Starting phenix.real_space_refine on Thu Jul 2 13:22:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb0_64911/07_2026/9vb0_64911.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb0_64911/07_2026/9vb0_64911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vb0_64911/07_2026/9vb0_64911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb0_64911/07_2026/9vb0_64911.map" model { file = "/net/cci-nas-00/data/ceres_data/9vb0_64911/07_2026/9vb0_64911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb0_64911/07_2026/9vb0_64911.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.077 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 60 5.16 5 C 5581 2.51 5 N 1491 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8758 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1758 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2585 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 410 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2190 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 1.93, per 1000 atoms: 0.22 Number of scatterers: 8758 At special positions: 0 Unit cell: (92.6833, 120.35, 127.267, 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 60 16.00 O 1626 8.00 N 1491 7.00 C 5581 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 304.9 milliseconds 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 13 sheets defined 39.7% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.511A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.823A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.069A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.676A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.517A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.667A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.134A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'R' and resid 62 through 91 Processing helix chain 'R' and resid 95 through 129 removed outlier: 3.588A pdb=" N THR R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 140 through 172 Processing helix chain 'R' and resid 172 through 177 Processing helix chain 'R' and resid 184 through 200 Processing helix chain 'R' and resid 229 through 273 Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 293 through 329 removed outlier: 4.067A pdb=" N VAL R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 367 removed outlier: 3.693A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.750A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 51 removed outlier: 4.852A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.736A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.131A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.785A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.560A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.506A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.711A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.512A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.512A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.426A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 3351 1.40 - 1.61: 5494 1.61 - 1.81: 74 1.81 - 2.02: 18 2.02 - 2.22: 1 Bond restraints: 8938 Sorted by residual: bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 2.223 -0.839 2.10e-02 2.27e+03 1.59e+03 bond pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 1.384 1.783 -0.399 2.10e-02 2.27e+03 3.61e+02 bond pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 1.528 1.308 0.220 1.56e-02 4.11e+03 1.99e+02 bond pdb=" CB LYS R 186 " pdb=" CG LYS R 186 " ideal model delta sigma weight residual 1.520 1.233 0.287 3.00e-02 1.11e+03 9.18e+01 bond pdb=" CB VAL R 64 " pdb=" CG1 VAL R 64 " ideal model delta sigma weight residual 1.521 1.228 0.293 3.30e-02 9.18e+02 7.87e+01 ... (remaining 8933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.28: 12063 9.28 - 18.56: 41 18.56 - 27.84: 3 27.84 - 37.12: 1 37.12 - 46.40: 1 Bond angle restraints: 12109 Sorted by residual: angle pdb=" CD1 PHE R 174 " pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 118.60 72.20 46.40 1.50e+00 4.44e-01 9.57e+02 angle pdb=" CB PHE R 174 " pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 120.70 88.52 32.18 1.70e+00 3.46e-01 3.58e+02 angle pdb=" CA LYS R 186 " pdb=" CB LYS R 186 " pdb=" CG LYS R 186 " ideal model delta sigma weight residual 114.10 138.04 -23.94 2.00e+00 2.50e-01 1.43e+02 angle pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " pdb=" CG PHE A 354 " ideal model delta sigma weight residual 113.80 124.41 -10.61 1.00e+00 1.00e+00 1.13e+02 angle pdb=" CD1 LEU R 118 " pdb=" CG LEU R 118 " pdb=" CD2 LEU R 118 " ideal model delta sigma weight residual 110.80 133.81 -23.01 2.20e+00 2.07e-01 1.09e+02 ... (remaining 12104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4752 17.91 - 35.83: 397 35.83 - 53.74: 117 53.74 - 71.66: 22 71.66 - 89.57: 7 Dihedral angle restraints: 5295 sinusoidal: 2028 harmonic: 3267 Sorted by residual: dihedral pdb=" N TRP R 129 " pdb=" C TRP R 129 " pdb=" CA TRP R 129 " pdb=" CB TRP R 129 " ideal model delta harmonic sigma weight residual 122.80 144.13 -21.33 0 2.50e+00 1.60e-01 7.28e+01 dihedral pdb=" C TRP R 129 " pdb=" N TRP R 129 " pdb=" CA TRP R 129 " pdb=" CB TRP R 129 " ideal model delta harmonic sigma weight residual -122.60 -143.67 21.07 0 2.50e+00 1.60e-01 7.10e+01 dihedral pdb=" C ILE R 374 " pdb=" N