.7459 (ptp-170) cc_final: 0.6845 (mmt90) REVERT: R 387 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5971 (mt-10) REVERT: R 418 GLU cc_start: 0.7283 (mm-30) cc_final: 0.7053 (tm-30) REVERT: B 42 ARG cc_start: 0.7622 (ttp-110) cc_final: 0.7164 (ttm-80) REVERT: B 70 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8613 (pt) REVERT: B 186 ASP cc_start: 0.8364 (m-30) cc_final: 0.7686 (m-30) REVERT: B 217 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7842 (pmm) REVERT: G 21 MET cc_start: 0.3466 (tmm) cc_final: 0.3251 (tpt) outliers start: 33 outliers final: 19 residues processed: 159 average time/residue: 0.6261 time to fit residues: 106.1680 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 38 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.192408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.135263 restraints weight = 10115.057| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.64 r_work: 0.3316 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9437 Z= 0.125 Angle : 0.557 7.625 12799 Z= 0.295 Chirality : 0.041 0.172 1412 Planarity : 0.005 0.065 1623 Dihedral : 4.929 49.364 1269 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.35 % Allowed : 22.66 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.04 (0.25), residues: 1133 helix: 1.38 (0.25), residues: 449 sheet: 0.08 (0.33), residues: 246 loop : -1.59 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 197 TYR 0.017 0.001 TYR R 148 PHE 0.014 0.001 PHE N 108 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9431) covalent geometry : angle 0.55683 (12787) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.92459 ( 12) hydrogen bonds : bond 0.03888 ( 424) hydrogen bonds : angle 4.17085 ( 1221) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8159 (mmm) cc_final: 0.7237 (mtt) REVERT: A 272 LEU cc_start: 0.8278 (mt) cc_final: 0.8046 (mp) REVERT: A 283 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7258 (mtm110) REVERT: A 308 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 331 ASP cc_start: 0.8044 (t0) cc_final: 0.7624 (t0) REVERT: A 343 ASP cc_start: 0.7422 (m-30) cc_final: 0.7090 (m-30) REVERT: A 356 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6824 (mtm110) REVERT: A 386 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8178 (ttm) REVERT: A 392 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: N 46 GLU cc_start: 0.8384 (mp0) cc_final: 0.8108 (mp0) REVERT: P 3 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6820 (mm-30) REVERT: R 41 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7816 (pp20) REVERT: R 44 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8052 (ptp-110) REVERT: R 109 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8064 (mm) REVERT: R 146 ILE cc_start: 0.8727 (mt) cc_final: 0.8453 (mp) REVERT: R 202 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7402 (tttp) REVERT: R 267 ARG cc_start: 0.7299 (tpt170) cc_final: 0.6268 (mpp80) REVERT: R 336 LYS cc_start: 0.7714 (mttp) cc_final: 0.7373 (mmtm) REVERT: R 348 ARG cc_start: 0.7316 (tpm-80) cc_final: 0.6067 (mtp180) REVERT: R 376 ARG cc_start: 0.7432 (ptp-170) cc_final: 0.6793 (mmt90) REVERT: R 387 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5869 (mt-10) REVERT: R 418 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6952 (tm-30) REVERT: B 42 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7183 (ttm-80) REVERT: B 70 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8624 (pt) REVERT: B 186 ASP cc_start: 0.8327 (m-30) cc_final: 0.7658 (m-30) REVERT: B 217 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7777 (pmm) REVERT: G 21 MET cc_start: 0.3485 (tmm) cc_final: 0.3249 (tpt) outliers start: 33 outliers final: 19 residues processed: 154 average time/residue: 0.6251 time to fit residues: 102.5207 Evaluate side-chains 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain P residue 19 GLN Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.192265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132682 restraints weight = 10185.993| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.77 r_work: 0.3266 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9437 Z= 0.148 Angle : 