Starting phenix.real_space_refine on Wed Mar 12 12:56:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cx2_30489/03_2025/7cx2_30489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cx2_30489/03_2025/7cx2_30489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cx2_30489/03_2025/7cx2_30489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cx2_30489/03_2025/7cx2_30489.map" model { file = "/net/cci-nas-00/data/ceres_data/7cx2_30489/03_2025/7cx2_30489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cx2_30489/03_2025/7cx2_30489.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 52 5.16 5 C 5027 2.51 5 N 1374 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2027 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.21, per 1000 atoms: 0.66 Number of scatterers: 7930 At special positions: 0 Unit cell: (77.064, 110.526, 125.736, 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 52 16.00 O 1477 8.00 N 1374 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.2 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'R' and resid 26 through 46 removed outlier: 3.910A pdb=" N VAL R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 83 removed outlier: 3.859A pdb=" N GLU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 94 removed outlier: 3.933A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 140 Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.685A pdb=" N VAL R 148 " --> pdb=" O TYR R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 171 through 174 Processing helix chain 'R' and resid 195 through 228 Processing helix chain 'R' and resid 258 through 277 removed outlier: 3.661A pdb=" N SER R 277 " --> pdb=" O PHE R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 284 removed outlier: 4.037A pdb=" N THR R 281 " --> pdb=" O SER R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 317 removed outlier: 3.821A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 305 " --> pdb=" O LEU R 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 319 through 330 Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.663A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.296A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.549A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.339A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.902A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.899A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.001A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.681A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.056A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.982A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.675A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.733A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.630A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.873A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.929A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.590A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.623A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.822A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1125 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: 2.37 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2222 1.44 - 1.57: 4495 1.57 - 1.70: 2 1.70 - 1.83: 74 Bond restraints: 8086 Sorted by residual: bond pdb=" C8 P2E R 401 " pdb=" C9 P2E R 401 " ideal model delta sigma weight residual 1.515 1.436 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C11 P2E R 401 " pdb=" O4 P2E R 401 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 P2E R 401 " pdb=" C11 P2E R 401 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.529 1.576 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C12 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.538 1.498 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 10881 2.97 - 5.95: 70 5.95 - 8.92: 7 8.92 - 11.89: 1 11.89 - 14.87: 4 Bond angle restraints: 10963 Sorted by residual: angle pdb=" N VAL R 156 " pdb=" CA VAL R 156 " pdb=" C VAL R 156 " ideal model delta sigma weight residual 110.62 116.74 -6.12 1.02e+00 9.61e-01 3.59e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C4 P2E R 401 " pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " ideal model delta sigma weight residual 127.52 112.65 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " pdb=" C7 P2E R 401 " ideal model delta sigma weight residual 125.83 111.98 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.71 116.83 -5.12 1.15e+00 7.56e-01 1.98e+01 ... (remaining 10958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4337 16.25 - 32.49: 395 32.49 - 48.74: 83 48.74 - 64.98: 17 64.98 - 81.23: 9 Dihedral angle restraints: 4841 sinusoidal: 1870 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -4.97 -81.03 1 1.00e+01 1.00e-02 8.10e+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 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.119: 206 0.119 - 0.178: 19 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C15 P2E R 401 " pdb=" C14 P2E R 401 " pdb=" C16 P2E R 401 " pdb=" O5 P2E R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.52 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 P2E R 401 " pdb=" C12 P2E R 401 " pdb=" C7 P2E R 401 " pdb=" C9 P2E R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 390 " pdb=" N GLN A 390 " pdb=" C GLN A 390 " pdb=" CB GLN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1249 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " -0.269 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C13 P2E R 401 " 0.249 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " 0.296 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 388 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.028 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C5 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " -0.028 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 93 2.65 - 3.21: 7115 3.21 - 3.78: 11836 3.78 - 4.34: 17133 4.34 - 4.90: 28054 Nonbonded interactions: 64231 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR R 82 " pdb=" O HOH R 501 " model vdw 2.133 3.040 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.247 3.120 nonbonded pdb=" O GLU A 50 " pdb=" NH2 ARG A 265 " model vdw 2.276 3.120 nonbonded pdb=" O LEU R 304 " pdb=" ND2 ASN R 307 " model vdw 2.280 3.120 ... (remaining 64226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.880 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:70.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.004 0.079 8086 Z= 0.283 Angle : 0.712 14.865 10963 Z= 0.396 Chirality : 0.047 0.297 1252 Planarity : 0.009 0.273 1402 Dihedral : 13.642 81.229 2908 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % 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: -2.13 (0.23), residues: 1002 helix: -0.55 (0.24), residues: 371 sheet: -0.79 (0.32), residues: 210 loop : -2.51 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.024 0.002 TYR B 59 ARG 0.007 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7395 (t80) cc_final: 0.6912 (t80) REVERT: R 116 MET cc_start: 0.7244 (tpp) cc_final: 0.6897 (tpp) REVERT: R 124 MET cc_start: 0.8306 (tpp) cc_final: 0.8033 (tpt) REVERT: R 126 MET cc_start: 0.8307 (tpt) cc_final: 0.8107 (tpt) REVERT: R 282 ILE cc_start: 0.8561 (tt) cc_final: 0.8311 (pt) REVERT: A 20 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6757 (tpp80) REVERT: A 24 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7567 (ttmm) REVERT: B 23 LYS cc_start: 0.8989 (tttp) cc_final: 0.8746 (ttpp) REVERT: B 32 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8284 (tp-100) REVERT: N 12 VAL cc_start: 0.9235 (p) cc_final: 0.9015 (m) REVERT: N 105 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7787 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 1.3636 time to fit residues: 246.6574 Evaluate side-chains 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 0.1980 chunk 41 optimal weight: 0.0020 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.0000 chunk 89 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 213 GLN B 17 GLN B 175 GLN B 176 GLN N 35 ASN N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105724 restraints weight = 9584.498| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.59 r_work: 0.3148 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8086 Z= 0.183 Angle : 0.548 7.752 