ILE R 374 " pdb=" CA ILE R 374 " pdb=" CB ILE R 374 " ideal model delta harmonic sigma weight residual -122.00 -140.84 18.84 0 2.50e+00 1.60e-01 5.68e+01 ... (remaining 5292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1342 0.316 - 0.632: 44 0.632 - 0.948: 1 0.948 - 1.264: 0 1.264 - 1.580: 2 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CG LEU R 71 " pdb=" CB LEU R 71 " pdb=" CD1 LEU R 71 " pdb=" CD2 LEU R 71 " both_signs ideal model delta sigma weight residual False -2.59 -4.17 1.58 2.00e-01 2.50e+01 6.24e+01 chirality pdb=" CG LEU R 118 " pdb=" CB LEU R 118 " pdb=" CD1 LEU R 118 " pdb=" CD2 LEU R 118 " both_signs ideal model delta sigma weight residual False -2.59 -1.23 -1.36 2.00e-01 2.50e+01 4.65e+01 chirality pdb=" CA TRP R 129 " pdb=" N TRP R 129 " pdb=" C TRP R 129 " pdb=" CB TRP R 129 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.87 2.00e-01 2.50e+01 1.87e+01 ... (remaining 1386 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " 0.255 2.00e-02 2.50e+03 2.62e-01 1.20e+03 pdb=" CG PHE R 174 " -0.567 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " 0.127 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " 0.251 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 299 " 0.676 9.50e-02 1.11e+02 3.12e-01 1.24e+02 pdb=" NE ARG R 299 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG R 299 " -0.151 2.00e-02 2.50e+03 pdb=" NH1 ARG R 299 " 0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG R 299 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 182 " -0.968 9.50e-02 1.11e+02 4.34e-01 1.14e+02 pdb=" NE ARG R 182 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG R 182 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG R 182 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 182 " -0.024 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 927 2.82 - 3.34: 9101 3.34 - 3.86: 14392 3.86 - 4.38: 17173 4.38 - 4.90: 28820 Nonbonded interactions: 70413 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.395 3.040 nonbonded pdb=" O ILE D 126 " pdb=" OG1 THR D 226 " model vdw 2.419 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.430 3.040 nonbonded pdb=" O ASP R 112 " pdb=" OG1 THR R 115 " model vdw 2.471 3.040 ... (remaining 70408 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: 0.090 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.018 0.839 8938 Z= 0.987 Angle : 2.428 46.403 12109 Z= 1.655 Chirality : 0.154 1.580 1389 Planarity : 0.024 0.434 1520 Dihedral : 15.482 89.573 3185 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 7.89 % Allowed : 8.53 % Favored : 83.58 % Cbeta Deviations : 4.36 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1099 helix: -0.23 (0.24), residues: 402 sheet: -0.42 (0.32), residues: 229 loop : -1.76 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.143 0.009 ARG R 299 TYR 0.056 0.009 TYR R 342 PHE 0.567 0.011 PHE R 174 TRP 0.051 0.009 TRP R 316 HIS 0.038 0.007 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.01807 / 0.99 ( 8938) covalent geometry : angle 2.42848 / 1.66 (12109) hydrogen bonds : bond 0.18361 / 12.79 ( 470) hydrogen bonds : angle 7.45422 / 5.36 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 354 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8223 (ttp80) REVERT: A 49 ILE cc_start: 0.9383 (pt) cc_final: 0.9123 (mm) REVERT: A 52 GLN cc_start: 0.8117 (mt0) cc_final: 0.7697 (mt0) REVERT: A 204 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8215 (tp40) REVERT: A 207 GLU cc_start: 0.7388 (tt0) cc_final: 0.6945 (tt0) REVERT: A 242 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7839 (mtt-85) REVERT: A 306 GLN cc_start: 0.8451 (mm110) cc_final: 0.8063 (mm110) REVERT: A 315 ASP cc_start: 0.7934 (p0) cc_final: 0.7577 (p0) REVERT: A 333 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8687 (tp-100) REVERT: A 346 ASN cc_start: 0.8786 (m-40) cc_final: 0.8514 (m-40) REVERT: B 4 LEU cc_start: 0.9171 (pp) cc_final: 0.8712 (tt) REVERT: B 16 ASN cc_start: 0.9300 (t0) cc_final: 0.8692 (t0) REVERT: B 17 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8792 (tp-100) REVERT: B 29 THR cc_start: 0.8995 (p) cc_final: 0.8654 (p) REVERT: B 78 LYS cc_start: 0.8762 (mttp) cc_final: 0.8554 (mttm) REVERT: B 217 MET cc_start: 0.8393 (pmm) cc_final: 0.7921 (ppp) REVERT: B 229 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7898 (mt) REVERT: B 261 LEU cc_start: 0.8263 (tp) cc_final: 0.7916 (tp) REVERT: B 268 ASN cc_start: 0.8492 (m110) cc_final: 0.8272 (t0) REVERT: C 14 LYS cc_start: 0.9160 (ttmp) cc_final: 0.8787 (mtpp) REVERT: C 18 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8513 (tp-100) REVERT: D 12 VAL cc_start: 0.9317 (t) cc_final: 0.9031 (m) REVERT: D 13 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8794 (pp30) REVERT: D 137 VAL cc_start: 0.8490 (t) cc_final: 0.7860 (t) REVERT: D 178 TYR cc_start: 0.8797 (p90) cc_final: 0.8595 (p90) REVERT: D 179 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7089 (mtm180) REVERT: D 232 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8419 (ttmm) REVERT: R 99 SER cc_start: 0.6513 (OUTLIER) cc_final: 0.6193 (t) REVERT: R 102 HIS cc_start: 0.8626 (m-70) cc_final: 0.8265 (m90) REVERT: R 112 ASP cc_start: 0.9005 (m-30) cc_final: 0.8532 (p0) REVERT: R 149 ASP cc_start: 0.7803 (m-30) cc_final: 0.7589 (m-30) REVERT: R 184 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6798 (ppt170) REVERT: R 187 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7940 (pttt) REVERT: R 266 MET cc_start: 0.1783 (mtm) cc_final: 0.1353 (mtm) REVERT: R 350 ASN cc_start: 0.8364 (m-40) cc_final: 0.7744 (m-40) REVERT: R 376 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7390 (mt) outliers start: 75 outliers final: 22 residues processed: 410 average time/residue: 0.0949 time to fit residues: 50.9052 Evaluate side-chains 251 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 98 GLN Chi-restraints excluded: chain R residue 99 SER Chi-restraints excluded: chain R residue 142 ARG Chi-restraints excluded: chain R residue 172 HIS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 187 LYS Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 339 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 357 SER Chi-restraints excluded: chain R residue 361 PRO Chi-restraints excluded: chain R residue 368 SER Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 373 HIS Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain L residue 9 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 44 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN R 104 HIS R 229 HIS ** R 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.120289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.080995 restraints weight = 19389.904| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.19 r_work: 0.3073 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8938 Z= 0.221 Angle : 0.807 13.494 12109 Z= 0.421 Chirality : 0.049 0.303 1389 Planarity : 0.005 0.055 1520 Dihedral : 9.108 58.451 1296 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.89 % Allowed : 16.74 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1099 helix: 1.37 (0.24), residues: 399 sheet: -0.47 (0.29), residues: 271 loop : -1.26 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 8 TYR 0.033 0.002 TYR R 339 PHE 0.077 0.003 PHE R 375 TRP 0.016 0.002 TRP B 82 HIS 0.010 0.002 HIS R 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 ( 8938) covalent geometry : angle 0.80723 / 0.42 (12109) hydrogen bonds : bond 0.05423 / 3.72 ( 470) hydrogen bonds : angle 5.54014 / 3.90 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7923 (ttp80) REVERT: A 242 ARG cc_start: 0.8180 (ttm170) cc_final: 0.7916 (ttm170) REVERT: A 243 MET cc_start: 0.8299 (tpp) cc_final: 0.7920 (tpp) REVERT: A 273 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8881 (tt) REVERT: A 310 LEU cc_start: 0.9100 (mp) cc_final: 0.8732 (mt) REVERT: A 315 ASP cc_start: 0.8457 (p0) cc_final: 0.7911 (p0) REVERT: A 333 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8812 (tp-100) REVERT: A 346 ASN cc_start: 0.9220 (m-40) cc_final: 0.8864 (m-40) REVERT: B 17 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8974 (tp-100) REVERT: B 74 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8580 (p) REVERT: B 188 MET cc_start: 0.8983 (mmm) cc_final: 0.8764 (mmm) REVERT: B 217 MET cc_start: 0.8965 (pmm) cc_final: 0.8698 (pmm) REVERT: B 268 ASN cc_start: 0.9155 (m110) cc_final: 0.8775 (t0) REVERT: C 14 LYS cc_start: 0.9027 (ttmp) cc_final: 0.8577 (mtpp) REVERT: C 17 GLU cc_start: 0.9117 (pt0) cc_final: 0.8827 (pp20) REVERT: C 18 GLN cc_start: 0.8945 (tp-100) cc_final: 0.7755 (tp-100) REVERT: C 21 MET cc_start: 0.9396 (tmm) cc_final: 0.9122 (tmm) REVERT: C 32 LYS cc_start: 0.8845 (tptp) cc_final: 0.8254 (tptt) REVERT: D 46 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8446 (pt0) REVERT: D 178 TYR cc_start: 0.9010 (p90) cc_final: 0.8797 (p90) REVERT: D 179 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6928 (mtm180) REVERT: D 222 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8419 (mt-10) REVERT: R 102 HIS cc_start: 0.8649 (m-70) cc_final: 0.8133 (m-70) REVERT: R 180 MET cc_start: 0.7649 (mtt) cc_final: 0.7342 (ttp) REVERT: R 184 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6986 (tmm160) REVERT: R 203 MET cc_start: 0.6033 (tpp) cc_final: 0.5472 (tpp) REVERT: R 249 MET cc_start: 0.8496 (tmm) cc_final: 0.8167 (ptm) REVERT: R 326 PHE cc_start: 0.9024 (t80) cc_final: 0.8678 (t80) REVERT: R 331 ASP cc_start: 0.7945 (p0) cc_final: 0.7738 (p0) REVERT: R 374 ILE cc_start: 0.5072 (OUTLIER) cc_final: 0.4811 (mm) REVERT: R 376 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7748 (mt) REVERT: L 12 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7283 (pp) outliers start: 56 outliers final: 26 residues processed: 263 average time/residue: 0.0952 time to fit residues: 33.0979 Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 361 PRO Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 374 ILE Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain L residue 12 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 30.0000 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 55 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 13 GLN R 98 GLN ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.119677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079716 restraints weight = 19216.997| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.25 r_work: 0.3048 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8938 Z= 0.184 Angle : 0.736 11.838 12109 Z= 0.376 Chirality : 0.047 0.212 1389 Planarity : 0.004 0.048 1520 Dihedral : 7.479 55.409 1253 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.16 % Allowed : 20.00 