Starting phenix.real_space_refine on Sat Dec 28 22:24:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbi_31880/12_2024/7vbi_31880.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbi_31880/12_2024/7vbi_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_31880/12_2024/7vbi_31880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbi_31880/12_2024/7vbi_31880.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbi_31880/12_2024/7vbi_31880.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbi_31880/12_2024/7vbi_31880.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 5.58, per 1000 atoms: 0.61 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: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.01 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: 2.47 Time building geometry restraints manager: 3.05 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: 8.320 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: 1.260 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 23.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.120 ------------------------------------------------------------------------------- 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 9431 Z= 0.738 Angle : 1.125 12.808 12787 Z= 0.633 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.004 TRP R 72 HIS 0.020 0.003 HIS A 357 PHE 0.044 0.004 PHE N 108 TYR 0.027 0.003 TYR R 148 ARG 0.014 0.001 ARG B 8 *********************** 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 : 1.042 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: 0.6697 (mttt) REVERT: B 42 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7059 (ttm-80) outliers start: 8 outliers final: 4 residues processed: 177 average time/residue: 1.4519 time to fit residues: 273.8302 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 : 0.978 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.6980 chunk 84 optimal weight: 0.0570 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 279 ASN A 371 ASN N 1 GLN N 31 ASN N 77 ASN R 37 GLN 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9431 Z= 0.202 Angle : 0.608 8.982 12787 Z= 0.327 Chirality : 0.041 0.150 1412 Planarity : 0.005 0.062 1623 Dihedral : 5.867 50.026 1273 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.76 % Allowed : 13.72 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.23), residues: 1133 helix: -0.50 (0.24), residues: 433 sheet: -0.52 (0.32), residues: 242 loop : -2.04 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 214 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.022 0.001 TYR R 148 ARG 0.007 0.000 ARG A 283 *********************** 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 184 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.187 Fit side-chains REVERT: A 272 LEU cc_start: 0.8107 (mt) cc_final: 0.7852 (mm) REVERT: A 339 TYR cc_start: 0.8607 (m-80) cc_final: 0.8386 (m-80) REVERT: A 347 ARG cc_start: 0.7263 (ttp-170) cc_final: 0.7047 (ttp80) REVERT: N 34 MET cc_start: 0.8198 (mmm) cc_final: 0.7765 (mmm) REVERT: N 39 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: N 46 GLU cc_start: 0.7479 (mp0) cc_final: 0.7231 (mp0) REVERT: P 3 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6898 (mm-30) REVERT: R 146 ILE cc_start: 0.8770 (mt) cc_final: 0.8540 (mp) REVERT: R 167 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7703 (pp) REVERT: R 202 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7447 (tttp) REVERT: R 267 ARG cc_start: 0.7017 (tpt170) cc_final: 0.6327 (mpp80) REVERT: R 376 ARG cc_start: 0.7625 (ptp-170) cc_final: 0.6922 (mtt90) REVERT: R 387 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5572 (mt-10) REVERT: B 111 TYR cc_start: 0.8606 (m-80) cc_final: 0.8368 (m-10) REVERT: G 21 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.5173 (tmm) outliers start: 37 outliers final: 14 residues processed: 165 average time/residue: 1.3520 time to fit residues: 237.3799 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 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 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 37 GLN R 47 GLN R 394 GLN B 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 9431 Z= 0.339 Angle : 0.659 10.625 12787 Z= 0.350 Chirality : 0.044 0.193 1412 Planarity : 0.005 0.062 1623 Dihedral : 5.733 41.152 1269 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.07 % Allowed : 15.75 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1133 helix: 0.23 (0.24), residues: 434 sheet: -0.46 (0.32), residues: 240 loop : -1.99 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 214 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE N 108 TYR 0.025 0.002 TYR R 148 ARG 0.007 0.000 ARG R 44 *********************** 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 174 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8054 (mt) cc_final: 0.7822 (mp) REVERT: A 283 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7205 (mtm110) REVERT: A 308 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 339 TYR cc_start: 0.8703 (m-80) cc_final: 0.8444 (m-80) REVERT: A 386 