10963 Z= 0.283 Chirality : 0.042 0.140 1252 Planarity : 0.004 0.054 1402 Dihedral : 5.541 54.988 1140 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.03 % Allowed : 13.47 % Favored : 84.51 % 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: -0.67 (0.25), residues: 1002 helix: 1.10 (0.27), residues: 382 sheet: -0.37 (0.33), residues: 211 loop : -2.01 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE R 119 TYR 0.011 0.001 TYR B 124 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: R 228 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.6636 (mtp85) REVERT: R 278 LEU cc_start: 0.7753 (mt) cc_final: 0.7478 (mt) REVERT: R 282 ILE cc_start: 0.8429 (tt) cc_final: 0.8110 (pt) REVERT: A 20 ARG cc_start: 0.7114 (mtp85) cc_final: 0.6864 (tpp80) REVERT: A 24 LYS cc_start: 0.7704 (ttpp) cc_final: 0.7125 (ttmm) REVERT: A 220 HIS cc_start: 0.8018 (m170) cc_final: 0.7515 (m-70) REVERT: A 318 TYR cc_start: 0.7076 (t80) cc_final: 0.6645 (t80) REVERT: A 356 ARG cc_start: 0.8385 (pmm-80) cc_final: 0.8180 (pmm-80) REVERT: B 23 LYS cc_start: 0.8532 (tttp) cc_final: 0.8210 (ttpp) REVERT: B 32 GLN cc_start: 0.8766 (tp-100) cc_final: 0.8546 (tp-100) REVERT: B 160 SER cc_start: 0.8915 (m) cc_final: 0.8457 (p) REVERT: B 170 ASP cc_start: 0.8033 (t0) cc_final: 0.7767 (t0) REVERT: B 175 GLN cc_start: 0.8775 (mt0) cc_final: 0.8541 (pt0) REVERT: B 217 MET cc_start: 0.8303 (ptm) cc_final: 0.7795 (pp-130) REVERT: B 259 GLN cc_start: 0.8165 (pt0) cc_final: 0.7928 (pt0) REVERT: N 73 ASP cc_start: 0.7026 (t70) cc_final: 0.6080 (p0) REVERT: N 78 THR cc_start: 0.8752 (m) cc_final: 0.8290 (m) REVERT: N 89 GLU cc_start: 0.9105 (mp0) cc_final: 0.8899 (mp0) REVERT: N 105 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7719 (mtm-85) outliers start: 17 outliers final: 6 residues processed: 153 average time/residue: 1.4210 time to fit residues: 228.5176 Evaluate side-chains 137 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN A 29 GLN B 9 GLN B 13 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105833 restraints weight = 9783.674| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.62 r_work: 0.3159 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 : 0.003 0.026 8086 Z= 0.173 Angle : 0.515 7.413 10963 Z= 0.266 Chirality : 0.041 0.140 1252 Planarity : 0.004 0.057 1402 Dihedral : 5.474 57.889 1140 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.62 % Allowed : 15.73 % Favored : 81.64 % 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: -0.05 (0.26), residues: 1002 helix: 1.70 (0.28), residues: 382 sheet: -0.19 (0.33), residues: 211 loop : -1.67 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.010 0.001 TYR B 124 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: R 116 MET cc_start: 0.7044 (tpp) cc_final: 0.6520 (tpp) REVERT: R 228 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6727 (mtp85) REVERT: R 282 ILE cc_start: 0.8393 (tt) cc_final: 0.8063 (pt) REVERT: A 20 ARG cc_start: 0.7014 (mtp85) cc_final: 0.6764 (tpp80) REVERT: A 24 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7092 (ttmm) REVERT: A 27 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 314 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 356 ARG cc_start: 0.8435 (pmm-80) cc_final: 0.8233 (pmm-80) REVERT: B 19 ARG cc_start: 0.7165 (ttm110) cc_final: 0.6824 (ttm110) REVERT: B 23 LYS cc_start: 0.8614 (tttp) cc_final: 0.8233 (ttpp) REVERT: B 32 GLN cc_start: 0.8801 (tp-100) cc_final: 0.8428 (tp40) REVERT: B 160 SER cc_start: 0.8886 (m) cc_final: 0.8499 (p) REVERT: B 170 ASP cc_start: 0.8021 (t0) cc_final: 0.7750 (t0) REVERT: B 260 GLU cc_start: 0.8591 (pt0) cc_final: 0.8019 (pt0) REVERT: B 266 HIS cc_start: 0.8425 (t70) cc_final: 0.8224 (t70) REVERT: G 17 GLU cc_start: 0.8215 (tp30) cc_final: 0.7986 (tp30) REVERT: N 73 ASP cc_start: 0.6981 (t70) cc_final: 0.6040 (p0) REVERT: N 78 THR cc_start: 0.8725 (m) cc_final: 0.8254 (m) REVERT: N 86 LEU cc_start: 0.9102 (mp) cc_final: 0.8873 (mp) REVERT: N 89 GLU cc_start: 0.9120 (mp0) cc_final: 0.8913 (mp0) REVERT: N 105 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7708 (mtm-85) outliers start: 22 outliers final: 9 residues processed: 151 average time/residue: 1.3413 