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.25), residues: 1099 helix: 1.67 (0.25), residues: 402 sheet: -0.16 (0.30), residues: 273 loop : -1.34 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.043 0.002 TYR R 339 PHE 0.040 0.002 PHE R 375 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 8938) covalent geometry : angle 0.73574 / 0.38 (12109) hydrogen bonds : bond 0.04908 / 3.32 ( 470) hydrogen bonds : angle 5.26720 / 3.71 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7969 (ttp80) REVERT: A 52 GLN cc_start: 0.8076 (mt0) cc_final: 0.7685 (mt0) REVERT: A 242 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7849 (ttm170) REVERT: A 243 MET cc_start: 0.8423 (tpp) cc_final: 0.8223 (tpp) REVERT: A 295 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (p) REVERT: A 306 GLN cc_start: 0.8928 (mm110) cc_final: 0.8458 (mm110) REVERT: A 310 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8601 (mt) REVERT: A 315 ASP cc_start: 0.8454 (p0) cc_final: 0.8014 (p0) REVERT: A 333 GLN cc_start: 0.9107 (tp-100) cc_final: 0.8768 (tp-100) REVERT: A 346 ASN cc_start: 0.9230 (m-40) cc_final: 0.8834 (m-40) REVERT: B 17 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8945 (tp-100) REVERT: B 74 SER cc_start: 0.9367 (OUTLIER) cc_final: 0.9047 (p) REVERT: B 217 MET cc_start: 0.8884 (pmm) cc_final: 0.8182 (ppp) REVERT: B 268 ASN cc_start: 0.9285 (m110) cc_final: 0.8847 (t0) REVERT: C 14 LYS cc_start: 0.9038 (ttmp) cc_final: 0.8663 (mtpp) REVERT: C 18 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8022 (tp40) REVERT: C 21 MET cc_start: 0.9452 (tmm) cc_final: 0.9124 (tmm) REVERT: C 32 LYS cc_start: 0.8811 (tptp) cc_final: 0.8281 (tptt) REVERT: D 222 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8759 (mt-10) REVERT: R 90 ARG cc_start: 0.5571 (OUTLIER) cc_final: 0.5242 (ptp-170) REVERT: R 102 HIS cc_start: 0.8540 (m-70) cc_final: 0.7892 (m90) REVERT: R 112 ASP cc_start: 0.9366 (m-30) cc_final: 0.8990 (t70) REVERT: R 180 MET cc_start: 0.7909 (mtt) cc_final: 0.7704 (ttp) REVERT: R 184 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6965 (tmm160) REVERT: R 192 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6638 (tt) REVERT: R 203 MET cc_start: 0.6025 (tpp) cc_final: 0.5567 (tpp) REVERT: R 249 MET cc_start: 0.8439 (tmm) cc_final: 0.8124 (ptm) REVERT: R 320 HIS cc_start: 0.7246 (m-70) cc_final: 0.6885 (m-70) REVERT: R 331 ASP cc_start: 0.7961 (p0) cc_final: 0.7750 (p0) REVERT: R 376 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7576 (mt) outliers start: 49 outliers final: 22 residues processed: 230 average time/residue: 0.1096 time to fit residues: 33.3251 Evaluate side-chains 211 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 TRP Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 376 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 chunk 82 optimal weight: 4.9990 chunk 80 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 119 ASN B 259 GLN D 219 GLN ** R 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.119310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.079619 restraints weight = 19661.347| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.32 r_work: 0.3024 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8938 Z= 0.193 Angle : 0.727 11.091 12109 Z= 0.367 Chirality : 0.047 0.269 1389 Planarity : 0.004 0.037 1520 Dihedral : 7.017 52.740 1246 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 6.63 % Allowed : 18.74 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.25), residues: 1099 helix: 1.69 (0.26), residues: 402 sheet: -0.11 (0.31), residues: 268 loop : -1.21 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.015 0.002 TYR R 167 PHE 0.026 0.002 PHE B 292 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 8938) covalent geometry : angle 0.72665 / 0.37 (12109) hydrogen bonds : bond 0.04565 / 3.03 ( 470) hydrogen bonds : angle 5.14291 / 3.65 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7815 (ttp80) REVERT: A 209 LYS cc_start: 0.9226 (ptmt) cc_final: 0.9021 (pttt) REVERT: A 243 MET cc_start: 0.8655 (tpp) cc_final: 0.8309 (tpp) REVERT: A 295 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 306 GLN cc_start: 0.8954 (mm110) cc_final: 0.8684 (mm-40) REVERT: A 310 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8447 (mt) REVERT: A 315 ASP cc_start: 0.8460 (p0) cc_final: 0.7998 (p0) REVERT: A 333 GLN cc_start: 0.9085 (tp-100) cc_final: 0.8623 (tp-100) REVERT: A 346 ASN cc_start: 0.9239 (m-40) cc_final: 0.8845 (m-40) REVERT: B 8 ARG cc_start: 0.8750 (mtm180) cc_final: 0.8372 (mtm180) REVERT: B 15 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8936 (mptt) REVERT: B 17 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8939 (tp-100) REVERT: B 74 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.9150 (p) REVERT: B 217 MET cc_start: 0.8925 (pmm) cc_final: 0.8718 (pmm) REVERT: B 234 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: B 280 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8186 (ttmt) REVERT: C 9 ILE cc_start: 0.9009 (pt) cc_final: 0.8430 (pt) REVERT: C 18 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8139 (tp40) REVERT: C 21 MET cc_start: 0.9451 (tmm) cc_final: 0.9033 (tmm) REVERT: C 32 LYS cc_start: 0.8766 (tptp) cc_final: 0.8386 (tptt) REVERT: C 59 ASN cc_start: 0.8838 (t0) cc_final: 0.8507 (t0) REVERT: D 87 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.6963 (mtm180) REVERT: D 179 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7028 (mtm180) REVERT: D 219 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8708 (pp30) REVERT: R 74 PHE cc_start: 0.9139 (t80) cc_final: 0.8885 (t80) REVERT: R 102 HIS cc_start: 0.8336 (m-70) cc_final: 0.7728 (m-70) REVERT: R 112 ASP cc_start: 0.9294 (m-30) cc_final: 0.8551 (t0) REVERT: R 192 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6821 (tt) REVERT: R 203 MET cc_start: 0.6441 (tpp) cc_final: 0.5974 (tpp) REVERT: R 320 HIS cc_start: 0.7010 (m-70) cc_final: 0.6800 (m-70) REVERT: R 325 MET cc_start: 0.9080 (tmm) cc_final: 0.8409 (mmt) REVERT: R 374 ILE cc_start: 0.5205 (OUTLIER) cc_final: 0.4936 (mm) outliers start: 63 outliers final: 31 residues processed: 237 average time/residue: 0.0891 time to fit residues: 27.8849 Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 337 PHE Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 374 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 102 optimal weight: 20.0000 chunk 54 optimal weight: 2.9990 chunk 95 optimal weight: 50.0000 chunk 87 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN B 220 GLN B 259 GLN B 266 HIS ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.119205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.079436 restraints weight = 19312.362| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.15 r_work: 0.3069 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8938 Z= 0.173 Angle : 0.742 11.444 12109 Z= 0.371 Chirality : 0.046 0.234 1389 Planarity : 0.004 0.038 1520 Dihedral : 6.461 55.798 1238 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.68 % Allowed : 19.89 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1099 helix: 1.64 (0.26), residues: 402 sheet: -0.12 (0.31), residues: 271 loop : -1.24 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 208 TYR 0.018 0.001 TYR R 339 PHE 0.024 0.002 PHE B 292 TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8938) covalent geometry : angle 0.74168 / 0.37 (12109) hydrogen bonds : bond 0.04399 / 2.97 ( 470) hydrogen bonds : angle 5.02426 / 3.58 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: A 243 MET cc_start: 0.8634 (tpp) cc_final: 0.8304 (tpp) REVERT: A 306 GLN cc_start: 0.8914 (mm110) cc_final: 0.8300 (mm110) REVERT: A 308 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8422 (mp0) REVERT: A 310 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8670 (mt) REVERT: A 315 ASP cc_start: 0.8433 (p0) cc_final: 0.7944 (p0) REVERT: A 333 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8548 (tp-100) REVERT: A 346 ASN cc_start: 0.9187 (m-40) cc_final: 0.8722 (m-40) REVERT: B 17 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8974 (tp-100) REVERT: B 74 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9173 (p) REVERT: B 234 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: B 280 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8310 (ttmm) REVERT: C 13 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8391 (mtm-85) REVERT: C 21 MET cc_start: 0.9395 (tmm) cc_final: 0.8967 (tmm) REVERT: C 32 LYS cc_start: 0.8918 (tptp) cc_final: 0.8537 (tptt) REVERT: D 12 VAL cc_start: 0.9177 (t) cc_final: 0.8871 (m) REVERT: D 179 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7124 (mtm180) REVERT: R 102 HIS cc_start: 0.8334 (m-70) cc_final: 0.7830 (m-70) REVERT: R 112 ASP cc_start: 0.9303 (m-30) cc_final: 0.8566 (t0) REVERT: R 203 MET cc_start: 0.6610 (tpp) cc_final: 0.6365 (tpp) REVERT: R 320 HIS cc_start: 0.6852 (m-70) cc_final: 0.6635 (m-70) REVERT: R 325 MET cc_start: 0.9010 (tmm) cc_final: 0.8420 (mmt) REVERT: R 374 ILE cc_start: 0.5533 (OUTLIER) cc_final: 0.5324 (mm) outliers start: 54 outliers final: 36 residues processed: 220 average time/residue: 0.0950 time to fit residues: 27.7288 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 374 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 0.0470 chunk 91 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.118186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078530 restraints weight = 19366.065| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.12 r_work: 0.3065 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8938 Z= 0.193 Angle : 0.739 11.164 12109 Z= 0.372 Chirality : 0.046 0.244 1389 Planarity : 0.004 0.039 1520 Dihedral : 6.189 58.302 1235 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.37 % Allowed : 20.63 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1099 helix: 1.39 (0.26), residues: 410 sheet: -0.19 (0.31), residues: 271 loop : -1.13 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.017 0.001 TYR R 354 PHE 0.024 0.002 PHE B 292 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 ( 8938) covalent geometry : angle 0.73869 / 0.37 (12109) hydrogen bonds : bond 0.04374 / 2.95 ( 470) hydrogen bonds : angle 5.03317 / 3.58 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7939 (ttp80) REVERT: A 243 MET cc_start: 0.8663 (tpp) cc_final: 0.8376 (tpp) REVERT: A 247 MET cc_start: 0.8974 (mtp) cc_final: 0.8708 (mtm) REVERT: A 306 GLN cc_start: 0.8910 (mm110) cc_final: 0.8539 (mm-40) REVERT: A 310 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8680 (mt) REVERT: A 315 ASP cc_start: 0.8443 (p0) cc_final: 0.7974 (p0) REVERT: A 333 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8532 (tp-100) REVERT: A 346 ASN