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7587 (ttm) REVERT: N 34 MET cc_start: 0.8141 (mmm) cc_final: 0.7719 (mmm) REVERT: N 39 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: N 46 GLU cc_start: 0.7573 (mp0) cc_final: 0.7217 (mp0) REVERT: N 95 TYR cc_start: 0.8461 (m-80) cc_final: 0.8257 (m-80) REVERT: P 3 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6831 (mm-30) REVERT: R 44 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8149 (ttp80) REVERT: R 146 ILE cc_start: 0.8772 (mt) cc_final: 0.8540 (mp) REVERT: R 167 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7732 (pp) REVERT: R 202 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7459 (tttp) REVERT: R 267 ARG cc_start: 0.7022 (tpt170) cc_final: 0.6344 (mpp80) REVERT: R 348 ARG cc_start: 0.7534 (tpm-80) cc_final: 0.6378 (mtp180) REVERT: R 376 ARG cc_start: 0.7634 (ptp-170) cc_final: 0.7012 (mtt90) REVERT: R 387 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5563 (mt-10) REVERT: B 70 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8633 (pt) REVERT: B 111 TYR cc_start: 0.8599 (m-80) cc_final: 0.8359 (m-10) REVERT: B 171 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8491 (mm) REVERT: G 21 MET cc_start: 0.5508 (tmt) cc_final: 0.5180 (tmm) outliers start: 40 outliers final: 17 residues processed: 158 average time/residue: 1.3529 time to fit residues: 227.6380 Evaluate side-chains 156 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 283 ARG 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 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 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 76 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 37 GLN B 230 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9431 Z= 0.330 Angle : 0.633 8.905 12787 Z= 0.337 Chirality : 0.044 0.154 1412 Planarity : 0.005 0.062 1623 Dihedral : 5.542 39.214 1269 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.88 % Allowed : 16.67 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1133 helix: 0.53 (0.25), residues: 436 sheet: -0.15 (0.33), residues: 232 loop : -1.89 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 214 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.023 0.002 TYR R 148 ARG 0.005 0.000 ARG A 356 *********************** 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 191 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 143 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6253 (tt0) cc_final: 0.6033 (pt0) REVERT: A 272 LEU cc_start: 0.8162 (mt) cc_final: 0.7945 (mp) REVERT: A 283 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7236 (mtm110) REVERT: A 308 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7798 (tp) REVERT: A 339 TYR cc_start: 0.8694 (m-80) cc_final: 0.8421 (m-80) REVERT: A 386 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7528 (ttm) REVERT: N 34 MET cc_start: 0.8095 (mmm) cc_final: 0.7762 (mmm) REVERT: N 39 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7751 (tt0) REVERT: N 46 GLU cc_start: 0.7618 (mp0) cc_final: 0.7373 (mp0) REVERT: N 95 TYR cc_start: 0.8407 (m-80) cc_final: 0.8188 (m-80) REVERT: P 3 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: R 146 ILE cc_start: 0.8770 (mt) cc_final: 0.8526 (mp) REVERT: R 167 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7750 (pp) REVERT: R 202 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7485 (tttp) REVERT: R 267 ARG cc_start: 0.7028 (tpt170) cc_final: 0.6364 (mpp80) REVERT: R 303 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7454 (mtt) REVERT: R 348 ARG cc_start: 0.7541 (tpm-80) cc_final: 0.6371 (mtp180) REVERT: R 376 ARG cc_start: 0.7630 (ptp-170) cc_final: 0.7017 (mtt90) REVERT: R 387 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5744 (mt-10) REVERT: B 70 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8631 (pt) REVERT: B 100 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8843 (p) REVERT: B 111 TYR cc_start: 0.8600 (m-80) cc_final: 0.8358 (m-10) REVERT: B 171 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8348 (mm) REVERT: B 279 SER cc_start: 0.8678 (OUTLIER) cc_final: 0.8440 (t) REVERT: G 21 MET cc_start: 0.5393 (OUTLIER) cc_final: 0.5101 (tmm) outliers start: 48 outliers final: 19 residues processed: 174 average time/residue: 1.2248 time to fit residues: 227.8473 Evaluate side-chains 159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 283 ARG 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 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 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 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 279 SER 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 61 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN N 77 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9431 Z= 0.257 Angle : 0.603 8.497 12787 Z= 0.319 Chirality : 0.042 0.152 1412 Planarity : 0.004 0.063 1623 Dihedral : 5.383 43.172 1269 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.98 % Allowed : 18.90 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.24), residues: 1133 helix: 0.78 (0.25), residues: 442 sheet: 0.01 (0.33), residues: 232 loop : -1.80 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 214 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.002 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.006 0.000 ARG R 44 *********************** 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 176 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.894 Fit side-chains REVERT: A 272 LEU cc_start: 0.8148 (mt) cc_final: 0.7931 (mp) REVERT: A 283 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7196 (mtm110) REVERT: A 308 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 339 TYR cc_start: 0.8653 (m-80) cc_final: 0.8420 (m-80) REVERT: N 34 MET cc_start: 0.8044 (mmm) cc_final: 0.7716 (mmm) REVERT: N 39 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: N 46 GLU cc_start: 0.7625 (mp0) cc_final: 0.7273 (mp0) REVERT: P 3 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: R 44 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8184 (ptp-110) REVERT: R 109 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8024 (mm) REVERT: R 146 ILE cc_start: 0.8783 (mt) cc_final: 0.8548 (mp) REVERT: R 167 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7709 (pp) REVERT: R 202 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7476 (tttp) REVERT: R 267 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6370 (mpp80) REVERT: R 348 ARG cc_start: 0.7501 (tpm-80) cc_final: 0.6318 (mtp180) REVERT: R 376 ARG cc_start: 0.7622 (ptp-170) cc_final: 0.7018 (mtt90) REVERT: R 387 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5750 (mt-10) REVERT: B 70 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8547 (pt) REVERT: B 100 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8834 (p) REVERT: B 111 TYR cc_start: 0.8569 (m-80) cc_final: 0.8335 (m-10) REVERT: B 171 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8317 (mm) REVERT: G 21 MET cc_start: 0.5232 (OUTLIER) cc_final: 0.5029 (tmm) outliers start: 49 outliers final: 22 residues processed: 160 average time/residue: 1.2092 time to fit residues: 207.0992 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 372 ILE 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 100 VAL Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 198 ASP 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9431 Z= 0.197 Angle : 0.573 8.440 12787 Z= 0.303 Chirality : 0.041 0.165 1412 Planarity : 0.004 0.064 1623 Dihedral : 5.210 45.888 1269 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.78 % Allowed : 19.72 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.24), residues: 1133 helix: 1.01 (0.25), residues: 442 sheet: 0.18 (0.33), residues: 227 loop : -1.77 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 214 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.001 PHE N 108 TYR 0.017 0.001 TYR R 145 ARG 0.005 0.000 ARG A 356 *********************** 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 182 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7554 (tpp) REVERT: A 272 LEU cc_start: 0.8112 (mt) cc_final: 0.7894 (mp) REVERT: A 283 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7143 (mtm110) REVERT: A 308 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7705 (tp) REVERT: N 34 MET cc_start: 0.8033 (mmm) cc_final: 0.7708 (mmm) REVERT: N 46 GLU cc_start: 0.7609 (mp0) cc_final: 0.7263 (mp0) REVERT: P 3 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6759 (mm-30) REVERT: R 41 GLU cc_start: 0.8269 (pp20) cc_final: 0.7679 (pp20) REVERT: R 88 TYR cc_start: 0.7459 (p90) cc_final: 0.7245 (p90) REVERT: R 109 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8044 (mm) REVERT: R 146 ILE cc_start: 0.8759 (mt) cc_final: 0.8521 (mp) REVERT: R 267 ARG cc_start: 0.7035 (tpt170) cc_final: 0.6358 (mpp80) REVERT: R 303 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7290 (mtt) REVERT: R 348 ARG cc_start: 0.7486 (tpm-80) cc_final: 0.6333 (mtp180) REVERT: R 376 ARG cc_start: 0.7412 (ptp-170) cc_final: 0.6812 (mtt90) REVERT: R 387 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.5630 (mt-10) REVERT: B 57 LYS cc_start: 0.9206 (pttm) cc_final: 0.8976 (pttt) REVERT: B 70 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8520 (pt) REVERT: B 111 TYR cc_start: 0.8539 (m-80) cc_final: 0.8313 (m-10) REVERT: G 21 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.5094 (tmm) outliers start: 47 outliers final: 22 residues processed: 163 average time/residue: 1.2604 time to fit residues: 220.0677 Evaluate side-chains 155 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER 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 91 THR Chi-restraints excluded: chain P residue 3 GLU Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 47 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS 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 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 50.