0.581 7.594 12799 Z= 0.306 Chirality : 0.042 0.174 1412 Planarity : 0.005 0.067 1623 Dihedral : 5.009 53.787 1269 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.05 % Allowed : 22.97 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.01 (0.25), residues: 1133 helix: 1.44 (0.25), residues: 444 sheet: 0.07 (0.32), residues: 246 loop : -1.58 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 197 TYR 0.019 0.001 TYR R 148 PHE 0.033 0.002 PHE B 235 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9431) covalent geometry : angle 0.58062 (12787) SS BOND : bond 0.00147 ( 6) SS BOND : angle 0.98170 ( 12) hydrogen bonds : bond 0.04109 ( 424) hydrogen bonds : angle 4.22814 ( 1221) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8155 (mmm) cc_final: 0.7341 (mtt) REVERT: A 272 LEU cc_start: 0.8250 (mt) cc_final: 0.8008 (mp) REVERT: A 283 ARG cc_start: 0.7630 (ptp-110) cc_final: 0.7260 (mtm110) REVERT: A 308 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7564 (tp) REVERT: A 331 ASP cc_start: 0.8057 (t0) cc_final: 0.7628 (t0) REVERT: A 343 ASP cc_start: 0.7384 (m-30) cc_final: 0.7006 (m-30) REVERT: A 356 ARG cc_start: 0.7124 (mtm110) cc_final: 0.6825 (mtm110) REVERT: A 386 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8213 (ttm) REVERT: A 392 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: N 46 GLU cc_start: 0.8410 (mp0) cc_final: 0.8096 (mp0) REVERT: R 38 LYS cc_start: 0.8659 (mtmt) cc_final: 0.8435 (ttmt) REVERT: R 41 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7745 (pp20) REVERT: R 44 ARG cc_start: 0.8287 (ttp80) cc_final: 0.8060 (ptp-110) REVERT: R 109 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8115 (mm) REVERT: R 146 ILE cc_start: 0.8741 (mt) cc_final: 0.8455 (mp) REVERT: R 202 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7397 (tttp) REVERT: R 267 ARG cc_start: 0.7337 (tpt170) cc_final: 0.6283 (mpp80) REVERT: R 336 LYS cc_start: 0.7723 (mttp) cc_final: 0.7371 (mmtm) REVERT: R 348 ARG cc_start: 0.7333 (tpm-80) cc_final: 0.6061 (mtp180) REVERT: R 376 ARG cc_start: 0.7513 (ptp-170) cc_final: 0.6858 (mmt90) REVERT: R 387 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5908 (mt-10) REVERT: R 418 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6914 (tm-30) REVERT: B 42 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7345 (tpt170) REVERT: B 70 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8700 (pt) REVERT: B 186 ASP cc_start: 0.8352 (m-30) cc_final: 0.7672 (m-30) REVERT: B 217 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7774 (pmm) REVERT: G 21 MET cc_start: 0.3396 (tmm) cc_final: 0.3124 (tpt) outliers start: 30 outliers final: 20 residues processed: 148 average time/residue: 0.6029 time to fit residues: 94.9636 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 19 GLN Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 72 TRP Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 382 ILE Chi-restraints excluded: chain R residue 387 GLU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.1980 chunk 88 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.194120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138229 restraints weight = 10063.851| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.63 r_work: 0.3346 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9437 Z= 0.111 Angle : 0.549 7.824 12799 Z= 0.289 Chirality : 0.040 0.172 1412 Planarity : 0.004 0.066 1623 Dihedral : 4.885 56.932 1269 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.64 % Allowed : 23.48 % Favored : 73.88 % 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: 0.16 (0.25), residues: 1133 helix: 1.57 (0.25), residues: 444 sheet: 0.27 (0.33), residues: 241 loop : -1.51 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 134 TYR 0.016 0.001 TYR R 148 PHE 0.026 0.001 PHE B 235 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9431) covalent geometry : angle 0.54840 (12787) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.86619 ( 12) hydrogen bonds : bond 0.03646 ( 424) hydrogen bonds : angle 4.08244 ( 1221) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.14 seconds wall clock time: 58 minutes 56.36 seconds (3536.36 seconds total)