cc_start: 0.9177 (m-40) cc_final: 0.8742 (m-40) REVERT: B 17 GLN cc_start: 0.9319 (tm-30) cc_final: 0.9000 (tp-100) REVERT: B 74 SER cc_start: 0.9435 (OUTLIER) cc_final: 0.9215 (p) REVERT: B 234 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: B 280 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8195 (ttmt) REVERT: C 21 MET cc_start: 0.9387 (tmm) cc_final: 0.9032 (tmm) REVERT: C 32 LYS cc_start: 0.8935 (tptp) cc_final: 0.8555 (tptt) REVERT: D 179 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7237 (mtm180) REVERT: D 222 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8852 (mt-10) REVERT: R 102 HIS cc_start: 0.8346 (m-70) cc_final: 0.7708 (m-70) REVERT: R 112 ASP cc_start: 0.9294 (m-30) cc_final: 0.8678 (t0) REVERT: R 146 PHE cc_start: 0.8246 (t80) cc_final: 0.7930 (m-80) REVERT: R 192 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.6940 (tt) REVERT: R 237 ILE cc_start: 0.7552 (mm) cc_final: 0.7319 (tt) REVERT: R 320 HIS cc_start: 0.6847 (m-70) cc_final: 0.6631 (m-70) REVERT: R 325 MET cc_start: 0.8993 (tmm) cc_final: 0.8465 (mmt) REVERT: R 370 ASN cc_start: 0.5472 (OUTLIER) cc_final: 0.4459 (p0) REVERT: R 374 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5358 (mm) outliers start: 51 outliers final: 32 residues processed: 216 average time/residue: 0.0952 time to fit residues: 27.0828 Evaluate side-chains 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 374 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 70 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.119229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079648 restraints weight = 19285.291| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.15 r_work: 0.3073 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8938 Z= 0.157 Angle : 0.735 12.132 12109 Z= 0.369 Chirality : 0.046 0.261 1389 Planarity : 0.004 0.038 1520 Dihedral : 6.035 59.528 1235 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.05 % Allowed : 22.32 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1099 helix: 1.50 (0.26), residues: 404 sheet: -0.01 (0.31), residues: 269 loop : -1.12 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 13 TYR 0.033 0.001 TYR R 354 PHE 0.023 0.002 PHE B 292 TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 ( 8938) covalent geometry : angle 0.73502 / 0.37 (12109) hydrogen bonds : bond 0.04179 / 2.82 ( 470) hydrogen bonds : angle 4.94101 / 3.51 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8995 (m-30) cc_final: 0.8771 (m-30) REVERT: A 32 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7743 (ttp80) REVERT: A 243 MET cc_start: 0.8651 (tpp) cc_final: 0.8360 (tpp) REVERT: A 306 GLN cc_start: 0.8913 (mm110) cc_final: 0.8292 (mm110) REVERT: A 308 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8517 (mp0) REVERT: A 310 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 315 ASP cc_start: 0.8405 (p0) cc_final: 0.7927 (p0) REVERT: A 333 GLN cc_start: 0.9078 (tp-100) cc_final: 0.8538 (tp-100) REVERT: A 346 ASN cc_start: 0.9170 (m-40) cc_final: 0.8722 (m-40) REVERT: B 8 ARG cc_start: 0.8636 (mtm180) cc_final: 0.8354 (mtm180) REVERT: B 13 GLN cc_start: 0.9022 (pp30) cc_final: 0.8764 (pp30) REVERT: B 17 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8924 (tp-100) REVERT: B 74 SER cc_start: 0.9398 (OUTLIER) cc_final: 0.9176 (p) REVERT: B 101 MET cc_start: 0.9078 (ptm) cc_final: 0.8860 (ptp) REVERT: B 234 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: B 280 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8168 (ttmt) REVERT: C 21 MET cc_start: 0.9383 (tmm) cc_final: 0.9057 (tmm) REVERT: C 32 LYS cc_start: 0.8921 (tptp) cc_final: 0.8544 (tptt) REVERT: D 151 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8830 (ttpt) REVERT: D 179 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7198 (mtm180) REVERT: D 222 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8657 (mt-10) REVERT: R 102 HIS cc_start: 0.8327 (m-70) cc_final: 0.7704 (m-70) REVERT: R 112 ASP cc_start: 0.9301 (m-30) cc_final: 0.8731 (t0) REVERT: R 118 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7961 (tp) REVERT: R 146 PHE cc_start: 0.8185 (t80) cc_final: 0.7838 (m-80) REVERT: R 325 MET cc_start: 0.8989 (tmm) cc_final: 0.8396 (mmt) REVERT: R 370 ASN cc_start: 0.5323 (OUTLIER) cc_final: 0.4432 (p0) REVERT: R 374 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.5326 (mm) REVERT: R 375 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6400 (p90) outliers start: 48 outliers final: 30 residues processed: 216 average time/residue: 0.0937 time to fit residues: 26.7122 Evaluate side-chains 217 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 261 ASN Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 370 ASN Chi-restraints excluded: chain R residue 374 ILE Chi-restraints excluded: chain R residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 0.0060 chunk 105 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 15 optimal weight: 30.0000 chunk 64 optimal weight: 0.3980 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 overall best weight: 2.