time to fit residues: 213.2450 Evaluate side-chains 140 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103239 restraints weight = 9797.595| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.59 r_work: 0.3114 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8086 Z= 0.259 Angle : 0.550 10.295 10963 Z= 0.281 Chirality : 0.042 0.175 1252 Planarity : 0.004 0.056 1402 Dihedral : 5.468 53.815 1140 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.34 % Allowed : 16.33 % Favored : 80.33 % 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: 0.18 (0.27), residues: 1002 helix: 1.86 (0.28), residues: 383 sheet: -0.10 (0.33), residues: 217 loop : -1.50 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE A 212 TYR 0.013 0.001 TYR B 105 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7180 (t80) cc_final: 0.6838 (t80) REVERT: R 116 MET cc_start: 0.7008 (tpp) cc_final: 0.6542 (tpt) REVERT: R 228 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6899 (mtp85) REVERT: R 282 ILE cc_start: 0.8399 (tt) cc_final: 0.8087 (pt) REVERT: A 20 ARG cc_start: 0.7200 (mtp85) cc_final: 0.6940 (tpp80) REVERT: A 24 LYS cc_start: 0.7699 (ttpp) cc_final: 0.7169 (ttmm) REVERT: A 220 HIS cc_start: 0.8032 (m170) cc_final: 0.7650 (m-70) REVERT: A 314 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 19 ARG cc_start: 0.7270 (ttm110) cc_final: 0.6992 (ttm110) REVERT: B 23 LYS cc_start: 0.8637 (tttp) cc_final: 0.8246 (ttpp) REVERT: B 32 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8407 (tp-100) REVERT: B 46 ARG cc_start: 0.8325 (ptp-110) cc_final: 0.7608 (mtt90) REVERT: B 214 ARG cc_start: 0.7681 (mpt180) cc_final: 0.7366 (mpt180) REVERT: B 260 GLU cc_start: 0.8624 (pt0) cc_final: 0.8036 (pt0) REVERT: B 266 HIS cc_start: 0.8450 (t70) cc_final: 0.8230 (t70) REVERT: G 17 GLU cc_start: 0.8343 (tp30) cc_final: 0.8108 (tp30) REVERT: N 89 GLU cc_start: 0.9111 (mp0) cc_final: 0.8895 (mp0) REVERT: N 105 ARG cc_start: 0.8322 (mtp180) cc_final: 0.7698 (mtm-85) outliers start: 28 outliers final: 13 residues processed: 147 average time/residue: 1.3521 time to fit residues: 209.2854 Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN B 340 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103783 restraints weight = 9716.567| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.57 r_work: 0.3095 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8086 Z= 0.210 Angle : 0.531 7.922 10963 Z= 0.274 Chirality : 0.042 0.144 1252 Planarity : 0.004 0.056 1402 Dihedral : 5.311 52.391 1140 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.34 % Allowed : 17.76 % Favored : 78.90 % 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: 0.35 (0.27), residues: 1002 helix: 1.99 (0.28), residues: 382 sheet: -0.01 (0.33), residues: 217 loop : -1.40 (0.28), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.030 0.001 PHE R 119 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7133 (t80) cc_final: 0.6752 (t80) REVERT: R 116 MET cc_start: 0.7049 (tpp) cc_final: 0.6584 (tpp) REVERT: R 228 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6865 (mtp85) REVERT: R 282 ILE cc_start: 0.8434 (tt) cc_final: 0.8162 (pt) REVERT: A 20 ARG cc_start: 0.7169 (mtp85) cc_final: 0.6925 (tpp80) REVERT: A 24 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7246 (ttmm) REVERT: A 220 HIS cc_start: 0.8013 (m170) cc_final: 0.7636 (m-70) REVERT: A 314 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 19 ARG cc_start: 0.7334 (ttm110) cc_final: 0.7044 (ttm110) REVERT: B 23 LYS cc_start: 0.8680 (tttp) cc_final: 0.8272 (ttpp) REVERT: B 32 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8378 (tp-100) REVERT: B 46 ARG cc_start: 0.8406 (ptp-110) cc_final: 0.7776 (mpp-170) REVERT: B 170 ASP cc_start: 0.8118 (t0) cc_final: 0.7883 (t0) REVERT: B 214 ARG cc_start: 0.7758 (mpt180) cc_final: 0.7388 (mpt180) REVERT: B 260 GLU cc_start: 0.8628 (pt0) cc_final: 0.8069 (pt0) REVERT: N 89 GLU cc_start: 0.9130 (mp0) cc_final: 0.8911 (mp0) REVERT: N 105 ARG cc_start: 0.8362 (mtp180) cc_final: 0.7751 (mtm-85) outliers start: 28 outliers final: 15 residues processed: 148 average time/residue: 1.3765 time to fit residues: 214.3663 Evaluate side-chains 140 