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 B 239 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9431 Z= 0.234 Angle : 0.582 8.474 12787 Z= 0.307 Chirality : 0.042 0.167 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.166 50.482 1269 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.27 % Allowed : 21.04 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1133 helix: 1.19 (0.25), residues: 442 sheet: 0.15 (0.33), residues: 234 loop : -1.71 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE N 108 TYR 0.018 0.001 TYR R 148 ARG 0.010 0.000 ARG R 44 *********************** 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 169 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8110 (mt) cc_final: 0.7897 (mp) REVERT: A 283 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7186 (mtm110) REVERT: A 308 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7732 (tp) REVERT: N 34 MET cc_start: 0.8090 (mmm) cc_final: 0.7782 (mmm) REVERT: N 46 GLU cc_start: 0.7623 (mp0) cc_final: 0.7367 (mp0) REVERT: P 3 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6719 (mm-30) REVERT: R 41 GLU cc_start: 0.8334 (pp20) cc_final: 0.7878 (pp20) REVERT: R 88 TYR cc_start: 0.7523 (p90) cc_final: 0.7245 (p90) REVERT: R 146 ILE cc_start: 0.8749 (mt) cc_final: 0.8474 (mp) REVERT: R 267 ARG cc_start: 0.7032 (tpt170) cc_final: 0.6354 (mpp80) REVERT: R 348 ARG cc_start: 0.7495 (tpm-80) cc_final: 0.6315 (mtp180) REVERT: R 376 ARG cc_start: 0.7394 (ptp-170) cc_final: 0.6803 (mtt90) REVERT: R 387 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5613 (mt-10) REVERT: B 57 LYS cc_start: 0.9205 (pttm) cc_final: 0.8948 (pttt) REVERT: B 70 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8519 (pt) outliers start: 42 outliers final: 23 residues processed: 155 average time/residue: 1.2954 time to fit residues: 214.4770 Evaluate side-chains 151 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER 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 17 SER 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 47 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS 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 181 THR Chi-restraints excluded: chain B residue 232 ILE 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 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9431 Z= 0.207 Angle : 0.584 8.243 12787 Z= 0.307 Chirality : 0.041 0.161 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.099 53.441 1269 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.56 % Allowed : 22.36 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1133 helix: 1.31 (0.25), residues: 442 sheet: 0.21 (0.33), residues: 229 loop : -1.64 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 33 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.018 0.001 TYR R 148 ARG 0.010 0.000 ARG A 356 *********************** 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 166 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8242 (mmm) cc_final: 0.7411 (mtt) REVERT: A 272 LEU cc_start: 0.8093 (mt) cc_final: 0.7888 (mp) REVERT: A 283 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7162 (mtm110) REVERT: N 34 MET cc_start: 0.8080 (mmm) cc_final: 0.7749 (mmm) REVERT: N 39 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: N 46 GLU cc_start: 0.7611 (mp0) cc_final: 0.7359 (mp0) REVERT: P 3 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6763 (mm-30) REVERT: R 41 GLU cc_start: 0.8333 (pp20) cc_final: 0.7871 (pp20) REVERT: R 44 ARG cc_start: 0.8619 (ttp80) cc_final: 0.8387 (ptp-110) REVERT: R 88 TYR cc_start: 0.7494 (p90) cc_final: 0.7251 (p90) REVERT: R 146 ILE cc_start: 0.8739 (mt) cc_final: 0.8483 (mp) REVERT: R 267 ARG cc_start: 0.7071 (tpt170) cc_final: 0.6422 (mpp80) REVERT: R 348 ARG cc_start: 0.7417 (tpm-80) cc_final: 0.6215 (mtp180) REVERT: R 376 ARG cc_start: 0.7397 (ptp-170) cc_final: 0.6815 (mtt90) REVERT: R 387 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5614 (mt-10) REVERT: B 57 LYS cc_start: 0.9192 (pttm) cc_final: 0.8967 (pttt) REVERT: B 70 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8511 (pt) REVERT: B 111 TYR cc_start: 0.8554 (m-80) cc_final: 0.8326 (m-10) REVERT: B 171 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8341 (mm) REVERT: G 21 MET cc_start: 0.3989 (tmm) cc_final: 0.3720 (tpt) outliers start: 35 outliers final: 21 residues processed: 154 average time/residue: 1.2982 time to fit residues: 213.0988 Evaluate side-chains 150 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER 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 47 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 382 ILE 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 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE 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 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 50.0000 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9431 Z= 0.192 Angle : 0.577 7.990 12787 Z= 0.305 Chirality : 0.041 0.187 1412 Planarity : 0.004 0.065 1623 Dihedral : 5.039 57.903 1269 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.25 % Allowed : 23.17 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1133 helix: 1.37 (0.25), residues: 442 sheet: 0.27 (0.33), residues: 229 loop : -1.59 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 