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.119441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.079739 restraints weight = 19220.894| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.14 r_work: 0.3077 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8938 Z= 0.160 Angle : 0.747 13.685 12109 Z= 0.369 Chirality : 0.046 0.263 1389 Planarity : 0.004 0.039 1520 Dihedral : 5.932 57.913 1235 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.21 % Allowed : 23.26 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1099 helix: 1.54 (0.26), residues: 403 sheet: 0.05 (0.31), residues: 269 loop : -1.09 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 13 TYR 0.016 0.001 TYR R 346 PHE 0.022 0.002 PHE B 292 TRP 0.017 0.001 TRP B 82 HIS 0.009 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 ( 8938) covalent geometry : angle 0.74707 / 0.37 (12109) hydrogen bonds : bond 0.04147 / 2.78 ( 470) hydrogen bonds : angle 4.90910 / 3.48 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9023 (m-30) cc_final: 0.8788 (m-30) REVERT: A 32 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7769 (tmm-80) REVERT: A 243 MET cc_start: 0.8672 (tpp) cc_final: 0.8382 (tpp) REVERT: A 306 GLN cc_start: 0.8897 (mm110) cc_final: 0.8279 (mm110) REVERT: A 308 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8542 (mp0) REVERT: A 310 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8689 (mt) REVERT: A 315 ASP cc_start: 0.8453 (p0) cc_final: 0.8014 (p0) REVERT: A 333 GLN cc_start: 0.9087 (tp-100) cc_final: 0.8539 (tp-100) REVERT: A 346 ASN cc_start: 0.9166 (m-40) cc_final: 0.8720 (m-40) REVERT: B 13 GLN cc_start: 0.9125 (pp30) cc_final: 0.8825 (pp30) REVERT: B 17 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8938 (tp-100) REVERT: B 25 CYS cc_start: 0.9161 (m) cc_final: 0.8811 (p) REVERT: B 74 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.9190 (p) REVERT: B 101 MET cc_start: 0.9087 (ptm) cc_final: 0.8836 (ptp) REVERT: B 234 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: B 280 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8161 (ttmt) REVERT: C 21 MET cc_start: 0.9400 (tmm) cc_final: 0.9054 (tmm) REVERT: C 32 LYS cc_start: 0.8952 (tptp) cc_final: 0.8542 (tptt) REVERT: D 179 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7203 (mtm180) REVERT: R 102 HIS cc_start: 0.8259 (m-70) cc_final: 0.7647 (m-70) REVERT: R 112 ASP cc_start: 0.9275 (m-30) cc_final: 0.8747 (t0) REVERT: R 120 MET cc_start: 0.7315 (mmt) cc_final: 0.7081 (mmt) REVERT: R 146 PHE cc_start: 0.8188 (t80) cc_final: 0.7836 (m-80) REVERT: R 325 MET cc_start: 0.9055 (tmm) cc_final: 0.8477 (tpt) REVERT: R 374 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.5055 (mm) REVERT: R 375 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6410 (p90) outliers start: 40 outliers final: 29 residues processed: 208 average time/residue: 0.1118 time to fit residues: 30.5607 Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 90 ARG Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 374 ILE Chi-restraints excluded: chain R residue 375 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 36 ASN R 95 GLN ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.117923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078266 restraints weight = 19265.546| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.10 r_work: 0.3053 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.6044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8938 Z= 0.207 Angle : 0.797 17.653 12109 Z= 0.391 Chirality : 0.047 0.269 1389 Planarity : 0.004 0.039 1520 Dihedral : 5.942 57.016 1233 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.32 % Allowed : 23.79 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1099 helix: 1.48 (0.26), residues: 403 sheet: -0.04 (0.31), residues: 269 loop : -1.16 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 13 TYR 0.036 0.002 TYR R 354 PHE 0.023 0.002 PHE B 292 TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.21 ( 8938) covalent geometry : angle 0.79708 / 0.39 (12109) hydrogen bonds : bond 0.04331 / 2.88 ( 470) hydrogen bonds : angle 4.96314 / 3.51 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7781 (ttp80) REVERT: A 243 MET cc_start: 0.8730 (tpp) cc_final: 0.8485 (tpp) REVERT: A 306 GLN cc_start: 0.8935 (mm110) cc_final: 0.8313 (mm-40) REVERT: A 310 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8749 (mt) REVERT: A 315 ASP cc_start: 0.8302 (p0) cc_final: 0.7828 (p0) REVERT: A 333 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8551 (tp-100) REVERT: A 346 ASN cc_start: 0.9207 (m-40) cc_final: 0.8953 (m110) REVERT: B 13 GLN cc_start: 0.9155 (pp30) cc_final: 0.8861 (pp30) REVERT: B 17 GLN cc_start: 0.9393 (tm-30) cc_final: 0.8936 (tp-100) REVERT: B 25 CYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8726 (p) REVERT: B 101 MET cc_start: 0.9099 (ptm) cc_final: 0.8847 (ptp) REVERT: B 234 PHE cc_start: 0.9133 (OUTLIER) cc_final: 0.8294 (m-80) REVERT: B 280 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8179 (ttmt) REVERT: C 21 MET cc_start: 0.9426 (tmm) cc_final: 0.9071 (tmm) REVERT: C 32 LYS cc_start: 0.8980 (tptp) cc_final: 0.8572 (tptt) REVERT: D 19 LYS cc_start: 0.9266 (ttpp) cc_final: 0.9050 (tttm) REVERT: D 87 ARG cc_start: 0.6943 (mtm180) cc_final: 0.6262 (mtm180) REVERT: D 89 GLU cc_start: 0.8744 (pm20) cc_final: 0.8464 (pm20) REVERT: D 179 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7204 (mtm180) REVERT: R 81 ASN cc_start: 0.7857 (m-40) cc_final: 0.7224 (m-40) REVERT: R 102 HIS cc_start: 0.8352 (m-70) cc_final: 0.7703 (m-70) REVERT: R 112 ASP cc_start: 0.9284 (m-30) cc_final: 0.8924 (t0) REVERT: R 320 HIS cc_start: 