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS R 307 ASN B 17 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105392 restraints weight = 9710.833| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.59 r_work: 0.3127 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8086 Z= 0.164 Angle : 0.516 9.209 10963 Z= 0.263 Chirality : 0.041 0.141 1252 Planarity : 0.004 0.056 1402 Dihedral : 4.939 49.748 1140 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.22 % Allowed : 18.12 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.27), residues: 1002 helix: 2.11 (0.28), residues: 382 sheet: 0.04 (0.33), residues: 223 loop : -1.28 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.035 0.001 PHE R 119 TYR 0.010 0.001 TYR N 80 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7137 (t80) cc_final: 0.6814 (t80) REVERT: R 116 MET cc_start: 0.6981 (tpp) cc_final: 0.6425 (tpt) REVERT: R 228 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6795 (mtp85) REVERT: R 278 LEU cc_start: 0.7755 (mt) cc_final: 0.7437 (mt) REVERT: R 282 ILE cc_start: 0.8414 (tt) cc_final: 0.8134 (pt) REVERT: A 20 ARG cc_start: 0.7138 (mtp85) cc_final: 0.6900 (tpp80) REVERT: A 24 LYS cc_start: 0.7712 (ttpp) cc_final: 0.7151 (ttmm) REVERT: A 27 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7421 (mm-30) REVERT: A 314 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7733 (tm-30) REVERT: A 356 ARG cc_start: 0.8449 (pmm-80) cc_final: 0.8102 (ptp-170) REVERT: B 19 ARG cc_start: 0.7263 (ttm110) cc_final: 0.6946 (ttm110) REVERT: B 32 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8397 (tp-100) REVERT: B 46 ARG cc_start: 0.8383 (ptp-110) cc_final: 0.7647 (mtt90) REVERT: B 214 ARG cc_start: 0.7837 (mpt180) cc_final: 0.7434 (mpt180) REVERT: B 234 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: B 260 GLU cc_start: 0.8559 (pt0) cc_final: 0.8004 (pt0) REVERT: N 86 LEU cc_start: 0.9117 (mp) cc_final: 0.8883 (mp) REVERT: N 89 GLU cc_start: 0.9119 (mp0) cc_final: 0.8907 (mp0) REVERT: N 105 ARG cc_start: 0.8344 (mtp180) cc_final: 0.7722 (mtm-85) outliers start: 27 outliers final: 17 residues processed: 145 average time/residue: 1.3193 time to fit residues: 201.4743 Evaluate side-chains 144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 ARG Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 73 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS B 266 HIS N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103533 restraints weight = 9691.228| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.59 r_work: 0.3117 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8086 Z= 0.263 Angle : 0.548 8.758 10963 Z= 0.281 Chirality : 0.042 0.146 1252 Planarity : 0.004 0.054 1402 Dihedral : 4.701 41.188 1140 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.98 % Allowed : 19.43 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.27), residues: 1002 helix: 2.09 (0.28), residues: 383 sheet: 0.12 (0.33), residues: 217 loop : -1.27 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.001 PHE R 119 TYR 0.013 0.001 TYR B 105 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7103 (t80) cc_final: 0.6754 (t80) REVERT: R 116 MET cc_start: 0.6954 (tpp) cc_final: 0.6411 (tpp) REVERT: R 130 MET cc_start: 0.7555 (ttm) cc_final: 0.7349 (mtm) REVERT: R 282 ILE cc_start: 0.8400 (tt) cc_final: 0.8113 (pt) REVERT: A 20 ARG cc_start: 0.7081 (mtp85) cc_final: 0.6840 (tpp80) REVERT: A 24 LYS cc_start: 0.7680 (ttpp) cc_final: 0.7157 (ttmm) REVERT: A 220 HIS cc_start: 0.8004 (m170) cc_final: 0.7743 (m-70) REVERT: A 314 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7739 (tm-30) REVERT: A 356 ARG cc_start: 0.8446 (pmm-80) cc_final: 0.8048 (pmm-80) REVERT: B 32 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8387 (tp-100) REVERT: B 46 ARG cc_start: 0.8302 (ptp-110) cc_final: 0.7482 (mtt90) REVERT: B 111 TYR cc_start: 0.8985 (m-80) cc_final: 0.8682 (m-80) REVERT: B 214 ARG cc_start: 0.7845 (mpt180) cc_final: 0.7454 (mpt180) REVERT: B 234 PHE cc_start: 0.9241 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: B 260 GLU cc_start: 0.8546 (pt0) cc_final: 0.7966 (pt0) REVERT: N 86 LEU cc_start: 0.9084 (mp) cc_final: 0.8828 (mp) REVERT: N 89 GLU cc_start: 0.9105 (mp0) cc_final: 0.8885 (mp0) REVERT: N 105 ARG cc_start: 0.8284 (mtp180) cc_final: 0.7676 (mtm-85) outliers start: 25 outliers final: 15 residues processed: 147 average time/residue: 1.3865 time to fit residues: 214.7961 Evaluate side-chains 145 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104727 restraints weight = 9713.509| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.61 r_work: 0.3092 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8086 Z= 0.196 Angle : 0.529 9.297 10963 Z= 0.269 Chirality : 0.041 0.147 1252 Planarity : 0.004 0.051 1402 Dihedral : 4.515 37.328 1140 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.98 % Allowed : 19.67 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.27), residues: 1002 helix: 2.18 (0.28), residues: 382 sheet: 0.11 (0.33), residues: 218 loop : -1.22 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.022 0.001 PHE R 119 TYR 0.012 0.001 TYR R 161 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7146 (t80) cc_final: 0.6811 (t80) REVERT: R 116 MET cc_start: 0.6979 (tpp) cc_final: 0.6448 (tpp) REVERT: R 228 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6804 (mtp85) REVERT: R 278 LEU cc_start: 0.7676 (mt) cc_final: 0.7344 (mt) REVERT: R 282 ILE cc_start: 0.8379 (tt) cc_final: 0.8099 (pt) REVERT: A 20 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6853 (tpp80) REVERT: A 24 LYS cc_start: 0.7695 (ttpp) cc_final: 0.7176 (ttmm) REVERT: A 220 HIS cc_start: 0.7957 (m170) cc_final: 0.7702 (m-70) REVERT: A 314 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 356 ARG cc_start: 0.8486 (pmm-80) cc_final: 0.7998 (pmm-80) REVERT: B 19 ARG cc_start: 0.7136 (ttm110) cc_final: 0.6859 (ttm110) REVERT: B 32 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8395 (tp-100) REVERT: B 46 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.7601 (mtt90) REVERT: B 111 TYR cc_start: 0.9003 (m-80) cc_final: 0.8724 (m-80) REVERT: B 214 ARG cc_start: 0.7886 (mpt180) cc_final: 0.7516 (mpt180) REVERT: B 234 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: N 86 LEU cc_start: 0.9071 (mp) cc_final: 0.8823 (mp) REVERT: N 88 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.9170 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9113 (mp0) cc_final: 0.8677 (mp0) REVERT: N 105 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7687 (mtm-85) outliers start: 25 outliers final: 20 residues processed: 148 average time/residue: 1.3720 time to fit residues: 213.4648 Evaluate side-chains 154 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 40.0000 chunk 80 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS A 29 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104554 restraints weight = 9856.928| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.59 r_work: 0.3102 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8086 Z= 0.189 Angle : 0.529 9.273 10963 Z= 0.269 Chirality : 0.041 0.143 1252 Planarity : 0.004 0.050 1402 Dihedral : 4.427 31.355 1140 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.62 % Allowed : 20.14 % Favored : 77.23 % 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: 0.63 (0.27), residues: 1002 helix: 2.18 (0.28), residues: 383 sheet: 0.15 (0.33), residues: 217 loop : -1.20 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.024 0.001 PHE R 119 TYR 0.011 0.001 TYR R 161 ARG 0.006 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7208 (t80) cc_final: 0.6868 (t80) REVERT: R 116 MET cc_start: 0.7032 (tpp) cc_final: 0.6497 (tpp) REVERT: R 228 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6860 (mtp85) REVERT: R 278 LEU cc_start: 0.7764 (mt) cc_final: 0.7444 (mt) REVERT: R 282 ILE cc_start: 0.8536 (tt) cc_final: 0.8280 (pt) REVERT: A 20 ARG cc_start: 0.7151 (mtp85) cc_final: 0.6911 (tpp80) REVERT: A 24 LYS cc_start: 0.7759 (ttpp) cc_final: 0.7242 (ttmm) REVERT: A 220 HIS cc_start: 0.7986 (m170) cc_final: 0.7731 (m-70) REVERT: A 314 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7876 (tm-30) REVERT: A 356 ARG cc_start: 0.8513 (pmm-80) cc_final: 0.7918 (pmm-80) REVERT: B 19 ARG cc_start: 0.7232 (ttm110) cc_final: 0.6953 (ttm110) REVERT: B 32 