33 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE N 108 TYR 0.017 0.001 TYR R 148 ARG 0.011 0.000 ARG A 356 *********************** 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 159 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8225 (mmm) cc_final: 0.7433 (mtt) REVERT: A 272 LEU cc_start: 0.8065 (mt) cc_final: 0.7855 (mp) REVERT: N 34 MET cc_start: 0.8076 (mmm) cc_final: 0.7745 (mmm) REVERT: N 39 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7684 (tt0) REVERT: N 46 GLU cc_start: 0.7607 (mp0) cc_final: 0.7332 (mp0) REVERT: P 3 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6749 (mm-30) REVERT: R 41 GLU cc_start: 0.8345 (pp20) cc_final: 0.7796 (pp20) REVERT: R 44 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8396 (ptp-110) REVERT: R 146 ILE cc_start: 0.8726 (mt) cc_final: 0.8462 (mp) REVERT: R 267 ARG cc_start: 0.7119 (tpt170) cc_final: 0.6444 (mpp80) REVERT: R 348 ARG cc_start: 0.7432 (tpm-80) cc_final: 0.6228 (mtp180) REVERT: R 376 ARG cc_start: 0.7424 (ptp-170) cc_final: 0.6846 (mtt90) REVERT: R 387 GLU cc_start: 0.6478 (OUTLIER) cc_final: 0.5617 (mt-10) REVERT: B 70 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8483 (pt) REVERT: B 111 TYR cc_start: 0.8554 (m-80) cc_final: 0.8333 (m-10) REVERT: G 21 MET cc_start: 0.3846 (tmm) cc_final: 0.3637 (tpt) outliers start: 32 outliers final: 22 residues processed: 149 average time/residue: 1.2560 time to fit residues: 199.9913 Evaluate side-chains 149 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 17 SER 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 47 GLN Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 382 ILE 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 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE 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 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9431 Z= 0.203 Angle : 0.586 7.713 12787 Z= 0.309 Chirality : 0.041 0.166 1412 Planarity : 0.004 0.065 1623 Dihedral : 4.979 56.248 1269 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.95 % Allowed : 23.88 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1133 helix: 1.43 (0.25), residues: 441 sheet: 0.27 (0.33), residues: 230 loop : -1.57 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP R 33 HIS 0.004 0.001 HIS A 357 PHE 0.025 0.001 PHE B 292 TYR 0.018 0.001 TYR R 148 ARG 0.015 0.000 ARG B 197 ********************** 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 154 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 60 MET cc_start: 0.8223 (mmm) cc_final: 0.7473 (mtt) REVERT: A 272 LEU cc_start: 0.8071 (mt) cc_final: 0.7865 (mp) REVERT: A 283 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7192 (mtm110) REVERT: A 343 ASP cc_start: 0.6833 (m-30) cc_final: 0.6461 (m-30) REVERT: N 34 MET cc_start: 0.8074 (mmm) cc_final: 0.7749 (mmm) REVERT: N 39 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: N 46 GLU cc_start: 0.7576 (mp0) cc_final: 0.7220 (mp0) REVERT: P 3 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: R 41 GLU cc_start: 0.8341 (pp20) cc_final: 0.7733 (pp20) REVERT: R 146 ILE cc_start: 0.8734 (mt) cc_final: 0.8471 (mp) REVERT: R 267 ARG cc_start: 0.7111 (tpt170) cc_final: 0.6444 (mpp80) REVERT: R 348 ARG cc_start: 0.7438 (tpm-80) cc_final: 0.6235 (mtp180) REVERT: R 387 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5610 (mt-10) REVERT: B 70 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8464 (pt) REVERT: B 111 TYR cc_start: 0.8571 (m-80) cc_final: 0.8349 (m-10) outliers start: 29 outliers final: 23 residues processed: 146 average time/residue: 1.3619 time to fit residues: 213.2743 Evaluate side-chains 147 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 283 ARG Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain N residue 17 SER 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 47 GLN Chi-restraints excluded: chain R residue 105 THR 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 382 ILE 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 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 232 ILE 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: 0.5980 chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.192085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137864 restraints weight = 10145.283| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.50 r_work: 0.3314 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9431 Z= 0.206 Angle : 0.580 7.668 12787 Z= 0.306 Chirality : 0.041 0.178 1412 Planarity : 0.005 0.066 1623 Dihedral : 4.881 48.444 1269 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.85 % Allowed : 24.09 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1133 helix: 1.39 (0.25), residues: 449 sheet: 0.26 (0.33), residues: 230 loop : -1.54 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP R 33 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE B 292 TYR 0.018 0.001 TYR R 148 ARG 0.015 0.001 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3730.17 seconds wall clock time: 68 minutes 10.76 seconds (4090.76 seconds total)