0.7455 (m-70) cc_final: 0.7036 (m-70) REVERT: R 325 MET cc_start: 0.9178 (tmm) cc_final: 0.8506 (tpt) REVERT: R 374 ILE cc_start: 0.5230 (OUTLIER) cc_final: 0.5008 (mm) REVERT: R 375 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.6298 (p90) outliers start: 41 outliers final: 29 residues processed: 203 average time/residue: 0.1089 time to fit residues: 29.2221 Evaluate side-chains 206 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 374 ILE Chi-restraints excluded: chain R residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 50 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 60 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 35 ASN B 36 ASN ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.119985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080056 restraints weight = 19214.249| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.19 r_work: 0.3084 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8938 Z= 0.155 Angle : 0.790 16.884 12109 Z= 0.389 Chirality : 0.047 0.355 1389 Planarity : 0.004 0.040 1520 Dihedral : 5.797 56.562 1233 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Rotamer: Outliers : 3.89 % Allowed : 24.63 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1099 helix: 1.49 (0.26), residues: 401 sheet: -0.03 (0.31), residues: 279 loop : -1.03 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.042 0.002 TYR R 339 PHE 0.022 0.002 PHE B 292 TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 8938) covalent geometry : angle 0.78980 / 0.39 (12109) hydrogen bonds : bond 0.04138 / 2.75 ( 470) hydrogen bonds : angle 4.90623 / 3.46 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2198 Ramachandran restraints generated. 1099 Oldfield, 0 Emsley, 1099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.9019 (m-30) cc_final: 0.8789 (m-30) REVERT: A 32 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7667 (tmm-80) REVERT: A 43 GLU cc_start: 0.8490 (mp0) cc_final: 0.7762 (tm-30) REVERT: A 243 MET cc_start: 0.8709 (tpp) cc_final: 0.8504 (tpp) REVERT: A 247 MET cc_start: 0.8893 (mtp) cc_final: 0.8616 (mtm) REVERT: A 306 GLN cc_start: 0.8852 (mm110) cc_final: 0.8448 (mm110) REVERT: A 308 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8516 (mp0) REVERT: A 310 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8783 (mt) REVERT: A 315 ASP cc_start: 0.8382 (p0) cc_final: 0.8032 (p0) REVERT: A 333 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8561 (tp-100) REVERT: A 346 ASN cc_start: 0.9208 (m-40) cc_final: 0.8751 (m-40) REVERT: B 13 GLN cc_start: 0.9146 (pp30) cc_final: 0.8844 (pp30) REVERT: B 17 GLN cc_start: 0.9387 (tm-30) cc_final: 0.8919 (tp-100) REVERT: B 25 CYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8747 (p) REVERT: B 101 MET cc_start: 0.9007 (ptm) cc_final: 0.8782 (ptp) REVERT: B 234 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8234 (m-80) REVERT: B 280 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8116 (ttmt) REVERT: C 21 MET cc_start: 0.9407 (tmm) cc_final: 0.9053 (tmm) REVERT: C 32 LYS cc_start: 0.8973 (tptp) cc_final: 0.8584 (tptt) REVERT: D 19 LYS cc_start: 0.9264 (ttpp) cc_final: 0.9000 (tttm) REVERT: D 83 MET cc_start: 0.9022 (ptp) cc_final: 0.8599 (mtm) REVERT: D 87 ARG cc_start: 0.7012 (mtm180) cc_final: 0.6218 (mtm180) REVERT: D 89 GLU cc_start: 0.8700 (pm20) cc_final: 0.8430 (pm20) REVERT: D 179 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7326 (mtm180) REVERT: R 102 HIS cc_start: 0.8176 (m-70) cc_final: 0.7506 (m-70) REVERT: R 112 ASP cc_start: 0.9344 (m-30) cc_final: 0.8693 (t0) REVERT: R 149 ASP cc_start: 0.8996 (m-30) cc_final: 0.8459 (m-30) REVERT: R 203 MET cc_start: 0.7982 (mmp) cc_final: 0.7782 (mmp) REVERT: R 325 MET cc_start: 0.9212 (tmm) cc_final: 0.8523 (tpt) REVERT: R 375 PHE cc_start: 0.6697 (OUTLIER) cc_final: 0.6448 (p90) outliers start: 37 outliers final: 27 residues processed: 203 average time/residue: 0.1019 time to fit residues: 27.2033 Evaluate side-chains 208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 92 LYS Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 174 PHE Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 341 PHE Chi-restraints excluded: chain R residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS B 35 ASN B 340 ASN ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 104 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.078389 restraints weight = 19317.437| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.12 r_work: 0.3055 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8938 Z= 0.216 Angle : 0.819 16.167 12109 Z= 0.406 Chirality : 0.048 0.332 1389 Planarity : 0.004 0.040 1520 Dihedral : 5.871 55.877 1233 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 4.00 % Allowed : 24.84 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.26), residues: 1099 helix: 1.44 (0.26), residues: 400 sheet: 0.03 (0.31), residues: 270 loop : -1.11 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.054 0.002 TYR R 339 PHE 0.022 0.002 PHE B 292 TRP 0.045 0.002 TRP B 211 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.22 ( 8938) covalent geometry : angle 0.81863 / 0.41 (12109) hydrogen bonds : bond 0.04295 / 2.86 ( 470) hydrogen bonds : angle 5.01244 / 3.52 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2171.77 seconds wall clock time: 37 minutes 59.60 seconds (2279.60 seconds total)