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8392 (tp-100) REVERT: B 46 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.7665 (mtt90) REVERT: B 111 TYR cc_start: 0.9058 (m-80) cc_final: 0.8793 (m-80) REVERT: B 214 ARG cc_start: 0.7937 (mpt180) cc_final: 0.7565 (mpt180) REVERT: B 234 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: N 86 LEU cc_start: 0.9122 (mp) cc_final: 0.8881 (mp) REVERT: N 88 PRO cc_start: 0.9473 (Cg_exo) cc_final: 0.9213 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9107 (mp0) cc_final: 0.8670 (mp0) REVERT: N 105 ARG cc_start: 0.8322 (mtp180) cc_final: 0.7737 (mtm-85) outliers start: 22 outliers final: 16 residues processed: 141 average time/residue: 1.3608 time to fit residues: 202.0425 Evaluate side-chains 146 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 0.0050 chunk 55 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS R 307 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.157701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106956 restraints weight = 9618.933| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.59 r_work: 0.3170 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8086 Z= 0.143 Angle : 0.519 11.613 10963 Z= 0.260 Chirality : 0.040 0.138 1252 Planarity : 0.004 0.051 1402 Dihedral : 4.207 28.433 1140 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.38 % Allowed : 20.14 % Favored : 77.47 % 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: 0.82 (0.27), residues: 1002 helix: 2.45 (0.28), residues: 376 sheet: 0.05 (0.33), residues: 219 loop : -1.02 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.024 0.001 PHE R 119 TYR 0.012 0.001 TYR R 161 ARG 0.006 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7231 (t80) cc_final: 0.6892 (t80) REVERT: R 116 MET cc_start: 0.7032 (tpp) cc_final: 0.6548 (tpt) REVERT: R 130 MET cc_start: 0.7475 (ttm) cc_final: 0.7270 (mtm) REVERT: R 228 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6796 (mtp85) REVERT: R 278 LEU cc_start: 0.7630 (mt) cc_final: 0.7291 (mt) REVERT: R 282 ILE cc_start: 0.8514 (tt) cc_final: 0.8248 (pt) REVERT: A 24 LYS cc_start: 0.7686 (ttpp) cc_final: 0.7151 (ttmm) REVERT: A 27 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 220 HIS cc_start: 0.7764 (m170) cc_final: 0.7513 (m-70) REVERT: A 314 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 356 ARG cc_start: 0.8341 (pmm-80) cc_final: 0.7744 (pmm-80) REVERT: B 19 ARG cc_start: 0.7101 (ttm110) cc_final: 0.6787 (ttm110) REVERT: B 32 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8374 (tp-100) REVERT: B 46 ARG cc_start: 0.8358 (ptp-110) cc_final: 0.7556 (mtt90) REVERT: B 214 ARG cc_start: 0.7973 (mpt180) cc_final: 0.7614 (mpt180) REVERT: B 234 PHE cc_start: 0.9279 (OUTLIER) cc_final: 0.7758 (m-80) REVERT: N 86 LEU cc_start: 0.9047 (mp) cc_final: 0.8796 (mp) REVERT: N 88 PRO cc_start: 0.9437 (Cg_exo) cc_final: 0.9202 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9095 (mp0) cc_final: 0.8601 (mp0) REVERT: N 105 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7670 (mtm-85) outliers start: 20 outliers final: 18 residues processed: 143 average time/residue: 1.3467 time to fit residues: 203.1244 Evaluate side-chains 148 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 25 optimal weight: 0.0770 chunk 51 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 68 HIS R 191 HIS N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107350 restraints weight = 9714.669| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.60 r_work: 0.3173 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8086 Z= 0.134 Angle : 0.524 9.579 10963 Z= 0.260 Chirality : 0.040 0.139 1252 Planarity : 0.004 0.051 1402 Dihedral : 4.150 29.353 1140 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.67 % Allowed : 21.10 % Favored : 77.23 % 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: 0.93 (0.27), residues: 1002 helix: 2.53 (0.28), residues: 376 sheet: 0.17 (0.33), residues: 217 loop : -0.99 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE R 119 TYR 0.010 0.001 TYR R 161 ARG 0.008 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7433.83 seconds wall clock time: 127 minutes 6.02 seconds (7626.02 seconds total)